Wikiomics:Bioinfo tutorial (exercises): Difference between revisions
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Latest revision as of 21:00, 19 November 2007
Sequence formats
text only/raw sequence
DNA
CGGGAGGCGGCAGCGGCTGCAGCGTTGGTAGCATCAGCATCAGCATCAGCGGCAGCGGCAGCGGCCTCGG GCGGGGCCGGCCGGACGGACAGGCGGACAGAAGGCGCCAGGGGCGCGCGTCCCGCCCGGGCCGGCCATGG AGGGCGCCTCCTTCGGCGCGGGCCGCGCAGGGGCCGCCCTGGACCCCGTGAGCTTTGCGCGGCGGCCCCA GACCCTGCTCCGGGTCGCGTCCTGGGTGTTCTCCATCGCCGTCTTCGGGCCCATCGTCAACGAGGGCTAC GTGAACACCGACAGCGGCCCCGAGCTGCGCTGCGTGTTCAACGGGAACGCGGGCGCCTGCCGCTTCGGCG
Protein
MEGASFGAGRAGAALDPVSFARRPQTLLRVASWVFSIAVFGPIV NEGYVNTDSGPELRCVFNGNAGACRFGVALGLGAFLACAAFLLLDVRFQQISSVRDRR RAVLLDLGFSGLWSFLWFVGFCFLTNQWQRTAPGPATTQAGDAARAAIAFSFFSILSW VALTVKALQRFRLGTDMSLFATEQLSTGASQAYPGYPVGSGVEGTETYQSPPFTETLD TSPKGYQVPAY
FASTA
single FASTA
>gi|22091456|ref|NM_004209.4| Homo sapiens synaptogyrin 3 (SYNGR3), mRNA CGGGAGGCGGCAGCGGCTGCAGCGTTGGTAGCATCAGCATCAGCATCAGCGGCAGCGGCAGCGGCCTCGG GCGGGGCCGGCCGGACGGACAGGCGGACAGAAGGCGCCAGGGGCGCGCGTCCCGCCCGGGCCGGCCATGG AGGGCGCCTCCTTCGGCGCGGGCCGCGCAGGGGCCGCCCTGGACCCCGTGAGCTTTGCGCGGCGGCCCCA GACCCTGCTCCGGGTCGCGTCCTGGGTGTTCTCCATCGCCGTCTTCGGGCCCATCGTCAACGAGGGCTAC GTGAACACCGACAGCGGCCCCGAGCTGCGCTGCGTGTTCAACGGGAACGCGGGCGCCTGCCGCTTCGGCG
multiple FASTA
>homoSYNGR1a_NP_004702.2 MEGGAYGAGKAGGAFDPYTLVRQPHTILRVVSWLFSIVVFGSIVNEGYLNSASEGEEFCIYNRNPNACSY GVAVGVLAFLTCLLYLALDVYFPQISSVKDRKKAVLSDIGVSAFWAFLWFVGFCYLANQWQVSKPKDNPL NEGTDAARAAIAFSFFSIFTWAGQAVLAFQRYQIGADSALFSQDYMDPSQDSSMPYAPYVEPTGPDPAGM GGTYQQPANTFDTEPQGYQSQGY >X.laev_syngr1_BAB79596.1 MEGGAYGAGKAGGAFDPQTFIRQPHTILRMVSWVFSIVVFGCIINEGYINSSTEEEEHCIFNRNPSACSY GVTVGVLAFLTCLLYLAVDIYFPQISSVKDRKKTVISDIAVSALWAFFWFVGFCFLANQWQVSNPNDNPM NEGADAARAAITFSFFSIFTWAGQAVLAYQQYRLGSDSALFSQDYMDPSQDQGPPYPPYASNEDLDPSAG YQQPPTEAYDAGSHGYQTQDY >X.trop_syngr1_NP_001016195.1 MEGGAYGAGKAGGAFDPQTFVRQPHTVLRMVSWVFSIVVFGCIINEGYINASTEAEEHCIFNRNSSACAY GVTVGVLAFLTCLLYLAVDVYFPQISSVKDRKKTVISDIAVSGLWAFFWFVGFCFLANQWQVSNPNDNPM NEGADAARAAIAFSFFSIFTWAGQAVLAYQRYRLGSDSALFSQDYMDPSQDQGPPYPPYASNEDLDPSAG YQQPPSDAYDAGSQGYQTQDY
GenBank format
LOCUS NM_004209 2054 bp mRNA linear PRI 24-SEP-2005
DEFINITION Homo sapiens synaptogyrin 3 (SYNGR3), mRNA.
ACCESSION NM_004209
VERSION NM_004209.4 GI:22091456
KEYWORDS .
SOURCE Homo sapiens (human)
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
REFERENCE 1 (bases 1 to 2054)
AUTHORS Kedra,D., Pan,H.Q., Seroussi,E., Fransson,I., Guilbaud,C.,
Collins,J.E., Dunham,I., Blennow,E., Roe,B.A., Piehl,F. and
Dumanski,J.P.
TITLE Characterization of the human synaptogyrin gene family
JOURNAL Hum. Genet. 103 (2), 131-141 (1998)
PUBMED 9760194
COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The
reference sequence was derived from BC014087.2 and BG699055.1.
On Aug 2, 2002 this sequence version replaced gi:21361084.
Summary: This gene encodes an integral membrane protein. The gene
belongs to the synaptogyrin gene family. Like other members of the
family the protein contains four transmembrane regions. The exact
function of this protein is unclear.
COMPLETENESS: complete on the 3' end.
FEATURES Location/Qualifiers
source 1..2054
/organism="Homo sapiens"
/mol_type="mRNA"
/db_xref="taxon:9606"
/chromosome="16"
/map="16p13"
gene 1..2054
/gene="SYNGR3"
/note="synonym: MGC:20003"
/db_xref="GeneID:9143"
/db_xref="HGNC:11501"
/db_xref="HPRD:06801"
/db_xref="MIM:603927"
CDS 137..826
/gene="SYNGR3"
/go_component="integral to plasma membrane [pmid 9760194];
membrane"
/codon_start=1
/product="synaptogyrin 3"
/protein_id="NP_004200.2"
/db_xref="GI:6631112"
/db_xref="CCDS:CCDS10456.1"
/db_xref="GeneID:9143"
/db_xref="HGNC:11501"
/db_xref="HPRD:06801"
/db_xref="MIM:603927"
/translation="MEGASFGAGRAGAALDPVSFARRPQTLLRVASWVFSIAVFGPIV
NEGYVNTDSGPELRCVFNGNAGACRFGVALGLGAFLACAAFLLLDVRFQQISSVRDRR
RAVLLDLGFSGLWSFLWFVGFCFLTNQWQRTAPGPATTQAGDAARAAIAFSFFSILSW
VALTVKALQRFRLGTDMSLFATEQLSTGASQAYPGYPVGSGVEGTETYQSPPFTETLD
TSPKGYQVPAY"
STS 1230..1360
/gene="SYNGR3"
/standard_name="D3S3542"
/db_xref="UniSTS:4004"
STS 1396..2025
/gene="SYNGR3"
/standard_name="SYNGR3_8904"
/db_xref="UniSTS:467928"
STS 1739..1859
/gene="SYNGR3"
/standard_name="RH66376"
/db_xref="UniSTS:7190"
STS 1914..2013
/gene="SYNGR3"
/standard_name="SHGC-61093"
/db_xref="UniSTS:61380"
polyA_signal 2001..2006
/gene="SYNGR3"
polyA_site 2029
/gene="SYNGR3"
/experiment="experimental evidence, no additional details
recorded"
ORIGIN
1 cgggaggcgg cagcggctgc agcgttggta gcatcagcat cagcatcagc ggcagcggca
61 gcggcctcgg gcggggccgg ccggacggac aggcggacag aaggcgccag gggcgcgcgt
121 cccgcccggg ccggccatgg agggcgcctc cttcggcgcg ggccgcgcag gggccgccct
<snip>
GCG
from [1]
!!NA_SEQUENCE 1.0 H.sapiens fau mRNA HSFAU Length: 518 Type: N Check: 2981 .. 1 ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc 51 gccaatatgc agctctttgt ccgcgcccag gagctacaca ccttcgaggt 101 gaccggccag gaaacggtcg cccagatcaa ggctcatgta gcctcactgg 151 agggcattgc cccggaagat caagtcgtgc tcctggcagg cgcgcccctg 201 gaggatgagg ccactctggg ccagtgcggg gtggaggccc tgactaccct 251 ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc 301 gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag 351 aagaagaaga agacaggtcg ggctaagcgg cggatgcagt acaaccggcg 401 ctttgtcaac gttgtgccca cctttggcaa gaagaagggc cccaatgcca 451 actcttaagt cttttgtaat tctggctttc tctaataaaa aagccactta 501 gttcagtcaa aaaaaaaa
XML
EXP
ID xb61c6.s1
EN xb61c6.s1
LN xb61c6.s1.ztr
LT ZTR
QR 446
AQ 54.180000
SQ
GCTTTACTGC CTTAGGGTCG ACTCTAGAGG ATCCCCTAAA TTATTATTTT AAATTGACAT
TTTGAAAATT TCCCCCGTAA TTTTATTGCA ATTTTAATTG AAAGTTTATT AATTGTGAAA
TGTGCTTTTT AAGATGTTGC AAACACCTAA TTACTATT-T CACTTTTGAG ATATGT-AAT
T-CTAAA-AA CTTTT-T--A ATTTCCTAA- --GAATTT-C AAAAG-CAAA A-AACAAACG
AATTT-ATAA AAG--AAAAG -GCAAACT-A CCTG-TAACT -ACA-T-CCG G-CCA-T-AT
CAAAATTAAT TTTTCCGTTG G-ATTAACTT TTT-G-AT-T TTCCT-GGGG GG-CTTGACT
TT-CCGC-AT TGGTTGGTT- GGGTTCGCGG AATTTTTTTA CCAGGGGTTC TTTGGG-GGA
G-G-AAG-C- TT-A-AAC-C GGGTT
//
SF /home6/jkb/work/course/t/m13mp18.vector
CF /home6/jkb/work/course/t/lorist6.vector
TN xb61c6
PR 1
SC 6249
SP 41
SI 1400..2000
CH 0
QR 159
QL 0
SL 36
SR 446
GFF
from [2]
##gff-version 3 ##sequence-region ctg123 1 1497228 ctg123 . gene 1000 9000 . + . ID=gene00001;Name=EDEN ctg123 . TF_binding_site 1000 1012 . + . ID=tfbs00001;Parent=gene00001 ctg123 . mRNA 1050 9000 . + . ID=mRNA00001;Parent=gene00001;Name=EDEN.1 ctg123 . five_prime_UTR 1050 1200 . + . Parent=mRNA0001 ctg123 . CDS 1201 1500 . + 0 Parent=mRNA0001 ctg123 . CDS 3000 3902 . + 0 Parent=mRNA0001 ctg123 . CDS 5000 5500 . + 0 Parent=mRNA0001 ctg123 . CDS 7000 7600 . + 0 Parent=mRNA0001 ctg123 . three_prime_UTR 7601 9000 . + . Parent=mRNA0001 ctg123 . cDNA_match 1050 1500 5.8e-42 + . ID=match0001;Target=cdna0123+12+462 ctg123 . cDNA_match 5000 5500 8.1e-43 + . ID=match0001;Target=cdna0123+463+963 ctg123 . cDNA_match 7000 9000 1.4e-40 + . ID=match0001;Target=cdna0123+964+2964
MSF
PileUp MSF: 265 Type: P Check: 214852 .. Name: homoSYNGR1a_NP_ Len: 265 Check: 17794 Weight: 1.000 Name: X_laev_syngr1_B Len: 265 Check: 17613 Weight: 1.000 Name: X_trop_syngr1_N Len: 265 Check: 17610 Weight: 1.000 Name: homo_SYNGR3_NP_ Len: 265 Check: 17422 Weight: 1.000 Name: homo_SYNGR2_AAH Len: 265 Check: 17128 Weight: 1.000 Name: D_rerio_XP_6969 Len: 265 Check: 18054 Weight: 1.000 Name: T_nigr_CAF89717 Len: 265 Check: 18574 Weight: 1.000 Name: D_mela_NP_61090 Len: 265 Check: 18339 Weight: 1.000 Name: D_rerio_syngr1_ Len: 265 Check: 16771 Weight: 1.000 Name: E_eleg_NP_50923 Len: 265 Check: 18759 Weight: 1.000 Name: A_gamb_EAA05258 Len: 265 Check: 16202 Weight: 1.000 Name: chick_syngr1_XP Len: 265 Check: 9780 Weight: 1.000 Name: bee_XP_624778_1 Len: 265 Check: 10806 Weight: 1.000 // homoSYNGR1a_NP_ .........M E.GGAYGAGK AGGAFDPYTL VRQPHTILRV VSWLFSIVVF X_laev_syngr1_B .........M E.GGAYGAGK AGGAFDPQTF IRQPHTILRM VSWVFSIVVF X_trop_syngr1_N .........M E.GGAYGAGK AGGAFDPQTF VRQPHTVLRM VSWVFSIVVF homo_SYNGR3_NP_ .........M E.GASFGAGR AGAALDPVSF ARRPQTLLRV ASWVFSIAVF homo_SYNGR2_AAH .........M E.SGAYGAAK AGGSFDLRRF LTQPQVVARA VCLVFALIVF D_rerio_XP_6969 .......MES R.SVAYGASL AGAGFDLVKF IKQPQTVVRF LSWVFAIVVF T_nigr_CAF89717 .........M DGVGSFGAGR TGSAVDPIAF AKQPQTILRV LSWIFSLVVF D_mela_NP_61090 MDMLNQILSI NNGGAYGGGK AGGAFDPLTF AMKPQVVIRA LCWLFSVVVF D_rerio_syngr1_ MDQ....... ....AYGAGK AGGTFDPITF FQQPQTILRI VSWIFSIVIF E_eleg_NP_50923 .........M ENVRAYGAGL AGANFDKNTF FKKPTVLFRC AALLFGLILW A_gamb_EAA05258 .NEANR.SKM DIGGAYGGGK AGGAFDPIAF VQRPTVILRA VCWLFAIIVF chick_syngr1_XP .......... .......... .......... .......... ...VFSIVVF bee_XP_624778_1 .......... .......... .......... .......... .......... homoSYNGR1a_NP_ GSIVNEGYLN SASEGEEFCI YNRNPNACSY GVAVGVLAFL TCLLYLALDV X_laev_syngr1_B GCIINEGYIN SSTEEEEHCI FNRNPSACSY GVTVGVLAFL TCLLYLAVDI X_trop_syngr1_N GCIINEGYIN ASTEAEEHCI FNRNSSACAY GVTVGVLAFL TCLLYLAVDV homo_SYNGR3_NP_ GPIVNEGYVN TDSGPELRCV FNGNAGACRF GVALGLGAFL ACAAFLLLDV homo_SYNGR2_AAH SCIYGEGYSN AHESKQMYCV FNRNEDACRY GSAIGVLAFL ASAFFLVVDA D_rerio_XP_6969 SSITAEGYVN STDEAEVRCV FNRNDGACHY GVGIGVIAFL ACVGFLLADA T_nigr_CAF89717 ASIVNEGYVN IGSE.RLYCV FNKNADACNY GVFVGLVGLL ACSFFGLLDY D_mela_NP_61090 GCISSEGWTE K.DG.KEYCL YNGDGMACKY GNMVGVFGFL ASMGFMGGEF D_rerio_syngr1_ GCIANEGYVN RPDEVEEFCI FNRNQNACNY AVGMGALDFL CCAAFLALDI E_eleg_NP_50923 YSVSKGGWHK PSDAIHPVCL YGRSSSTCSF ATAVGFFAVC GAIVLIVLDA A_gamb_EAA05258 GCISSEGWRE EANG.KEYCI INRDGNACNY AVGIGVIAFL AAMGFIAGEY chick_syngr1_XP GSIVNEGYVN RLDESEEHCI FNRNRNACNY GITVGVLAFL SCLLYLALDA bee_XP_624778_1 .......... .......... .......... .......... .......... homoSYNGR1a_NP_ YFPQISSVKD RKKAVLSDIG VSAFWAFLWF VGFCYLANQ. ..WQVSKPKD X_laev_syngr1_B YFPQISSVKD RKKTVISDIA VSALWAFFWF VGFCFLANQ. ..WQVSNPND X_trop_syngr1_N YFPQISSVKD RKKTVISDIA VSGLWAFFWF VGFCFLANQ. ..WQVSNPND homo_SYNGR3_NP_ RFQQISSVRD RRRAVLLDLG FSGLWSFLWF VGFCFLTNQ. ..WQRTAPGP homo_SYNGR2_AAH YFPQISNATD RKYLVIGDLL FSALWTFLWF VGFCFLTNQ. ..WAVTNPKD D_rerio_XP_6969 ILPLISNAQE RKYIVMADLA FSGCWTFLWF VCFCLTADQ. ..WSKTSDRS T_nigr_CAF89717 KFSSISSIKD RKKAVMLEIG FSGFWTFLYF VSFCFLANQ. ..WSRTTPDE D_mela_NP_61090 LFERMSSVKS RKRYVMADMG FSALWTFMYF VAFLYLWSQ. ..WSSSAPPP D_rerio_syngr1_ YFPQISSVKD RKKAVLADIG VSAFWSFVWF VGFCFLANQ. ..WQVANPED E_eleg_NP_50923 KMDQISSVPT RRRAVLADLV VSAIFTAIFL IGFFTFWSKL SAFEVDEDDE A_gamb_EAA05258 LFEQMSSVKT RKHYVLADLG FSAFWSFLFF IGFCYLTNQ. ..WGKADDPP chick_syngr1_XP YFPQISSVKD RKKAVLSDIG VSAFWAFLWF VGFCFLTNQ. ..WQASKEED bee_XP_624778_1 ....MSSVKT RKHFVLLDLG FSGFWAFLYF VGFCYLTNA. ..WNKSETPK homoSYNGR1a_NP_ NPLNEGTDAA RAAIAFSFFS IFTWAGQAVL AFQRYQIGAD SAL...FSQD X_laev_syngr1_B NPMNEGADAA RAAITFSFFS IFTWAGQAVL AYQQYRLGSD SAL...FSQD X_trop_syngr1_N NPMNEGADAA RAAIAFSFFS IFTWAGQAVL AYQRYRLGSD SAL...FSQD homo_SYNGR3_NP_ ATTQ.AGDAA RAAIAFSFFS ILSWVALTVK ALQRFRLGTD M.....SLFA homo_SYNGR2_AAH VLV..GADSV RAAITFSFFS IFSWGVLASL AYQRYKAGVD D.....FIQN D_rerio_XP_6969 GI...PTDAV HAVIAFSFFS IASWGALTYF AVVRFRQGVE E.....VTQS T_nigr_CAF89717 VPLDQGADAA RAAIAFSFFS IITWAGLTVR AVQKYLLGTD MSL...FTTE D_mela_NP_61090 LGI..GAGSM KTAIWFCLFS IVSWALCALM AYKRFLIGAG DEF...TSAF D_rerio_syngr1_ NPLKEGADAA RAAITFAFFS IFTWAGQAFF GFQRYKLGSS SSL...FSQD E_eleg_NP_50923 NPI..KTNNA KFGILSALLS FLAWGGAAFF AWRRYEEGNQ ATHEPNYDEH A_gamb_EAA05258 NGE..GVNNV QASIVFSFFS IFTWAGCAYF AFLRFKAGVD PSF...SSTY chick_syngr1_XP NPMNEGGDAA RAAITFSFFS IFTWV..... .......... .......... bee_XP_624778_1 DNY..GVNNV QSAIAFSFFS IFTWAACAWF AFQRFKQGTD AAF...APSY homoSYNGR1a_NP_ YMDPSQDSSM PYAP..YVEP TGPDPAGMGG TYQQPANTF. DTEP..QGYQ X_laev_syngr1_B YMDPSQDQGP PYPP..YASN EDLDPS...A GYQQPPTEAY DAGS..HGYQ X_trop_syngr1_N YMDPSQDQGP PYPP..YASN EDLDPS...A GYQQPPSDAY DAGS..QGYQ homo_SYNGR3_NP_ TEQLSTGASQ AYPG..YPVG SGVEGT...E TYQSPPFTET LDTSP.KGYQ homo_SYNGR2_AAH YVDPTPDPNT AYAS..YPGA S....V...D NYQQPPFTQN AETT..EGYQ D_rerio_XP_6969 YTDPPPDLSS PYPSTYTPPT YPSFQNTGAD IYQQPPFTPN PDPSGQTSFQ T_nigr_CAF89717 HLDGAAPTQR LPLQLTCRRH RRDHGGLPEP PLHREQRSTH LPGSHLLDQG D_mela_NP_61090 ETDPANV... VHQQAYGYSM DNDNDQYSAS PFGQPQQGGM EQQQSGMEYQ D_rerio_syngr1_ YTDPSQDPAA APSE...... .....GTEYT GYNADMEANY DGS...GGYQ E_eleg_NP_50923 FGQVSTDVQD GYGY...... .GGDSTGIGH VGAPPPQSSY QSGAAPQTMQ A_gamb_EAA05258 ESDPSAAQQY AAYP...... ....ASNEND QFQEAPF... .......... chick_syngr1_XP .......... .......... .......... .......... .......... bee_XP_624778_1 EADPVGGTGY TSYP...... .....DATDT GYQEPPFGQQ QQQQQ.QQQQ homoSYNGR1a_NP_ .SQGY..... ..... X_laev_syngr1_B .TQDY..... ..... X_trop_syngr1_N .TQDY..... ..... homo_SYNGR3_NP_ .VPAY..... ..... homo_SYNGR2_AAH PPPVY..... ..... D_rerio_XP_6969 .PPVY..... ..... T_nigr_CAF89717 .SPRRARSSA K.... D_mela_NP_61090 .QPTY..... ..... D_rerio_syngr1_ .NQDY..... ..... E_eleg_NP_50923 QPPSNPYTQS EGYGY A_gamb_EAA05258 .......... ..... chick_syngr1_XP .......... ..... bee_XP_624778_1 QQQQQRMPDF RAPAY
ALN
CLUSTAL FORMAT for T-COFFEE Version_3.93, CPU=12.81 sec, SCORE=52, Nseq=13, Len=276
A.gamb_EAA05258.2 -NEANRS-KMDIG-GAYGGGKAGGAFDPIAFVQRPTVILRAVCWLFAIIVFGCISSEGWR
bee_XP_624778.1 ------------------------------------------------------------
D.mela_NP_610908.1 MDMLNQILSINNG-GAYGGGKAGGAFDPLTFAMKPQVVIRALCWLFSVVVFGCISSEGWT
E.eleg_NP_509239.1 ---------MENV-RAYGAGLAGANFDKNTFFKKPTVLFRCAALLFGLILWYSVSKGGWH
D.rerio_XP_696934.1 --------MESRS-VAYGASLAGAGFDLVKFIKQPQTVVRFLSWVFAIVVFSSITAEGYV
homo_SYNGR2_AAH00407.1 ----------MES-GAYGAAKAGGSFDLRRFLTQPQVVARAVCLVFALIVFSCIYGEGYS
D.rerio_syngr1_AAH83255.1 ----------M-D-QAYGAGKAGGTFDPITFFQQPQTILRIVSWIFSIVIFGCIANEGYV
X.laev_syngr1_BAB79596.1 ----------MEG-GAYGAGKAGGAFDPQTFIRQPHTILRMVSWVFSIVVFGCIINEGYI
X.trop_syngr1_NP_001016195.1 ----------MEG-GAYGAGKAGGAFDPQTFVRQPHTVLRMVSWVFSIVVFGCIINEGYI
chick_syngr1_XP_423200.1 --------------------------------------------VFSIVVFGSIVNEGYV
homoSYNGR1a_NP_004702.2 ----------MEG-GAYGAGKAGGAFDPYTLVRQPHTILRVVSWLFSIVVFGSIVNEGYL
T.nigr_CAF89717.1 ----------MDGVGSFGAGRTGSAVDPIAFAKQPQTILRVLSWIFSLVVFASIVNEGYV
homo_SYNGR3_NP_004200.2 ----------MEG-ASFGAGRAGAALDPVSFARRPQTLLRVASWVFSIAVFGPIVNEGYV
A.gamb_EAA05258.2 EEANG-KEYCIINRDGNACNYAVGIGVIAFLAAMGFIAGEYLFEQMSSVKTRKHYVLADL
bee_XP_624778.1 ---------------------------------------------MSSVKTRKHFVLLDL
D.mela_NP_610908.1 EKD-G-KEYCLYNGDGMACKYGNMVGVFGFLASMGFMGGEFLFERMSSVKSRKRYVMADM
E.eleg_NP_509239.1 KPSDAIHPVCLYGRSSSTCSFATAVGFFAVCGAIVLIVLDAKMDQISSVPTRRRAVLADL
D.rerio_XP_696934.1 NSTDEAEVRCVFNRNDGACHYGVGIGVIAFLACVGFLLADAILPLISNAQERKYIVMADL
homo_SYNGR2_AAH00407.1 NAHESKQMYCVFNRNEDACRYGSAIGVLAFLASAFFLVVDAYFPQISNATDRKYLVIGDL
D.rerio_syngr1_AAH83255.1 NRPDEVEEFCIFNRNQNACNYAVGMGALDFLCCAAFLALDIYFPQISSVKDRKKAVLADI
X.laev_syngr1_BAB79596.1 NSSTEEEEHCIFNRNPSACSYGVTVGVLAFLTCLLYLAVDIYFPQISSVKDRKKTVISDI
X.trop_syngr1_NP_001016195.1 NASTEAEEHCIFNRNSSACAYGVTVGVLAFLTCLLYLAVDVYFPQISSVKDRKKTVISDI
chick_syngr1_XP_423200.1 NRLDESEEHCIFNRNRNACNYGITVGVLAFLSCLLYLALDAYFPQISSVKDRKKAVLSDI
homoSYNGR1a_NP_004702.2 NSASEGEEFCIYNRNPNACSYGVAVGVLAFLTCLLYLALDVYFPQISSVKDRKKAVLSDI
T.nigr_CAF89717.1 NIGSE-RLYCVFNKNADACNYGVFVGLVGLLACSFFGLLDYKFSSISSIKDRKKAVMLEI
homo_SYNGR3_NP_004200.2 NTDSGPELRCVFNGNAGACRFGVALGLGAFLACAAFLLLDVRFQQISSVRDRRRAVLLDL
:*. *: *: ::
A.gamb_EAA05258.2 GFSAFWSFLFFIGFCYLTNQWGK---AD--DPPNGEGVNNVQASIVFSFFSIFTWAGCAY
bee_XP_624778.1 GFSGFWAFLYFVGFCYLTNAWNK---SE--TPKDNYGVNNVQSAIAFSFFSIFTWAACAW
D.mela_NP_610908.1 GFSALWTFMYFVAFLYLWSQWSS---SA--PPPLGIGAGSMKTAIWFCLFSIVSWALCAL
E.eleg_NP_509239.1 VVSAIFTAIFLIGFFTFWSKLSAFEVDE--DDENPIKTNNAKFGILSALLSFLAWGGAAF
D.rerio_XP_696934.1 AFSGCWTFLWFVCFCLTADQWSK---TSDRS---GIPTDAVHAVIAFSFFSIASWGALTY
homo_SYNGR2_AAH00407.1 LFSALWTFLWFVGFCFLTNQWAV---TNPKD--VLVGADSVRAAITFSFFSIFSWGVLAS
D.rerio_syngr1_AAH83255.1 GVSAFWSFVWFVGFCFLANQWQV---ANPEDNPLKEGADAARAAITFAFFSIFTWAGQAF
X.laev_syngr1_BAB79596.1 AVSALWAFFWFVGFCFLANQWQV---SNPNDNPMNEGADAARAAITFSFFSIFTWAGQAV
X.trop_syngr1_NP_001016195.1 AVSGLWAFFWFVGFCFLANQWQV---SNPNDNPMNEGADAARAAIAFSFFSIFTWAGQAV
chick_syngr1_XP_423200.1 GVSAFWAFLWFVGFCFLTNQWQA---SKEEDNPMNEGGDAARAAITFSFFSIFTWV----
homoSYNGR1a_NP_004702.2 GVSAFWAFLWFVGFCYLANQWQV---SKPKDNPLNEGTDAARAAIAFSFFSIFTWAGQAV
T.nigr_CAF89717.1 GFSGFWTFLYFVSFCFLANQWSR---TTPDEVPLDQGADAARAAIAFSFFSIITWAGLTV
homo_SYNGR3_NP_004200.2 GFSGLWSFLWFVGFCFLTNQWQR---TAPGPATTQAG-DAARAAIAFSFFSILSWVALTV
.*. :: .::: * . . : * .::*: :*
A.gamb_EAA05258.2 FAFLRFKAGVDPSFSSTYESDPSAAQQ--------------YAAYP-ASNE-----ND-Q
bee_XP_624778.1 FAFQRFKQGTDAAFAPSYEADPVGGTG--------------YTSYP-DATD-----TG--
D.mela_NP_610908.1 MAYKRFLIGAGDEFTSAFETDPANVVH--QQ----------AYGYS-MDND-----ND-Q
E.eleg_NP_509239.1 FAWRRYEEGNQATHEPNYDEHFGQVSTDVQD----------GYGYGGDSTG-----IG-H
D.rerio_XP_696934.1 FAVVRFRQGVEEV--TQSYTDPPPDLSSPYPS--TYTP----PTYP-SFQNT-GAD---I
homo_SYNGR2_AAH00407.1 LAYQRYKAGVDDF--IQNYVDPTPDPNTAYAS----------------YPGA-SVD---N
D.rerio_syngr1_AAH83255.1 FGFQRYKLGSSSSLFSQDYTDPSQDPAAA------------PSEGT-EYT---------G
X.laev_syngr1_BAB79596.1 LAYQQYRLGSDSALFSQDYMDPSQDQGPP------------YPPYA-SNEDLDPSA---G
X.trop_syngr1_NP_001016195.1 LAYQRYRLGSDSALFSQDYMDPSQDQGPP------------YPPYA-SNEDLDPSA---G
chick_syngr1_XP_423200.1 ------------------------------------------------------------
homoSYNGR1a_NP_004702.2 LAFQRYQIGADSALFSQDYMDPSQDSSMP------------YAPYV-EPTGPDPAGMGGT
T.nigr_CAF89717.1 RAVQKYLLGTDMSLFTTEHLDGAAPTQRLPLQLTCRRHRRDHGGLP-EPPLHREQR---S
homo_SYNGR3_NP_004200.2 KALQRFRLGTDMSLFATEQLSTGASQA--------------YPGYP-VGSGVEGTE---T
A.gamb_EAA05258.2 FQEAPF------------------------------
bee_XP_624778.1 YQEPPFGQQQQQQQQQQQQQQQQRMPDFRAPA-Y--
D.mela_NP_610908.1 YSASPFGQPQQGGMEQQQSGM-----EYQQPT-Y--
E.eleg_NP_509239.1 VGAPPPQSSYQSGAAPQTMQQPPSNPYTQSEG-YGY
D.rerio_XP_696934.1 YQQPPFTPNPDPSGQ----------TSFQPPV-Y--
homo_SYNGR2_AAH00407.1 YQQPPFTQNAETT------------EGYQPPPVY--
D.rerio_syngr1_AAH83255.1 YNADM-EANYD-GS-----------GGYQNQD-Y--
X.laev_syngr1_BAB79596.1 YQQPP-TEAYDAGS-----------HGYQTQD-Y--
X.trop_syngr1_NP_001016195.1 YQQPP-SDAYDAGS-----------QGYQTQD-Y--
chick_syngr1_XP_423200.1 ------------------------------------
homoSYNGR1a_NP_004702.2 YQQP--ANTFDTEP-----------QGYQSQG-Y--
T.nigr_CAF89717.1 THLPGSHLLDQGSP-----------RRARSSA-K--
homo_SYNGR3_NP_004200.2 YQSPPFTETLDTSP-----------KGYQVPA-Y--
Promoter analysis
- go to
- humNSG2ex1 + 2000bp 5'
>chromosome:NCBI36:5:173403330:173468885:1 CTCCTGCCTCAGCCTCCCAAGTAGTTAGGATTACAGGCATGCGCCACCATGCCTGGCTAA TTTTTGTATTTTTAGTAGAGACGGGATTTCACCATGTTGGTCAGGCTGGTCTCGAACTCC TGACCTTGTGATCCACCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCAC TGCTCCCGGCTGCCAATTTTTAAATCAGATTTTTGTTTTTTGGCTGTTGTTTGAGTTTCT TATATATTCTGGGTATTAACCCCTGGTCAGATGCATAGTTTGCAGATATTTTCTTCCATT TTGTAGGTTGTCTCTTTAGTCTGTTAATTATTTCCTTTGCTGTGCAGAAGCTTGGCTTGA AATTATTAAAAGTGTGATTTCTATGTGTGAATCAATCACAAGACATGTCAAAAGGAATTT CTTTTTCCTCTGGAGGAAAAAGATTAAACACAAGGGTTCACAATTGACTCCACGTGGTTA TCCACATTGTGTTGTCACAATGATTGCACCTGAAAACTCATCTAGGTCTTTGGAAAGAAG AGAATGGAGGACTAACATTTACTGGGACACTCCCATATTATGTATCTGCCTACTTCTATT AATATAGCCCTGTGCAGCTCAGATGTGCTAGCTTTTGTTGTCTCAGAAAATGTCTCTCTC TCTGTCTCTCCACACACGTGTCCCCCCCCCCCACACGTTTCATTACTGAACAATATATAT AATACTTACGTTTTCTCCTGACCTTTTAGCTAGCAGAGTGTATGCTCAGCACATGAGCAC TAACTAGGGTGACCTAACAATTTATCACATAAACTAGAATACTTTTGAAAGCAAAAGGGG ACCCTATGACAAATGCCAAGACAGCTGGGCCTCATGAAGTGCATCATAAGCAGCACTGCA GCTGGGAATGAACAACCATCAGTGACTTGAACCACAGCTTGGTGAAGACAGTGGCAACAG CCTTGACCTCAGAGGATTTGAAGAGAATCTGTGAGCAATCCCCGGGGATGAAATAATGCA GCCATTCAGAACCTTGTCCCTGAGCAGTAAGGGGTTTCCTTGAGCACAATCTCTTCTCAT ATTTACAATCGCTCTCCTGAGCAATAAGGGGTTTCCTTGAGCACAATCTCTTCTCATATT TACAATCGCTCTGCAAGAGAGATATTATTATTCTTACGCCAGAGAAAAGGAAATGGAGGT TTAAAGAATAAATGCAAAATGTCCAAAATCCATACAGCCAGAATTTGGTAGAGCAGACAC TAGGACTTTGCCCTGTCTGATTCCAGGCACCAACTTGGAAGCCATGCAATGTCCTGGGCT GGATACAAATTTTGGTGGCCACCGATCAGGGTTCAAATTCCAGCTCTGGTTACCGTGGCT GCCCTGTATGATCACAGTGCAATGTTGAGTGTAGTAGCTCATGTGAATACAGTGCTTGCC ATAGTCCCTGCTCTGTACTACATGCATTCCCTATGCTATCCCATTTCATGCTTTGTACTA ACCCCATCATGTGTGTACTATTAGAAACACCATTTTGCAAATGAGGGAGATAGTCTGAAA GAGGCTGGAAAAGTGCCCACTGCATGAAAGATACACAATAAATATATTTCCCTTCTGTCC TGACCACAGGGTCAGAGCACAGTAGAGGTCTTGAACCATTCTGTGTTTTATGATATTGTT CTGGAAGGTCTTAGGAGGCAATGCCCTCTCCTAATGAATGTGCCTGCTTTTCCAGTTTTT CCAAAGGCTCAAGGATTACTTGTTATATGGTGCATATTAATTATTTTTTTGGTGTGGCCA AAATCCTTCCCACTTTCTTGAAACCATTTTGTCCCGTGCAGTGGTTGTGGCCATGCATAA GAAACAGCAGGTGGTGCCAGATGACAGATGGTGTGGGAGCGCGTTCCCCGGTAGGAGGGG GCGCGAGCGAGCAAGCAGGCAGGCAGCTGCCAGGAGCTCTTCCCTGCTCGCTCACGCCTG CTCTCAGAAGCTCCGATCCAGACACACGCGAGGCGCTGTCCTTTCAGCACCACAAGCTCG GGCTGAGGAGGGAGGACTCCTGGCCGTCCTCCTCCTCTTCAAATTGGCTTGAATCTGCTC TGACCCCCCACGAGTGCAGCACA
- humSYNGR3 exon1 + 2000bp 5'
>chromosome:NCBI36:16:1977969:1984376:1 GTGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCATGAACCACCCACCTCAGCTTCCCAA GGTGCTGAGATTACAAGCGTGAGCCACTGCGCCAGGCCAGAGTCTGTTTTTGAAGGCATC CAGGCCAGTGGAACTCTAGTGCAAGGAAAAGTTCTGGCTTGAGCTGGTGTTCCAGAGCTG TTGACACGCAGACCAAAGGAGTTAGCACAGAGGGAGAGACCTCCCCAGGATCGCGCCCTG GGCTCCTAAGGCTCACAGGTCACAGAGGAAGGACCCATGAGGGAGGAGGACCTCCAGGAG GGGCATAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAAACCAAGGTGGGCAGATCAC TTGAAGTCAGGAGTTCGAGACCAGCCTGGTCAACATGGCGAAACCCCGTCTCTACTAAAA ATACAAAAAAAAAAAAAAAAAAAATTAGCTGGGTGCGGTGGCACACCTGGAATCCCAGCT ACTCCAGTGGCTGAGGTAGGAGAATCACTTGAGCCCCTGAGGCAAAGCTTGCAGTGAGCC AAGATTGCGCCACTGCACTCCAGCCTGGGTAACAGAGTGCGACTGTAACTCAAAAAATAA ATAAATAACTAAAGAAATAAATGAGTCGACAGCAGCATCAGACTTGCCCTTGGGATTGGC ACGGAGAGGTCAGTGGCAACCTTGAGTTTAGGTGGCGGTGGGAGCTGATTCTGCCGGGTC AGAGGGAGAGAGAGGAGGGTGTTGCAGGCAGAGTTTGCTGCTAAAGGAAGCAGTAACGTA AGGCAGCTGGAGGGGAGGTGGGGTCAACAGTGTTTGGCTTTTAGGAGAAAGTGCAGCATG TCTGGGTGCTGATGTTAGTGATGAAGTAGAGAATGAATGACACAGAGGGGAGGTCTGTGG CCAACAGGTGAGAGGGGTTGTGATCGGACGCACAGTGTGATGGACTTGGAACACAGTGAG TAGCGCCTCTGGCAACACCTGCTCTGCCCACCTGTGCCCAGCAAGGCTGAAGAATGAGCT CCAGGGGGGCTGGGCCACGCAGCACCATCTGTGCACCCGGCTCGTGTAGCAGGGACCTGG GTTGCTTATTATCTGAAGTACAGGGTGGTAACAGTCTCCGCCACTACACAGGTCAAGCGC TTGGCGCTGTAAATGTCAGTGCAGACATCTCAGTGCTCTAGACAGAAACCTAGGAGTCAT CTGAACTTCCAGCCTGCTAGGAACATGAGGAGAGGGACCTTGTTGCACCCAAGGCTGGGG TCTGTGGAGGGGACTCAGCGGGACACAGGGCAGCCAGGCACCACCCCCACCCGACTCCTA GTCTCTGATGCCGCTCCCTGCCCTCCATTCCAGACTAGGCGCCGCAAGTACGCTGGGGAG ACCCAGGAGTAGGGAGGGCATTGGGAGCACCACCACCTGGCCACGGGCAAGGAGCGGAGA CACCGAAACCAACACTCCCAGCGGCGCTGGCCACGGTGGCTCTGTCCCCTCCCTCAACAG GTGCTCCTGGGGCCAACGCCTTTCTTCCCACCAGATCCTCCCCGCCAGAGGCTAGAAGCT GTGATAGCAGCTAGAGCACAGTGGGGGGCCATGAGAAAGACCCCAGTTATCCATCTGGTC TTCTTGGGACCAGGGCCAGGGAGCCGGTCCCCTCTCCCGTGGGTTGGGGGAAGATGCTGC AGCCCGTGGACCTCCTACCCCTTTACTCCCTCACCCAAGTGCCCTTCCCAGAGGAGCGGA CTCCTCCTGTCTGTCCTCCCGGCTCTAGCAAAGTCTGCGCCCAGCACCCGAGCCCCACCC TGCCCCCGGGGACCTGGCTGGTGGGTTCCTGAGGATGGTCTCCATCTCGGGACCGGGGCA GGCAGGTGAGGGTGGGGGATGGGAGGTGGGCGCGGCGGAGGGAGAGGAGGGACCCGGCCC CGCGCGCATGGACCCAGTGGGGGGCGCGGGCGCGGCCCCGCCCCGTCCCGCGCGTCCCCG CCGCGGCCGGCGCGCGCTCCCGGGAGGCGGCAGCGGCTGCAGCGTTGGTAGCATCAGCAT CAGCATCAGCGGCAGCGGCAGCGGCCTCGGGCGGGGCCGGCCGGACGGACAGGCGGACAG AAGGCGCCAGGGGCGCGCGTCCCGCCCGGGCCGGCCATGGAGGGCGCCTCCTTCGGCGCG GGCCGCGCAGGGGCCGCCCTGGACCCCGTGAGCTTTGCGCGGCGGCCCCAGACCCTGCTC CGGGTCGCGTCCTGG
- mus Syngr3 exon1 + 2000bp 5'
>chromosome:NCBIM35:17:22866087:22874033:-1 CTGTGGAAAGCTGGTTTTCACTCTTTCAGCAATTCCTAATCGCGGGCACCTTCTGTGATT CCTGGCCAGGAGCAACCCTGTCTCAAAAAATCAAAACAAAATAAACAAACAAACAAAAAA ACCCGACAATAACTTTATTCACTTACTTTTGGTTTTTTGAGACACAGTTTCTCTGCCTAC ATCTGCCTCCAAAGTGCTGGGATTAAAGGCATGCGTTACCACTGCCCAGCCAATAAATTT ATTTTTAGAAAGTAAATCAAGCCAGGCGTGGTGACACATGCCTATAATCCCAGCACTTGG GAGGCAGAAGCCAGTGAATTTCTGAGTTAGAGGCCAGCCTAGTCTACAGAGTTAGTTCCA GGACAGCCACGGCTACACAGAGAAGAGAAACCCTGTCTTGAAAACCCAAAAAAAAAAAAA AAAAAAAAAAAAGCTTCATTTTGTCCCTGTTCACAGAGCATCTGGGTCAAGACAAGCAGA ACTTGTGTGAAGGAAGGTTATGGTTTGAGCTGGCATTTGAGAGCGGTCAGCACAGACAGA GGGATAAGTACTCAGCAATGAAAAAAGGTAAACAGCAGAAGTGTAAGCTCATGGGTGAAC CGGAAGCAAACATTTCCAAAATGCAGGGTAGGGGCTTGGTTATACTGGGTTTTGAGGGAA TGGAGGAAGAGGCACTAGAAATAGATGGGCAACAGCTTGAGTTTGCTGCTAAGGGAGACA GAAGTATGAGCACGAACTGTTTGTTTTGGTGATAATTGGGAATTTAAAACCCCATGCATG CTACTAGCTAAGCAGGCATTCTACCACTGAGCTCAATACTCAGCCCAGGAATGGTGTTTT TCAAAGAATATGCTGCATTGTTTGGGTGTTGATGAAAATGACGGAGGAGAAGGACAAAAT GGGTGATCACACAGATCTGTTAATAGCTAAAGGAGATGGGATGGGATGCTCACCTGCATC CAACTAGACTGAAACAAGACAGACCAGAGCCAGTGGTTCCTCCAGCTACACTTTCCTCTG AAGAATGAACAACAGATCACACAAAGTAAAGTGTGTAGTCTCTATATGTGGGAGCTTTCC TTATACCCAGCTCTGGTCCCAGGAAGACAGAGATAGGTAACTGGGGCCTTACCCATGATC AACTACACCCTAGCTTCTGTGACCATGAAGGTGAAGCCATTCAGTCTCTTACCAGCCTGG CACTGAAAGAGCATCAAGTGGCTCTGTTAGTCAGGCTGTGGGGCAGAGGAATCCCAGCAG AGGTCAGGATAATTAGGCAACAGCTGGGACAAGATCTTATCTCTGGTAATTCTCCCCTCC CAGAACTCAGGATTAATTAGCTACAGATCAACCCAGACCAGAGATGGAAAGGGCTTTTGG AAGAAATGACTTGGCCTGAGGAGAACAGGCATGCTCAACCTTAACTTCTGCTGGCCACAG TGGACTCTGCTTCCCAGACAGTACCCCTGACAGTGACAGAACTGCCACTCTCCCCACCTG ACCCTGTTAGGAAGGTACAACCTATGAAGAAAAAGCCAGAATACAGGGGACATGTGAGCC ACAGACAACACAAGTGTGCACAACACCTCTGAGCTGAGCTTTTCTTGATTCAAGGGCTAG TGAGAACGCCCCGCCAGAGATTTACCTCTGGTCTTCTGAGGTTGAGGGCTCGTTCTCTCT TCCTGAATGTAAAGGTCAAGATGCTGGGCCTCAGTTTCCTCTTACATACTCACCAAAAGG CTCTCCTGATCAGAGAAGCAGGATGCTGCACTTGTCCTCCTGTCGATGCTCTTGGCTATG ACAAAATCTGAGCTTACCTTCTCTTGCCCACCTCTAAACCCCATAAGGGCTTCGTTCTGT GTCTCTTGAGAATGTCCCTATCTCCAACTCTGTCATACGGGGGAGAGCGAGTGGGAAGGA TCCAGGGCAGGGCTCAGACCCCGGCGCATGGACCTAGTCGGGGGCGCTGGCTCAGCCCCG CCCCGCGCGCCCCCGTCGCAGCCGACGCGCGCTCCCGGGAGGCGGCGGCAGAGGCAGCAT CCACAGCATCAGCAGCCTCAGCTTCATCCCCGGGCGGTCTCCGGCGGGGAAGGCCGGTGG GACAAACGGACAGAAGGCAAAGTGCCCGCAATGGAGGGAGCATCCTTTGGCGCGGGCCGT GCGGGAGCTGCCTTTGATCCCGTGAGCTTTGCGCGGCGGCCCCAGACCCTGTTGCGGGTC GTGTCCTGG
Batch Entrez Acc nos
AAA40104 AAH05595 AAH12710 AAH14854 AAH24644 AAH28901 AAH31452 AAH46616 AAH49971 AAH50927
