>retro_sscr_50
ATGGAAATCCCGAGGCTGCTCCCGGCTCGCGGGACGCGACAGGGCGGCGGCGCTGGCAGCCCCGGGGGCGGCGGCCGGAT
CCACGGAGGTCCTGACCCGCGGGCGGGCCAGGCCCCCGCGCGCCGCCTCCTGCTGCTCCGGGGCCCCCAAGATGGCGGGT
CCGGGCGGCGGCGTGAGGAGGCCCGCGCGGCCTCCTCGGGCCCCGGCCAGAGCCCGTCGGCGCCTAGGCCCGATCGCGGC
AGCGGCGGCGGCGGCAGTGGCGGCGGCGATGACTTCTTCCTGGTGCTTCTGGACCCGGTGGGTGGAGACGTAGAGACCGC
GGGCGCGGGCCAGGCCGCAGGGCCCGTGTGGAGGGAGGAGGCCGGGCTGGGCCCGCGGCTCCAGGGGGGCGAAAGCGGCG
CGAACCCTGAGGGCCGCCCTGCGCTGGGCCCCAGCTGCCTGTCTGTTATCCCCGCCCCAGTCCCGGCCCTGGCCCCGATC
CCCGCCCCAGGCCTGGGCCCCGCCGCGGCCTTCGCGGGCACCGTCACTATTCACAACCAAAACCTGCTGTTGCGTTTGGA
GAACGGCGTCCTCACCCTGGCCACGCCCCCGCCGCCAGCCTGGGCGCCTGGGGTCGCCCCTACCCCTCAGCCCCGGGGTC
TGATCGCCCCGCAAGCGGGTATCCCGCATGCCGCGCAGCCTGGCGACTGTCCCGAGCTGCCGCCAGACCTCCTGCTGGCC
GAGCGGGCGGAACCCGCGCCGGCCCCAGCGCCCGAGGCGGAGGCGGAGGGCCCAGCTGCTGCTGAGAGCCCCCGCGGGCC
CCCTGGGCCGGGCCAGGGCGTGGTGCTGTACCTGTGTCCCGAGGCGCAGTGCGGACAAACCTTCGCCAAGAAGCACCAGC
TGAAGGTGCACCTGCTGACGCACAGCAGCAGCCAGGGCCAGCGGCCCTTCAAGTGCCCCCTGGGCGGCTGCGGCTGGACT
TTCACCACCTCGTACAAGCTCAAGAGACACCTGCAGTCACACGACAAACTGAGGCCCTTTGGGTGCCCTGCAGAGGGCTG
TGGCAAGAGCTTCACCACCGTGTATAACCTCAAAGCACACATGAAGGGCCACGAACAGGAGAACTCATTCAAATGTGAGG
TGTGTGAGGAGACTTTCCCCACACAGGCCAAACTCAGCGCCCACCAGCGCAGCCACTTTGAGCCAGAGAGGCCCTATCAG
TGCGCGTTTTCGGGCTGCAAGAAGACGTTTATCACAGTGAGTGCCCTCTTTTCCCATAACCGCGCCCACTTCAGGGAACA
GGAACTCTTTTCCTGCTCCTTCCCTGGTTGCAGCAAACAGTACGACAAGGCTTGTAGGCTGAAAATTCACCTTCGGAGCC
ACACTGGCGAGAGACCGTTCCTTTGTGATTTTGAGGGCTGTGGCTGGAACTTCACCAGCATGTCCAAACTCCTAAGGCAC
AAAAGGAAGCACGATGATGATCGGAGGTTCATGTGCCCTGTGGAAGGCTGTGGGAAATCTTTCACAAGGGCCGAGCATCT
CAAAGGCCACAGCATAACCCACCTGGGCACAAAGCCTTTTGTGTGTCCCGTGGAGGGCTGTTGTGCCAGGTTCTCTGCTC
GCAGTAGTCTCTACATTCACTCCAAAAAACACTTGCAGGATGTGGACACTTGGAAAAGCCGATGCCCAGTCTCCACTTGT
AATAAACTCTTCACATCCAAGCATAGCATGAAGACCCACATGGCCAAAAGGCACAACCTGCGCCAGGATCTCCTAGCTCA
GCTAGAAGCTGCAAATTCTCTTACGCCCAGCAGTGAACTTACCAGCCAGGGGCAGAATGACCTCAGTGAGGCAGAGCTTG
TGTCTCTCTTCTCTGATGCACCTGGTAATAGTTCTGCTGCAGTCCTGGACACAGCATTGGTGAACTCTGGGATCTTGACT
ATTGATGTGGCTTCTGTGAACTCAACTCTGGCAGGGAACCATGTCCCTGCTAGTAATAATAATTCCTTAGGGCAGGCAGT
GGATCCTCCCGCCTTGATGGCCACAGGTGACCTTCCTCAAAGTCTGGATACCTCACTCTTTTTTGGAACAACAGCCGCCG
GTTTTCAGCAGAGCCCCTTAGATATGGATGATGTCTCAACTCTAAGTGTGGGGACATTGGGATCTCTGGGCTCTTTGGCT
ATGAAAAACTCGAGTCAAGAGCCCCAGGCGTTGACTCCCAGCAGTAAGCTAACAGCAGACACAGATGCTCTGACTCCTTC
AAGCACCCTTTGTGAAAGCAGTGTCTCAGAACTACTGCCGCCAACCAAAACGGAATGGAATGTACATCCTGACTCTGACT
TTTTTGGACAAGAGGAAGAAACCCAGTTTGGATTCTCCAATCCAGCAGGGAACCATGGGTCTCAGAAAGAAACAGATCTT
ATCACAGTGACTGGCAGCTCATTTTTGGTATAA
ORF - retro_sscr_50 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: |
66.54 % |
Parental protein coverage: |
59.86 % |
Number of stop codons detected: |
0 |
Number of frameshifts detected |
0 |
Retrocopy - Parental Gene Alignment:
Parental | YRCPEPQCALLFAKKHQLKVHLLTHSGGQGRRPFKCPLDGCGWAFTTSYKLKRHLQSHDKLRPFGCPVGG |
| Y.CPE.QC...FAKKHQLKVHLLTHS..QG.RPFKCPL.GCGW.FTTSYKLKRHLQSHDKLRPFGCP..G |
Retrocopy | YLCPEAQCGQTFAKKHQLKVHLLTHSSSQGQRPFKCPLGGCGWTFTTSYKLKRHLQSHDKLRPFGCPAEG |
|
Parental | CGKKFTTVYNLKAHMKGHEQESLFKCEVCAERFPTHAKLSSHQRSHFEPERPYKCDYPGCEKTFITVSAL |
| CGK.FTTVYNLKAHMKGHEQE..FKCEVC.E.FPT.AKLS.HQRSHFEPERPY.C...GC.KTFITVSAL |
Retrocopy | CGKSFTTVYNLKAHMKGHEQENSFKCEVCEETFPTQAKLSAHQRSHFEPERPYQCAFSGCKKTFITVSAL |
|
Parental | FSHNRAHFREQELFSCSFPGCSKQYDKACRLKIHLRSHTGERPFICDSDSCGWTFTSMSKLLRHKRKHED |
| FSHNRAHFREQELFSCSFPGCSKQYDKACRLKIHLRSHTGERPF.CD...CGW.FTSMSKLLRHKRKH.D |
Retrocopy | FSHNRAHFREQELFSCSFPGCSKQYDKACRLKIHLRSHTGERPFLCDFEGCGWNFTSMSKLLRHKRKHDD |
|
Parental | DRRFACPVEGCGKSFTRAEHLKGHSVTHLGTKPFVCPVEGCCARFSARSSLYIHSKKHLQDVAP-KSRCP |
| DRRF.CPVEGCGKSFTRAEHLKGHS.THLGTKPFVCPVEGCCARFSARSSLYIHSKKHLQDV...KSRCP |
Retrocopy | DRRFMCPVEGCGKSFTRAEHLKGHSITHLGTKPFVCPVEGCCARFSARSSLYIHSKKHLQDVDTWKSRCP |
|
Parental | ASSCDRLFASKHNGKAHVGRQPRRHPDLFPPLGAPSALTPSSDLSGPGQSEFSNVDLALLFSDTPGDNSG |
| .S.C..LF.SKH..K.H.........DL...L.A...LTPSS.L...GQ...S...L..LFSD.PG.NS. |
Retrocopy | VSTCNKLFTSKHSMKTHMAKRHNLRQDLLAQLEAANSLTPSSELTSQGQNDLSEAELVSLFSDAPG-NSS |
|
Parental | AAGASDEALSAGILTIDVTSMSSSLGGD-LPTS-HTSLG-PMDPLVLVAHSDVPPGPDSPLVLGTAATVL |
| AA.........GILTIDV.S..S.L.G...P.S...SLG...DP..L.A..D.P...D..L..GT.A... |
Retrocopy | AAVLDTALVNSGILTIDVASVNSTLAGNHVPASNNNSLGQAVDPPALMATGDLPQSLDTSLFFGTTAAGF |
|
Parental | QQRSFAMDDTQGVGAGALGCLVAVPVKSLSLDPPALTSGSSSAANTCMPASASSTQGNTSVPELLVPIKV |
| QQ....MDD......G.LG.L.....K..S..P.ALT..S...A.T......SST....SV.ELL.P.K. |
Retrocopy | QQSPLDMDDVSTLSVGTLGSLGSLAMKNSSQEPQALTPSSKLTADT-DALTPSSTLCESSVSELLPPTKT |
|
Parental | EADSPPGPDTIRQQERSR |
| E....P..D...Q.E... |
Retrocopy | EWNVHPDSDFFGQEEETQ |
|
Legend:
* | Stop codon |
> | Forward frameshift by one nucleotide |
< | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
Library |
Retrocopy expression |
Parental gene expression |
SRP014902_placenta |
5 .31 RPM |
80 .30 RPM |
SRP014902_testis |
41 .02 RPM |
132 .11 RPM |
SRP018288_heart |
5 .47 RPM |
14 .41 RPM |
SRP018288_kidney |
6 .50 RPM |
36 .35 RPM |
SRP018288_liver |
2 .88 RPM |
16 .31 RPM |
SRP018288_lung |
16 .09 RPM |
46 .94 RPM |
SRP018856_adipose |
11 .63 RPM |
22 .13 RPM |
SRP035408_brain |
3 .59 RPM |
38 .30 RPM |
SRP035408_liver |
1 .41 RPM |
19 .40 RPM |
Sus scrofa was not studied using ChIP-Seq data.
2 EST(s) were mapped to retro_sscr_50 retrocopy
EST ID |
Start |
End |
Identity |
Match |
Mis-match |
Score |
BI346972 |
56142725 |
56143267 |
99.9 |
541 |
1 |
540 |
EW000871 |
56142712 |
56143316 |
99.9 |
603 |
1 |
602 |
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_50 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_50 has 0 orthologous retrocopies within eutheria group .
Parental genes homology:
Parental genes homology involve
6 parental genes, and
7 retrocopies.