RetrogeneDB ID: | retro_ecab_516 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 2:61577889..61578994(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SSRP1 | ||
| Ensembl ID: | ENSECAG00000016612 | ||
| Aliases: | None | ||
| Description: | structure specific recognition protein 1 [Source:HGNC Symbol;Acc:11327] |
Retrocopy-Parental alignment summary:
>retro_ecab_516
CTTACAAGCAAGGCCTTTGACTACAAGATCTCCTACACTTCAGTACCTAATCTCTTTTTGTTGCGTCACAAGGACCATCA
CCAGATATTCTTTGTGATCAGGCTGTATCCCTCCATCAAGCAGGGCAAAACCTGGTACCGCTTCCTGATCCTCCTTTTCT
CCAAGGACAAGGACATTTCCTTGACTTCCAACAAGAACAAGGAAGAAATGGAGAAGCACTTTGATAGGCAGTTCACTAAG
AACATGTTGGGATCCCTCCAAGAGATGGTTGGCCAAGTCATGAAAGCATTGGTGAACCACAAGGTCACACTCCCAGGCAA
CTTCCAAGGACATTTAGGGGCCCAGTGTTTCACTTGCTCCTACAAGGTGAGCTCAGGACTGCTCTACCTGCTCAGTGGGG
CTTCATCTAGGTTCACAAGCCACCCAGACAGATCTGCTTTGACAAAATCTCTTTCATCAACTTTGCCAATGGCACCACTG
CCACTTGCTCCTTTGACTTTGAAATTGAGACCAAGCAGGCACTCAGTATACCTTCGGCAGCATTGAGAGGGAGGAGTATG
AGAAACCATTTGATTTTGTCAATGCAAAAAAGCTCAACATCAAAAACCAAATATTAAAAGAGAAGATGAACCAAAACTAC
AATGAATAGGCCTCTAACTCTGATGAAGATGAGTGTGATGTCTTCATGGAACTGATAAAAGATGCCTGCTTAGAGAATGC
CACCAAAAACTATAGTGACTCAGGAGAATAAACTGATAAGTCATTCTAGTCAGGTGGAGAAAAGCAGGAAATGGCAGAGA
AGTTTAACAGTAACGCCTCTGCCAGCCAGCTCTTCCAGTAATGATGGTGACAGTGATTGGGATGAGACGAAGAGAAAACA
GCTCAAAACAGCTGAAACAGTCAAGGATCACAATGGTCTCAAGAAGTCTGTGGAGGTGGAGAAGGGCAAAGTCCTCAATG
CCCCCAAAAGGCACATGTCTGCATACATGCTGTGCTCAATGCTACTTGAGAGAAGATCAAGCCTGCCCATCTTGGCATCA
GTATCATGGATATTTCCAAGAAGGCATACAAGATCTGGAAGGGGATGCCCAAGGAGAAGAAAGAG
ORF - retro_ecab_516 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 67.02 % |
| Parental protein coverage: | 62.29 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | LHGKTFDYKIPYTTVLRLFLLPHKDQRQMFFVISLDPPIKQGQTRYHFLILLFSKDEDISLTLNMNEEEV |
| L..K.FDYKI.YT.V..LFLL.HKD..Q.FFVI.L.P.IKQG.T.Y.FLILLFSKD.DISLT.N.N.EE. | |
| Retrocopy | LTSKAFDYKISYTSVPNLFLLRHKDHHQIFFVIRLYPSIKQGKTWYRFLILLFSKDKDISLTSNKNKEEM |
| Parental | EKRFEGRLTKNMSGSLYEMVSRVMKALVNRKITVPGNFQGHSGAQCITCSYKASSGLLY-PLERGFIYVH |
| EK.F....TKNM.GSL.EMV..VMKALVN.K.T.PGNFQGH.GAQC.TCSYK.SSGLLY.P...GFI.VH | |
| Retrocopy | EKHFDRQFTKNMLGSLQEMVGQVMKALVNHKVTLPGNFQGHLGAQCFTCSYKVSSGLLY<PAQWGFI*VH |
| Parental | KPPVHIRFDEISFVNFARGTTTTRSFDFEIETKQ-GTQYTFSSIEREEYGKLFDFVNAKKLNIKNRGLKE |
| KPP..I.FD.ISF.NFA.GTT.T.SFDFEIETKQ.GTQYTF.SIEREEY.K.FDFVNAKKLNIKN..LKE | |
| Retrocopy | KPPRQICFDKISFINFANGTTATCSFDFEIETKQ<GTQYTFGSIEREEYEKPFDFVNAKKLNIKNQILKE |
| Parental | GMNPNYDEYA-DSDEDQHDAYLERMKEEGKIREENANDSSDDSGEETDESFNPGEEEEDVAEEFDSNASA |
| .MN.NY.E.A..SDED..D...E..K......E......SD.SGE.TD.SF..G.E....AE.F.SNASA | |
| Retrocopy | KMNQNYNE*ASNSDEDECDVFMELIKD--ACLENATKNYSD-SGE*TDKSF*SGGEKQEMAEKFNSNASA |
| Parental | S-SS-SNEGDSDRDEKKRKQLKKAKMAKDRKSRKKPMEVKKGKDPNAPKRPMSAYMLW-LNASREKIKSD |
| S.SS.SN.GDSD.DE.KRKQLK.A...KD....KK..EV.KGK..NAPKR.MSAYML..LNA..EKIK.. | |
| Retrocopy | S>SSSSNDGDSDWDETKRKQLKTAETVKDHNGLKKSVEVEKGKVLNAPKRHMSAYMLC<LNAT*EKIKPA |
| Parental | HPGISITDLSKKAGEIWKGMSKEKKE |
| H.GISI.D.SKKA..IWKGM.KEKKE | |
| Retrocopy | HLGISIMDISKKAYKIWKGMPKEKKE |
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 |
|---|---|---|
| SRP021940_articular_cartilage | 0 .18 RPM | 78 .86 RPM |
| SRP021940_cerebellum | 0 .42 RPM | 96 .44 RPM |
| SRP021940_embryo | 0 .92 RPM | 229 .80 RPM |
| SRP021940_placental_villous | 0 .38 RPM | 65 .05 RPM |
| SRP021940_synovial_membrane | 0 .47 RPM | 76 .37 RPM |
| SRP021940_testis | 0 .51 RPM | 82 .36 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_516 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_516 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_516 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000000375 | 1 retrocopy | |
| Cavia porcellus | ENSCPOG00000000480 | 1 retrocopy | |
| Equus caballus | ENSECAG00000016612 | 1 retrocopy |
retro_ecab_516 ,
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