RetrogeneDB ID: | retro_ecab_807 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 4:31874048..31875299(-) | ||
| Located in intron of: | ENSECAG00000017842 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CDCP1 | ||
| Ensembl ID: | ENSECAG00000025146 | ||
| Aliases: | None | ||
| Description: | CUB domain containing protein 1 [Source:HGNC Symbol;Acc:24357] |
Retrocopy-Parental alignment summary:
>retro_ecab_807
TGCACGGACCACCGGTACTGCCACAAGAAGTCTTACCCACTCCGGGTGCCCAGCAACATCCTCCAGCTGGCTGTGCAGCT
GCACAGCTTCTCCTGGAAGCTGCTGGTGCCCAAGGACAGTCTCAGCCTGGCACGGGTGCCAGTCCAGAAGCTGCAGCAGC
ACTCACACAAGAGGGCCTGCAACACCAGCTTCAGCTACTTCGTGGCCAGTGCTGTTCCCGGCCAGGACCTTTACTTCTGC
TCCGGAGGCTCCAGTGAGCAGATCCAGGTGAAGCAGAACATCTCGGTGACTCTCCACACCTTTGCCTCCAGCTTCCAACA
GGATGTCTCCAGGCAGGGCCTGACCGTGTCCTTTAGACCGTACTTCACAGAGGAAGCTGTTTTCACTGTGACCCTGGACA
TGAAAAGCAAGGTCTATCTGAGGACCCCTAACTGGGACTGGGGCCTGCTGTCCCTCGCCTCGGTGTCCTGGAACATCAGT
GTGCCCAGAGACCAGGTGGCCTGCCTGACCTTCTTAAAGGAGTGGACTGACCTGGTCTGCCAGACAGGGCGTGCATTCAT
GATCATCCAGGAGCAGCGGATGTGGGCTGAGGAGATCTTTAGCCTGGAGGATGTGCTCCCCAAGCCAAGATTCCACCATC
ATGGTTTCTGGGTCAACATCTCCAATTGCAGCCCTGTGAGCAGCAAGCAGCTGGACATGCTCTTCTGGGTGTCACTTTCC
CTGAGGACAACGGACGTGACTGTTGTCATCATTGCAGTGGTGGGAGGTGGCGCCTTACTGATGTTTGCCCTCGGACTCAT
CATTTGCCTCGTGAAAAAGAAGAGGAAAAAGGAGATAAACAAGGGCCCGGCCGTAGGTATCTACAATGGCAATGTCAATA
CCTAGACGCTGATGCAGCCAAAAAAGTTTCAGAAGAGGTGAAAGGACAATGACTCCCATGTGTATGCAGTCATCGATGAC
ACTATGGTATATGGGCATCTGCTGCAGGATTCCAACAGGTCCTTCCTCCAGCCAGAGGTGGACACCTACCAGCCCTTCCA
GGGCCCCATGGGGGACTGCCCTCCCTCCCCACCCCCCGTATGCTCCAGGGCCCCGACTGTAAAGTTGATCATAGATGAAC
CACCCCCTGACATTCCTCCTGAGTCTGAGAGCAAACCATGCATCTTCTCCCACCCCAACATAGAGAATGTAAGCAACGGG
AACACAGACATTCCCTTGCTGGATGCCCACAAGCCAGTGGAGCCGGGGGAA
ORF - retro_ecab_807 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.67 % |
| Parental protein coverage: | 50.24 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | CTDRRYCHKKSYPLQVPSNILQLPVQLHNFSWKLLVPKDSLSLVLVPVQKLQQHTYERACNTSFRYLVAS |
| CTD.RYCHKKSYPL.VPSNILQL.VQLH.FSWKLLVPKDSLSL..VPVQKLQQH...RACNTSF.Y.VAS | |
| Retrocopy | CTDHRYCHKKSYPLRVPSNILQLAVQLHSFSWKLLVPKDSLSLARVPVQKLQQHSHKRACNTSFSYFVAS |
| Parental | AVPSQDLYFGSFCSGGSIEQIQVKQNISVTLRTFSPSYQQDISRQGLTVSFRPYFTEEAVFTVTPDVKSK |
| AVP.QDLY...FCSGGS.EQIQVKQNISVTL.TF..S.QQD.SRQGLTVSFRPYFTEEAVFTVT.D.KSK | |
| Retrocopy | AVPGQDLY---FCSGGSSEQIQVKQNISVTLHTFASSFQQDVSRQGLTVSFRPYFTEEAVFTVTLDMKSK |
| Parental | VYLRTPNWDRGLPSLASVSWNISVPRDQVACLTFLKERTGLVCQTGRAFMIIQEQRMRAEEIFSLEEVLP |
| VYLRTPNWD.GL.SLASVSWNISVPRDQVACLTFLKE.T.LVCQTGRAFMIIQEQRM.AEEIFSLE.VLP | |
| Retrocopy | VYLRTPNWDWGLLSLASVSWNISVPRDQVACLTFLKEWTDLVCQTGRAFMIIQEQRMWAEEIFSLEDVLP |
| Parental | KPRFHHHSFWVNISNCSPVSGKQLDMLFWVLLSPRTTDMTVIIIAVVGGGALLMFALGLIICLVKKKKKK |
| KPRFHHH.FWVNISNCSPVS.KQLDMLFWV.LS.RTTD.TV.IIAVVGGGALLMFALGLIICLVKKK.KK | |
| Retrocopy | KPRFHHHGFWVNISNCSPVSSKQLDMLFWVSLSLRTTDVTVVIIAVVGGGALLMFALGLIICLVKKKRKK |
| Parental | EINKGPAVGIYNGNVNTQMPMQSKKFQKRRKDNDSHVYAVIDDTMVYGHLLQDSNGSFVQPEVDTYRPFQ |
| EINKGPAVGIYNGNVNT...MQ.KKFQKR.KDNDSHVYAVIDDTMVYGHLLQDSN.SF.QPEVDTY.PFQ | |
| Retrocopy | EINKGPAVGIYNGNVNT*TLMQPKKFQKR*KDNDSHVYAVIDDTMVYGHLLQDSNRSFLQPEVDTYQPFQ |
| Parental | GPTGDCPPSPPPIGFRAPTAKLTTDEPPPDIPPESESEPYTFSHPNKENVSNGNTDIPLLDAHKPAEPGE |
| GP.GDCPPSPPP...RAPT.KL..DEPPPDIPPESES.P..FSHPN.ENVSNGNTDIPLLDAHKP.EPGE | |
| Retrocopy | GPMGDCPPSPPPVCSRAPTVKLIIDEPPPDIPPESESKPCIFSHPNIENVSNGNTDIPLLDAHKPVEPGE |
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 .00 RPM | 0 .41 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 1 .66 RPM |
| SRP021940_embryo | 0 .08 RPM | 3 .66 RPM |
| SRP021940_placental_villous | 0 .05 RPM | 23 .57 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 1 .59 RPM |
| SRP021940_testis | 0 .00 RPM | 1 .21 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_807 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_807 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_807 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000025146 | 1 retrocopy |
retro_ecab_807 ,
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