RetrogeneDB ID: | retro_ecab_342 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 15:1177155..1177744(-) | ||
| Located in intron of: | ENSECAG00000008458 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSECAG00000008327 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ecab_342
GAGCCATATGGCACATTAATCCTAAGTGGACCAGGTGGCTGCAGAAGCTGTGTAGTCCCTGCTGCTTTGGCTGTGATTGC
CTTGTCCTCAACCAGGGCTATCTCTCAGAGGCAGGGGCCAGCCTGGTGGACCAAAAACTGGAACTCAACATTGTGCCCCG
TACAAAGGTAGTATACCTGGCCAGTGAGACTTTCAACTATAGTGCCATTGACCGAGTGAAGTCCAAGGGCAAGCAGCTTG
CACTGGAGAAGGTGCCAAAACTTGGGCAGCAGTTTAACCACATTGGGCTACGGCTGAGGCCAAAGGTTAGTTCATTCCTG
CTCTTTGTTGAAGGCTACAAAGATGCAGATTACTGGCTACAGTGTTTTGAAGCAGAACCTCTCCCTGAGAACACTAACTG
GCAACTACTGCTTCAGTTTGAGCAGTTGTGGTACTGGATTACATCATCCGCAATACTGATCGAGGCAGTGACAACTGGCT
GATTAAATACCACTGTCCAATGGATAGTTCTAGCTCTCGGGACACAGACTGGGTGGTGGTGAAGGAGCCTGTTATCAAGG
TGGCTGCCATAGACAATGGGCTGGCTTTC
ORF - retro_ecab_342 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.44 % |
| Parental protein coverage: | 54.62 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | EPYG-HLNPKWTKWLQKLCCPCCFGRDCLVLNQGYLSEAGASLVDQKLELNIVPRTKVVYLASETFNYSA |
| EPYG.H.NPKWT.WLQKLC.PCCFG.DCLVLNQGYLSEAGASLVDQKLELNIVPRTKVVYLASETFNYSA | |
| Retrocopy | EPYG<HINPKWTRWLQKLCSPCCFGCDCLVLNQGYLSEAGASLVDQKLELNIVPRTKVVYLASETFNYSA |
| Parental | IDRVKSRGKRLALEKVPKVGARFNRIG--LPPKVGSFQLFVEGYKDADYWLRRFEAEPLPENTNRQLLLQ |
| IDRVKS.GK.LALEKVPK.G..FN.IG..L.PKV.SF.LFVEGYKDADYWL..FEAEPLPENTN.QLLLQ | |
| Retrocopy | IDRVKSKGKQLALEKVPKLGQQFNHIGLRLRPKVSSFLLFVEGYKDADYWLQCFEAEPLPENTNWQLLLQ |
| Parental | FERL-VVLDYIIRNTDRGNDNWLIKYDCPMDSSSSRDTDWVVVKEPVIKVAAIDNGLAF |
| FE.L.VVLDYIIRNTDRG.DNWLIKY.CPMDSSSSRDTDWVVVKEPVIKVAAIDNGLAF | |
| Retrocopy | FEQL<VVLDYIIRNTDRGSDNWLIKYHCPMDSSSSRDTDWVVVKEPVIKVAAIDNGLAF |
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 .06 RPM | 10 .21 RPM |
| SRP021940_cerebellum | 0 .05 RPM | 19 .47 RPM |
| SRP021940_embryo | 0 .08 RPM | 12 .40 RPM |
| SRP021940_placental_villous | 0 .10 RPM | 24 .54 RPM |
| SRP021940_synovial_membrane | 0 .03 RPM | 16 .44 RPM |
| SRP021940_testis | 0 .00 RPM | 12 .85 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_342 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_342 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_342 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 | ENSECAG00000008327 | 1 retrocopy |
retro_ecab_342 ,
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