RetrogeneDB ID: | retro_ecab_990 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 8:37009018..37009830(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSECAG00000012757 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ecab_990
AATGAAACAGAAATAAGTGACCTACCTGACAAAGAGTTCAAACAAAAACTCCTAAGGATGCTCACAGATATTGGGAGAAG
ACTGGATGAACACAGTGAGCTCATCAACAAGGAACTGGAAAATATAAAAAAAAAAAACCAATCAGAAATGAAGACTACAA
TACTGGAAATGAAAAATTCACTAGAGGGACTCAATAGCTGAGTAGAGGATGCAGAAGAATGGATCAGCGAGCTAGATGAA
AGACTAGAGGAAATCACCCAAGCTGAACAGAAAAAAGAAAAAAGAATTACAGTGAGAACAATCTAAGGGAACTCTGGAAC
AATATCAAGCACATTAACATTCAGAGTATAGGTGTCCCAGAAGGAGAAGACAGAGACAAAGGGGCAGAAAATTTATTTGA
AGAAATAATAGATGAAAATTTTCCTAAGCTAAGGAAGGAAACAGACATCCAAGTACAGGAAGCACAGAGAGCTCCAAACA
AGATAAGCCCAAAGAGGCCCACACCAAGACACATTATAAATAAAAGGTCCAAAATTAAAGATAAAGAGGAATCCTAAAAG
TGGCAAGAGAAAGGCAACAATTGACATACAAAGGAAAGCCCATAAGGCTATCAGTGTACTTCTCAGTTGAAACCGTACAG
GTGAGAAGAGAATGGCATGACATATTTAAAGTGCTAAAAGGAAAAAAACCTACAGCCAAGAATACTCTATCCATCAAGGG
TGTCATTCAGAATGGAAGGAGAAATAAAGAGCTTCCCAGACAAACAAAAATTAAAAGAGTTTACCACCAAGAAACCAGTT
CTACAAGAAATG
ORF - retro_ecab_990 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 60.36 % |
| Parental protein coverage: | 98.18 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | NEKEINNVTDEEYKLTVIRVLTNLGRRMDELSENFKKELENKKRTNQK--KTTILEIKNSLEGLNGRVDD |
| NE.EI....D.E.K....R.LT..GRR.DE.SE...KELEN.....Q...KTTILE.KNSLEGLN..V.D | |
| Retrocopy | NETEISDLPDKEFKQKLLRMLTDIGRRLDEHSELINKELENXXXXXQSEMKTTILEMKNSLEGLNS*VED |
| Parental | TEEWISELDERLEEITQASQIKETRIIKNT-NMVKELWDNIKHNNIRLVGVPEGAERDKGAENLFEEVIA |
| .EEWISELDERLEEITQA.Q.....I...T.N...ELW.NIKH.NI...GVPEG..RDKGAENLFEE.I. | |
| Retrocopy | AEEWISELDERLEEITQAEQXXXXXITVRT<NL-RELWNNIKHINIQSIGVPEGEDRDKGAENLFEEIID |
| Parental | ENFPNLRKETDWKTKKANRSPNFTNVKRPTPRHIVVKLAKVNDKEK-ILRAARQ-NKITYKGTSIRLSEN |
| ENFP.LRKETD.....A.R.PN....KRPTPRHI..K..K..DKE..IL..AR.....TYKG..IRLS.. | |
| Retrocopy | ENFPKLRKETDIQVQEAQRAPNKISPKRPTPRHIINKRSKIKDKEE<ILKVARERQQLTYKGKPIRLSVY |
| Parental | FSADTLQARREWNDIFRTL-KDKNLQPRILYAVKISFKYDGEIKTFQDKQKLREFIATRPPLQEM |
| FS..T.Q.RREW.DIF..L.K.KNLQPRILY....SF...GEIK.F.DKQKL.EF....P.LQEM | |
| Retrocopy | FSVETVQVRREWHDIFKVL>KEKNLQPRILYPSRVSFRMEGEIKSFPDKQKLKEFTTKKPVLQEM |
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 .00 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 0 .00 RPM |
| SRP021940_embryo | 0 .05 RPM | 0 .10 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 0 .00 RPM |
| SRP021940_synovial_membrane | 0 .05 RPM | 0 .00 RPM |
| SRP021940_testis | 0 .00 RPM | 0 .00 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_990 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_990 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_990 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000012757 | 4 retrocopies |