RetrogeneDB ID: | retro_ecab_290 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 13:42390704..42391237(-) | ||
| Located in intron of: | ENSECAG00000000792 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ACER3 | ||
| Ensembl ID: | ENSECAG00000026842 | ||
| Aliases: | None | ||
| Description: | alkaline ceramidase 3 [Source:HGNC Symbol;Acc:16066] |
Retrocopy-Parental alignment summary:
>retro_ecab_290
CTACTGGATGAACTCCCAATGATGTACAGCTGTTGTGTATTTGTGTACTGCATGTTTGAACGTTTCAAGATGAAGAACTC
AGTAAACTATCATCTGCGTTTTACCTTAATTCTCTTCAGTTTAAAGTCACCACAGTTTGCCTTAAGGTAAAGGAGCCTGT
ATTTCAGCAGGTCATGCATGGAATGTTGGTCTTCACATTAGCACTTCCATCTGTTTATATTGTTACATAGGTTTATCCAT
GGCTAAGAGGACTCGGTTTTACATCCTTGGGTCTATTTTTATTGGGATCTTTATTATAGAACACAGATAACATCTTTTGC
GAATCACTAAGGAACTTTCGAAAGAAGGTGCCACCTATCATAGGTGTTACCACACAATTTCAGGCATGGTGGCATATTTT
AACTGGCCTTGGTTCTTATCTTCACATCCTTTTCAATTTATATACAAGAACACTTTACCTGAGATACAGGCCAAAAGTGA
AGTTTCTCTTGGGAATCTGGCCAGTGATCCTGTTTGAGCCTCTCAGGAAGCAC
ORF - retro_ecab_290 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.68 % |
| Parental protein coverage: | 76.52 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LLDELPMIYSCCIFVYCMFECFKMKNSVNYHLLFTLVLFSLI-VTTVYLKVKEPIFQQVMYGMLVFTLVL |
| LLDELPM.YSCC.FVYCMFE.FKMKNSVNYHL.FTL.LFSL..VTTV.LKVKEP.FQQVM.GMLVFTL.L | |
| Retrocopy | LLDELPMMYSCCVFVYCMFERFKMKNSVNYHLRFTLILFSLK<VTTVCLKVKEPVFQQVMHGMLVFTLAL |
| Parental | RSVYIVTWVYPWLRGLGYTSLGLFLLGFLLWNIDNIFCESLRNFRKKVPPIIGVTTQFHAWWHILTGLGS |
| .SVYIVT.VYPWLRGLG.TSLGLFLLG.LL.N.DNIFCESLRNFRKKVPPIIGVTTQF.AWWHILTGLGS | |
| Retrocopy | PSVYIVT*VYPWLRGLGFTSLGLFLLGSLL*NTDNIFCESLRNFRKKVPPIIGVTTQFQAWWHILTGLGS |
| Parental | YLHILFR-EIETFSLNLFPK-QFLFGIWPVILFEPLRKH |
| YLHILF.....T..L...PK..FL.GIWPVILFEPLRKH | |
| Retrocopy | YLHILFNLYTRTLYLRYRPKVKFLLGIWPVILFEPLRKH |
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 .41 RPM | 2 .83 RPM |
| SRP021940_cerebellum | 0 .52 RPM | 3 .22 RPM |
| SRP021940_embryo | 0 .28 RPM | 2 .61 RPM |
| SRP021940_placental_villous | 0 .87 RPM | 4 .86 RPM |
| SRP021940_synovial_membrane | 0 .69 RPM | 5 .33 RPM |
| SRP021940_testis | 1 .47 RPM | 10 .10 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_290 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_290 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_290 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000026842 | 1 retrocopy |
retro_ecab_290 ,
|
| Sus scrofa | ENSSSCG00000014873 | 1 retrocopy |