RetrogeneDB ID: | retro_cjac_4210 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:105184983..105185592(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000022501 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | WDYHV1 | ||
| Ensembl ID: | ENSCJAG00000000865 | ||
| Aliases: | None | ||
| Description: | WDYHV motif containing 1 [Source:HGNC Symbol;Acc:25490] |
Retrocopy-Parental alignment summary:
>retro_cjac_4210
ATGGAGGGTAATGGCCCTGCTGCCACCCAGTACCAGCCGGCCAGCCCCCCGCAGGATGCCTGTGTCTACAGCAGCTGCTA
CTGTGAAGAAAATATTTGGAAGCTCTGTGAATACATCAAAAACCATGACCAGTATCCTTTAGAAGAATGTTATGCTGTCT
TCATATCTATTGAGAAGATGATCCCTATCTGGAAGCAACAGGCAAGACCTGGAGATGGACCTGTGATCTGGGATTACCAT
GTCGTTTTGCTTCATGTTTCAAGTGGAGGACAGAGCTTCATTTATGACCTCGATACTGTCTTGCTGTTTCCCTGCCCTAT
TGACACTTATGTAGAAGATGCCTTTAAGTCTGATGAAGACATTCATCCACAGTTTAAAAGGAAATTTAGAGTGATCCATG
CAGATTCATATTTGAAGAACTTTGCTTCTGACCAATGTCACATGAAAGACTCCAGTGGGAATTGGAGAGAGCCTCCTCTA
CCATATCCCTGCATTGAGACTGGAGATTCCAAAACAAACCTGAATGATTTCATCAGCATGGACCCCGAGGTAGGGTGGGG
CACTGTCTACACACTTTCTGAATTTACACATTGGTTTGGCAGTAAAAAC
ORF - retro_cjac_4210 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.63 % |
| Parental protein coverage: | 99.51 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MEGNGPAAAQYQPASPPRDACVYSSCYCEENIWKLCEYIKNHDQYPLEECYAVFISNERKMIPIWKQQAR |
| MEGNGPAA.QYQPASPP.DACVYSSCYCEENIWKLCEYIKNHDQYPLEECYAVFIS.E.KMIPIWKQQAR | |
| Retrocopy | MEGNGPAATQYQPASPPQDACVYSSCYCEENIWKLCEYIKNHDQYPLEECYAVFISIE-KMIPIWKQQAR |
| Parental | PGDGPVIWDYHVVLLHVSSGGQSFIYDLDSVLPFPCPFDTYVEDAFKSDEDIHPQFRRKFRVIRADSYLK |
| PGDGPVIWDYHVVLLHVSSGGQSFIYDLD.VL.FPCP.DTYVEDAFKSDEDIHPQF.RKFRVI.ADSYLK | |
| Retrocopy | PGDGPVIWDYHVVLLHVSSGGQSFIYDLDTVLLFPCPIDTYVEDAFKSDEDIHPQFKRKFRVIHADSYLK |
| Parental | NFASDRSHMKDSSGNWREPPPPYPCIETGDSKMNLNDFISMDPEVGWGTVYTLSEFTHWFGSKN |
| NFASD..HMKDSSGNWREPP.PYPCIETGDSK.NLNDFISMDPEVGWGTVYTLSEFTHWFGSKN | |
| Retrocopy | NFASDQCHMKDSSGNWREPPLPYPCIETGDSKTNLNDFISMDPEVGWGTVYTLSEFTHWFGSKN |
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 |
|---|---|---|
| SRP051959_colon | 0 .00 RPM | 2 .00 RPM |
| SRP051959_heart | 0 .02 RPM | 3 .79 RPM |
| SRP051959_kidney | 0 .00 RPM | 4 .88 RPM |
| SRP051959_liver | 0 .02 RPM | 4 .35 RPM |
| SRP051959_lung | 0 .00 RPM | 2 .93 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 2 .72 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 1 .62 RPM |
| SRP051959_spleen | 0 .00 RPM | 3 .34 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4210 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4210 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4210 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000000865 | 1 retrocopy |
retro_cjac_4210 ,
|
| Macropus eugenii | ENSMEUG00000008130 | 3 retrocopies | |
| Oryctolagus cuniculus | ENSOCUG00000014201 | 1 retrocopy |