RetrogeneDB ID: | retro_cjac_3146 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 8:69531731..69532040(-) | ||
| Located in intron of: | ENSCJAG00000006304 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | UFC1 | ||
| Ensembl ID: | ENSCJAG00000005303 | ||
| Aliases: | None | ||
| Description: | ubiquitin-fold modifier conjugating enzyme 1 [Source:HGNC Symbol;Acc:26941] |
Retrocopy-Parental alignment summary:
>retro_cjac_3146
AAGAAAGGGACTCGGTGGTTTGGAAAATGTTGGTATATCTATAACCTCCTGAAATGTCAGTTTGACATTCCTGTCACATA
TCCTACTACTTCCCCAGAAATTGCAGTCCCTGAGCTGGATGGAAAGACAGCAAAGACATACAGAGGTTGCAAAATATACC
TGACAGTTCATTTCAATTCTTCGTGAGCCGGGAATGTGGCCAAATTTGGACTAGCTCATATTGTGCCTCTGGGGTTGGGT
TCAGGGCTGGCAGTGGAAATCCCTGGTCTGATTCAGAAGGGTGTCATCCAGCACAAAGAGAAATGCAAC
ORF - retro_cjac_3146 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.77 % |
| Parental protein coverage: | 64.46 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | KEGTRWFGKCWYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKMYRGGKICLTDHFKPLWARNV |
| K.GTRWFGKCWYI..LLK......FDIP.TYPTT.PEIAVPELDGKTAK.YRG.KI.LT.HF....A.NV | |
| Retrocopy | KKGTRWFGKCWYIYNLLK----CQFDIPVTYPTTSPEIAVPELDGKTAKTYRGCKIYLTVHFNSS*AGNV |
| Parental | PKFGLAHLMALGLGPWLAVEIPDLIQKGVIQHKEKCN |
| .KFGLAH...LGLG..LAVEIP.LIQKGVIQHKEKCN | |
| Retrocopy | AKFGLAHIVPLGLGSGLAVEIPGLIQKGVIQHKEKCN |
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 .09 RPM | 13 .91 RPM |
| SRP051959_heart | 0 .82 RPM | 8 .72 RPM |
| SRP051959_kidney | 0 .27 RPM | 20 .17 RPM |
| SRP051959_liver | 0 .17 RPM | 17 .98 RPM |
| SRP051959_lung | 0 .13 RPM | 14 .46 RPM |
| SRP051959_lymph_node | 0 .05 RPM | 14 .50 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 11 .40 RPM |
| SRP051959_spleen | 0 .17 RPM | 18 .42 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3146 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3146 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3146 has 5 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3753 |
| Pan troglodytes | retro_ptro_2547 |
| Gorilla gorilla | retro_ggor_2525 |
| Pongo abelii | retro_pabe_3164 |
| Macaca mulatta | retro_mmul_1727 |