RetrogeneDB ID: | retro_cjac_656 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:202785070..202785494(-) | ||
| Located in intron of: | ENSCJAG00000009771 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | COA1 | ||
| Ensembl ID: | ENSCJAG00000007826 | ||
| Aliases: | None | ||
| Description: | cytochrome c oxidase assembly factor 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21868] |
Retrocopy-Parental alignment summary:
>retro_cjac_656
CAAAAGTATCCAGGAAGCAGGATGCCAGTGCCTCAAGGAAAATGGTCCTTTTCAGCAGTATATTTGGTACCTGGGGCTTG
GCCCTTGTGTATTACCTCACACAAAAGACTTTTCCAGGGCTTCGTTTTACTAGTTGGCATTGGAGCATGTGCGTAGCCAT
CCCAAGGCACGGGGAGCTCTGGGCCCTCCTTCAACATTTACATTCTCAAACTCAGTGACAAGCAAGACTTTGTGGACATT
GCTGATGCCAAGTTGAAGATTTCCTATCTCTGGATCCAAGTCAGAGGGCCATCTCCAGGTCAGCTCATCCAGAAGTGGCC
CCATTCAGAGGTGTTGCCTTGATGATATCTTCTTAGAGCTCAAGGATGGTCAACAGATTCCCATGTTCAAGCTCAGTGGG
GAGAATGGTGAAGAAGTGAGAAAG
ORF - retro_cjac_656 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 58.9 % |
| Parental protein coverage: | 97.93 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | QTHPRSRMSM-SPAKMIIYGSVLCTGGFSLAYFIIQKTY-SRSLYYQLALEQLQIHPGAQEALGPP-VSV |
| Q..P.SRM......KM....S...T.G..L.Y...QKT..SR...Y.LALE....HP.A..ALGPP.... | |
| Retrocopy | QKYPGSRMPV<ASRKMVLFSSIFGTWGLALVYYLTQKTF<SRASFY*LALEHVRSHPKARGALGPP<FNI |
| Parental | HHLKLTGKDNFVDIADAKLKI-PVSGSKSEGHLHVHSTRSGPFQRWHLDEVFLELKDGQQIPVFNLSGEN |
| ..LKL..K..FVDIADAKLKI.P.SGSKSEGHL.V.S.RSGP.QR..LD..FLELKDGQQIP.F.LSGEN | |
| Retrocopy | YILKLSDKQDFVDIADAKLKI>PISGSKSEGHLQVSSSRSGPIQRCCLDDIFLELKDGQQIPMFKLSGEN |
| Parental | GDEVKK |
| G.EV.K | |
| Retrocopy | GEEVRK |
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 .42 RPM | 2 .46 RPM |
| SRP051959_heart | 0 .33 RPM | 3 .51 RPM |
| SRP051959_kidney | 0 .49 RPM | 3 .37 RPM |
| SRP051959_liver | 0 .39 RPM | 2 .62 RPM |
| SRP051959_lung | 0 .24 RPM | 6 .78 RPM |
| SRP051959_lymph_node | 0 .18 RPM | 11 .96 RPM |
| SRP051959_skeletal_muscle | 0 .24 RPM | 2 .66 RPM |
| SRP051959_spleen | 0 .38 RPM | 7 .69 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_656 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_656 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_656 has 4 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_2595 |
| Pan troglodytes | retro_ptro_1520 |
| Gorilla gorilla | retro_ggor_1624 |
| Pongo abelii | retro_pabe_1914 |
Parental genes homology:
Parental genes homology involve 10 parental genes, and 10 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000009377 | 1 retrocopy | |
| Canis familiaris | ENSCAFG00000031110 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000007826 | 1 retrocopy |
retro_cjac_656 ,
|
| Homo sapiens | ENSG00000106603 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000034928 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000019023 | 1 retrocopy | |
| Mustela putorius furo | ENSMPUG00000018149 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000003316 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000017606 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000019125 | 1 retrocopy |