RetrogeneDB ID: | retro_cjac_513 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:32724677..32725308(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | KIAA1704 | ||
| Ensembl ID: | ENSCJAG00000019204 | ||
| Aliases: | None | ||
| Description: | KIAA1704 [Source:HGNC Symbol;Acc:20298] |
Retrocopy-Parental alignment summary:
>retro_cjac_513
ATGGCAAGGGACCTGATCAGACTGGCCCTGCTGCTTGGCTTCAAGGTCTCGGGAACAGCAGAGGATGAGGAGCGGGACCC
AAGCCCCATTGCAGGACCAGCTCTAATTACTAATTATAAAAGCAGTAGTTCAGATTCATCAGACAGCAATGAAGACAGTA
GTTCTTTGTACAACAAAGGAAATAAAGAATGTGAGGAAGATGACACTGGTCCAACTGAAAGAAAACAGGAAAGATCAGTA
TGATGACAATGATGAAGATGATGATGGGTTTTTTGGACCAGCCCTTCCTCCTGGATTTTAAAAGCAGGATGATTTTCCTC
CAAGGCCTATAATAGGTCCTGCATTGCCACCTGGTTTCATTAAATCTACACAGAAACGTAATGAGCAGAGATGATCCAGG
GCAAAAGGAAACAGAGAGCAGTGAAGATGAGGACATTGTTGGACCATTGCCCACAGAAGGACCAGTTAACTATAATGTAA
AGACAGAATTTGAAAAAAGATCCCAGAGAATGAAAGAAAAACTGACCAAGGAGATGATGATTCTTCTAATCCCATTGTAA
GAGAGTCATAGATGACTGAACTTCCTCCAGAAATGAAAGACTTTGGTCTTGGGCCAAGGACTTTTAAGAGA
ORF - retro_cjac_513 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.1 % |
| Parental protein coverage: | 62.06 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MARDLIGPALPPGFKARGTAEDEERDPSPVAGPALPPNYKSSSSDSSDSDEDSSSLYEEGNQESEDDDTG |
| MARDLI..AL..GFK..GTAEDEERDPSP.AGPAL..NYKSSSSDSSDS.EDSSSLY..GN.E.E.DDTG | |
| Retrocopy | MARDLIRLALLLGFKVSGTAEDEERDPSPIAGPALITNYKSSSSDSSDSNEDSSSLYNKGNKECEEDDTG |
| Parental | PTARKQRKN-QDDDEDDDDGFFGPALPPGFKKQDDSPPRPMIGPALPPGFIKATRKSDKGR-DDPEQQET |
| PT.RKQ.....DD...DDDGFFGPALPPGF.KQDD.PPRP.IGPALPPGFIK.T.K....R.D......T | |
| Retrocopy | PTERKQERS>YDDNDEDDDGFFGPALPPGF*KQDDFPPRPIIGPALPPGFIKSTQKRNEQR>DPGQKE-T |
| Parental | DSSEDEDIVGPMPAKGPVNYNVTTEFEKRAQRMKEKLTK-GDDDSSKPIVRESWMTELPPEMKDFGLGPR |
| .SSEDEDIVGP.P..GPVNYNV.TEFEKR.QRMKEKLTK.GDDDSS.PIVRES.MTELPPEMKDFGLGPR | |
| Retrocopy | ESSEDEDIVGPLPTEGPVNYNVKTEFEKRSQRMKEKLTK<GDDDSSNPIVRES*MTELPPEMKDFGLGPR |
| Parental | TFKR |
| TFKR | |
| Retrocopy | TFKR |
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 | 5 .57 RPM |
| SRP051959_heart | 0 .00 RPM | 5 .93 RPM |
| SRP051959_kidney | 0 .00 RPM | 9 .27 RPM |
| SRP051959_liver | 0 .00 RPM | 6 .58 RPM |
| SRP051959_lung | 0 .00 RPM | 9 .70 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 8 .36 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 5 .18 RPM |
| SRP051959_spleen | 0 .00 RPM | 9 .64 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_513 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_513 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_513 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 | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000019204 | 1 retrocopy |
retro_cjac_513 ,
|
| Otolemur garnettii | ENSOGAG00000012513 | 1 retrocopy |