RetrogeneDB ID: | retro_cjac_2682 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 5:150903553..150903945(-) | ||
| Located in intron of: | ENSCJAG00000017909 | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000017967 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CRTC1 | ||
| Ensembl ID: | ENSCJAG00000007421 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2682
AGAGAGGTGCAGTCTGACAAACAAGGCCGACAGGTCGACAGCTGCCCCTACAGCACCGTGGACCTCTCGACACCCGCGGA
CACCAGCTGGAGAAGGACCAATTCTGACTCCGCCCTGCACCAGAGCACAATGATGCCCACACAGCCAGAATCCTTTACCA
GTGGGTCCCAGGACATGCACCAGAAAAGAGTCTTACTGTTAACAGTCCCAGGAATGGAAGAGAACATGTCAGAGGCAGAC
AAAAACCTTTCCAAGCAAGCGTGGCATACCAAGAAGACCGGGTGCAGGCCCAAGTCCTGTGAGGTCCCCGGAATCAACAT
CTTCCCATCCGCCAACCAGGAAAACACTACAGCCCTGATCCCCGCCACCCACAACACTGGGGCTCCCTCCCC
ORF - retro_cjac_2682 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.12 % |
| Parental protein coverage: | 59.55 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RPLSVDKHGRQADSCPYGTVYLSPPADTSWRRTNSDSALHQSTMTPTQPESFTSGSQDVHQKRVLLLTVP |
| R....DK.GRQ.DSCPY.TV.LS.PADTSWRRTNSDSALHQSTM.PTQPESFTSGSQD.HQKRVLLLTVP | |
| Retrocopy | REVQSDKQGRQVDSCPYSTVDLSTPADTSWRRTNSDSALHQSTMMPTQPESFTSGSQDMHQKRVLLLTVP |
| Parental | GMEETTSEADKNLSKQAWDTKKTGSRPKSCEVPGINIFPSADQENTTALIPATHNTG-GSLP |
| GMEE..SEADKNLSKQAW.TKKTG.RPKSCEVPGINIFPSA.QENTTALIPATHNTG.GSLP | |
| Retrocopy | GMEENMSEADKNLSKQAWHTKKTGCRPKSCEVPGINIFPSANQENTTALIPATHNTG<GSLP |
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 .02 RPM | 0 .95 RPM |
| SRP051959_heart | 0 .02 RPM | 1 .16 RPM |
| SRP051959_kidney | 0 .00 RPM | 1 .13 RPM |
| SRP051959_liver | 0 .02 RPM | 0 .41 RPM |
| SRP051959_lung | 0 .00 RPM | 1 .29 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 1 .44 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .87 RPM |
| SRP051959_spleen | 0 .00 RPM | 1 .20 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2682 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2682 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2682 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 | ENSCJAG00000007421 | 3 retrocopies |
retro_cjac_2682 , retro_cjac_595, retro_cjac_666,
|
| Homo sapiens | ENSG00000105662 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000010719 | 1 retrocopy |