RetrogeneDB ID: | retro_cjac_3095 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 8:107321283..107321832(+) | ||
| Located in intron of: | ENSCJAG00000013046 | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | MRPS15 | ||
| Ensembl ID: | ENSCJAG00000001852 | ||
| Aliases: | None | ||
| Description: | mitochondrial ribosomal protein S15 [Source:HGNC Symbol;Acc:14504] |
Retrocopy-Parental alignment summary:
>retro_cjac_3095
ATGCTGAGGGCTGCGTGGAGGACGCTGAGTTTGATTCAGACCCAGGCAGTTACTCAGGTCCCAGTCCCCGGGCTGCTGGG
CAGTGGGAGCGTCAGGTTTCCTTCCAGCCAGTGGGGCCTGCAACCTCGAAGTCTCCTCCTCCAGGCTGTGCACAGGTATG
TCATCCAGAAACCAGCCCAGCCCAGGTGAGATGATGACCCATCTCCTACACTACTCAAAGACTACCAGAATGTCCCTGGA
ATAGAGAAGGTTGATGATGTTGTGAGAAGACTCTTGTTTTTGGAAATGGCCAACACAAAGGAGAAGCTGAAAGTCATGCA
AGAACTGTTGATGAAGAAGATTGCTGCAAACCCAGAGGACACCAGATCCCTGGAGGCTCGAATTGTTCCCTTGACCATCA
AGATCCGCAGTTGTGAAGAACACCTGCAGACACATTGAAAGGACAAAGCGCACAAATGCTATTTGCTGATGAGCATTGAC
CAGAGGAAAAAGATGCTCAAAAACCTCTGTAACACCAACTATGATGTCTTTGAGAAGGTTTTCCAGGAG
ATGCTGAGGGCTGCGTGGAGGACGCTGAGTTTGATTCAGACCCAGGCAGTTACTCAGGTCCCAGTCCCCGGGCTGCTGGG
CAGTGGGAGCGTCAGGTTTCCTTCCAGCCAGTGGGGCCTGCAACCTCGAAGTCTCCTCCTCCAGGCTGTGCACAGGTATG
TCATCCAGAAACCAGCCCAGCCCAGGTGAGATGATGACCCATCTCCTACACTACTCAAAGACTACCAGAATGTCCCTGGA
ATAGAGAAGGTTGATGATGTTGTGAGAAGACTCTTGTTTTTGGAAATGGCCAACACAAAGGAGAAGCTGAAAGTCATGCA
AGAACTGTTGATGAAGAAGATTGCTGCAAACCCAGAGGACACCAGATCCCTGGAGGCTCGAATTGTTCCCTTGACCATCA
AGATCCGCAGTTGTGAAGAACACCTGCAGACACATTGAAAGGACAAAGCGCACAAATGCTATTTGCTGATGAGCATTGAC
CAGAGGAAAAAGATGCTCAAAAACCTCTGTAACACCAACTATGATGTCTTTGAGAAGGTTTTCCAGGAG
ORF - retro_cjac_3095 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.43 % |
| Parental protein coverage: | 71.48 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MLRAAWRMLSLIRTQAVTQAPGPGLPSCGSARFPSNQWGLQPRSLL-QATRRYVIQKPVLPRQDDDPPPS |
| MLRAAWR.LSLI.TQAVTQ.P.PGL...GS.RFPS.QWGLQPRSLL.QA..RYVIQKP..PR.DDDP.P. | |
| Retrocopy | MLRAAWRTLSLIQTQAVTQVPVPGLLGSGSVRFPSSQWGLQPRSLLLQAVHRYVIQKPAQPR*DDDPSP- |
| Parental | TLLQDYQNVPGIEKVDDVVKRLLSLEMAKKKEKLKVIQEQLMKKIVENPEDTRSLEARIVALTIKIRSYE |
| TLL.DYQNVPGIEKVDDVV.RLL.LEMA..KEKLKV.QE.LMKKI..NPEDTRSLEARIV.LTIKIRS.E | |
| Retrocopy | TLLKDYQNVPGIEKVDDVVRRLLFLEMANTKEKLKVMQELLMKKIAANPEDTRSLEARIVPLTIKIRSCE |
| Parental | EHMQKHRKDKAHKRYLLMSIDQRKKMLKNLRNTNYDVYEKVCKE |
| EH.Q.H.KDKAHK.YLLMSIDQRKKMLKNL.NTNYDV.EKV..E | |
| Retrocopy | EHLQTH*KDKAHKCYLLMSIDQRKKMLKNLCNTNYDVFEKVFQE |
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 | 3 .62 RPM |
| SRP051959_heart | 0 .02 RPM | 7 .33 RPM |
| SRP051959_kidney | 0 .18 RPM | 6 .68 RPM |
| SRP051959_liver | 0 .00 RPM | 5 .63 RPM |
| SRP051959_lung | 0 .00 RPM | 5 .32 RPM |
| SRP051959_lymph_node | 0 .11 RPM | 4 .89 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 14 .70 RPM |
| SRP051959_spleen | 0 .04 RPM | 7 .65 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3095 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3095 was not experimentally validated.