RetrogeneDB ID: | retro_cjac_3018 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 7:118091621..118092164(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MRPL46 | ||
| Ensembl ID: | ENSCJAG00000013019 | ||
| Aliases: | None | ||
| Description: | mitochondrial ribosomal protein L46 [Source:HGNC Symbol;Acc:1192] |
Retrocopy-Parental alignment summary:
>retro_cjac_3018
AAAGAAAAAAAGGCTGACTTCTATGATGAAGAAGATGAACAGGATATATTACTGGTTGCAAGATCTGGAAGATATGTGGG
AACAGAGATTCGTACAGTTCAAACTTGGAGCTCGTGTAACAGAAGCTGACGAAAGAATGACCGAACATCCCTGAACCGGA
AGCTAGACAGGAACCTTGTTCTGTTAGTCAGAGAGAAGCTTGGAGATGAGGATGTTTGGATGCTGCCCCAGGCGGAATGG
CAGCCTGGGGAGACCCTTCGAGGAACTGCTGAACGAACCCTAGTGACACTCTCAGAAAACAATATGGAAGCCAAGTTCCT
GGGAAATGCACCCTGTGGGCACTACAAATTCAAGTTCCCCCAGGCAATGCGGACAGAGAGTAACCTCGGGGCCAAGGTGT
TCTTCTTCAAAGCACTGCTGTTAACTGGAGACTTTTCAGAGGCCGGGAAGAAGGGCCAGCATGTGTGGGTCACTAAGGAT
GAGCTGAGTGATTATTTGAAACCAAAATACCTGGCCCAAGTTAGGAGGTTTCTTTTGGACCTC
ORF - retro_cjac_3018 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.72 % |
| Parental protein coverage: | 65.11 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | EKKKADLYDEEDEQDILLV-QDLEDMWEQRFVQFKLGARVTEADE-KNDRTSLNRKLDRNLVLLVREKLG |
| ..KKAD.YDEEDEQDILLV.QDLEDMWEQRFVQFKLGARVTEADE.KNDRTSLNRKLDRNLVLLVREKLG | |
| Retrocopy | KEKKADFYDEEDEQDILLV>QDLEDMWEQRFVQFKLGARVTEADE<KNDRTSLNRKLDRNLVLLVREKLG |
| Parental | DEDVWMLPQAEWQPGETLRGTAERTLVTLSENNMEAKFLGNAPCGHYKFKFPQAMRTESNLGAKVFFFKA |
| DEDVWMLPQAEWQPGETLRGTAERTLVTLSENNMEAKFLGNAPCGHYKFKFPQAMRTESNLGAKVFFFKA | |
| Retrocopy | DEDVWMLPQAEWQPGETLRGTAERTLVTLSENNMEAKFLGNAPCGHYKFKFPQAMRTESNLGAKVFFFKA |
| Parental | LLLTGDFSQAGKKGQHVWVTKDELSDYLKPKYLAQVRRFLLDL |
| LLLTGDFS.AGKKGQHVWVTKDELSDYLKPKYLAQVRRFLLDL | |
| Retrocopy | LLLTGDFSEAGKKGQHVWVTKDELSDYLKPKYLAQVRRFLLDL |
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 .90 RPM |
| SRP051959_heart | 0 .00 RPM | 5 .12 RPM |
| SRP051959_kidney | 0 .02 RPM | 6 .01 RPM |
| SRP051959_liver | 0 .02 RPM | 5 .72 RPM |
| SRP051959_lung | 0 .00 RPM | 3 .61 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 4 .54 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 6 .79 RPM |
| SRP051959_spleen | 0 .02 RPM | 3 .78 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3018 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3018 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3018 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000013019 | 1 retrocopy |
retro_cjac_3018 ,
|
| Felis catus | ENSFCAG00000014966 | 1 retrocopy | |
| Microcebus murinus | ENSMICG00000015826 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000004736 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000018547 | 1 retrocopy |