RetrogeneDB ID: | retro_cjac_3933 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL286325.1:13648..14142(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000003712 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LMO4 | ||
| Ensembl ID: | ENSCJAG00000007385 | ||
| Aliases: | None | ||
| Description: | LIM domain only 4 [Source:HGNC Symbol;Acc:6644] |
Retrocopy-Parental alignment summary:
>retro_cjac_3933
ATGATGAATCCGGGCAGCAGCTAGCAGCAGCCCCTGGTGACGGCCGGCTCCCTCTCCTGGAGGCGGTGCGCAGGCTGCGG
GGGCAAGATTGCGGACCGTTTCTGCTCTATGCCATGGACAGCTACTGGCACAGCCGGTGCCTCAAGTGCTCCTGCTGCCA
GGCGCAACTGGGCGACATCGGCATGTCCTGTTACACCAAGAGCGGCATGATCCTTTGCAGAAATGACTACATTAGGTTAT
TTGGGAATAGCGGTGCTTGCAGCGCTTGTGGACAGTCGATTCCTGGGAGCGAACTCGTCATAAGGGCGCAAGGCAATGTG
TATCATCTTAAGTGTTTTACATGCTCTACCTGCCGGAATCGCCTGGTCCCGGGAGATCGGTTTCACTACATCAATTTCAG
TTTATTTTGTGAACATAATAGACCTACAGCTCTCATCAATGGCCATTTGAATTTACTTCAGAGCAATCCTCTACTGCCAG
ACCAGAAGGTCTGC
ORF - retro_cjac_3933 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.77 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MVNPGSSSQPPPVTAGSLSWKRCAGCGGKIADRF-LLYAMDSYWHSRCLKCSCCQAQLGDIGTSCYTKSG |
| M.NPGSS.Q.P.VTAGSLSW.RCAGCGGKIADRF.LLYAMDSYWHSRCLKCSCCQAQLGDIG.SCYTKSG | |
| Retrocopy | MMNPGSS*QQPLVTAGSLSWRRCAGCGGKIADRF<LLYAMDSYWHSRCLKCSCCQAQLGDIGMSCYTKSG |
| Parental | MILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEH |
| MILCRNDYIRLFGNSGACSACGQSIP.SELV.RAQGNVYHLKCFTCSTCRNRLVPGDRFHYIN.SLFCEH | |
| Retrocopy | MILCRNDYIRLFGNSGACSACGQSIPGSELVIRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINFSLFCEH |
| Parental | DRPTALINGHLNSLQSNPLLPDQKVC |
| .RPTALINGHLN.LQSNPLLPDQKVC | |
| Retrocopy | NRPTALINGHLNLLQSNPLLPDQKVC |
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 | 8 .10 RPM |
| SRP051959_heart | 0 .00 RPM | 10 .28 RPM |
| SRP051959_kidney | 0 .02 RPM | 12 .56 RPM |
| SRP051959_liver | 0 .00 RPM | 1 .80 RPM |
| SRP051959_lung | 0 .02 RPM | 9 .26 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 11 .80 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 2 .99 RPM |
| SRP051959_spleen | 0 .00 RPM | 6 .28 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3933 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3933 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3933 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 | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000000305 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000007385 | 1 retrocopy |
retro_cjac_3933 ,
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