RetrogeneDB ID: | retro_cjac_2525 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 5:63577512..63578053(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RQCD1 | ||
| Ensembl ID: | ENSCJAG00000011079 | ||
| Aliases: | None | ||
| Description: | RCD1 required for cell differentiation1 homolog (S. pombe) [Source:HGNC Symbol;Acc:10445] |
Retrocopy-Parental alignment summary:
>retro_cjac_2525
CCCACATTGACAGCACACCAAATTAACAGAGTTTGCAATGCTCTGGCATTACTGCAATGTGTAGCATCACATCCAGAAGC
CAGGTCAGCGTTTCTTGCAGCACACATCCACTTTTTTGTACCCCTTTTTTGCACACACGTCCCTTTGAGTATCTTTGACT
CACCAGCCTTGGAGTTATTGGGACCCTGGTGAAAACAGATGAACAAGGAGTAATCAACTTTTTACTGACAACAGAAATTA
TCCCTTTATGTTTGCGAATTATGGAATCTGGAAGTGAACTTTCTAAAACAGTTGCCACATTCATCCTCCAGAAGATCTTC
TTAGATGACACTGGTTTGGCTTATATATGTCAGACGTATGAGCGTTTCTCCCTTGTTGCCATGATCTTGGGTAAGATGGT
CCTGCAGTTATCCAAAGAGCCTTCTGCCCATCTGCTGAAGCATGTAGTGAGATGTTACATTCAACTCTCAGATAACCCAG
GGCACCTGAAGCACTCAGGCAGTGCCTCTCTGACCAGCTGAAGGACACAACCTTTGCTAAA
ORF - retro_cjac_2525 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.77 % |
| Parental protein coverage: | 61.87 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | PTLTAHQSNRVCNALALLQCVASHPETRSAFLAAHI-PLFLYPFLHTVSKTRPFEYLRLTSLGVIGALVK |
| PTLTAHQ.NRVCNALALLQCVASHPE.RSAFLAAHI.PLF..PFLH....TRPFEYL.LTSLGVIG.LVK | |
| Retrocopy | PTLTAHQINRVCNALALLQCVASHPEARSAFLAAHI<PLFCTPFLH----TRPFEYL*LTSLGVIGTLVK |
| Parental | TDEQEVINFLLTTEIIPLCLRIMESGSELSKTVATFILQKILLDDTGLAYICQTYERFSHVAMILGKMVL |
| TDEQ.VINFLLTTEIIPLCLRIMESGSELSKTVATFILQKI.LDDTGLAYICQTYERFS.VAMILGKMVL | |
| Retrocopy | TDEQGVINFLLTTEIIPLCLRIMESGSELSKTVATFILQKIFLDDTGLAYICQTYERFSLVAMILGKMVL |
| Parental | QLSKEPSARLLKHVVRCYLRLSDN-PRAREALRQCLPDQLKDTTFAQ |
| QLSKEPSA.LLKHVVRCY..LSDN.PRA.EALRQCL.DQLKDTTFA. | |
| Retrocopy | QLSKEPSAHLLKHVVRCYIQLSDN<PRAPEALRQCLSDQLKDTTFAK |
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 .86 RPM |
| SRP051959_heart | 0 .00 RPM | 4 .35 RPM |
| SRP051959_kidney | 0 .00 RPM | 5 .79 RPM |
| SRP051959_liver | 0 .00 RPM | 3 .77 RPM |
| SRP051959_lung | 0 .00 RPM | 6 .98 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 7 .44 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 5 .28 RPM |
| SRP051959_spleen | 0 .00 RPM | 6 .68 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2525 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2525 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2525 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 | ENSCJAG00000011079 | 1 retrocopy |
retro_cjac_2525 ,
|
| Drosophila melanogaster | FBgn0031047 | 1 retrocopy |