RetrogeneDB ID: | retro_cjac_3886 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL285818.1:49130..49673(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DERL2 | ||
| Ensembl ID: | ENSCJAG00000011304 | ||
| Aliases: | LOC100400027, DERL2, derlin-2 | ||
| Description: | derlin 2 [Source:HGNC Symbol;Acc:17943] |
Retrocopy-Parental alignment summary:
>retro_cjac_3886
TCAGCTGTGCCTACACCACTGCCCATGCACTTGGAATTGATCACTGCTTTTCAGTTGTACTTCAATCCTGAATTAATCTT
TAAACACTTTAAAATATTGAGATTAATCACCAATTTCTTATTTTTTGAGCCAGTTGGATTCAATTTTTTATTTAACATGA
TTTTTCTATATTGTTACTGTCCAATGCTAGAAGGCTCTTTCTGGGGTTGGACAGCAAACTTGGTATTTATATTCCTTTTT
GGTGGATTCTTAATGACCCTTCTTAGTTTGTTTTTGAGCTTAGTTTTCATGGGCCAGGCCTTTACAATAATGCTCGTCTA
TGTGTGGAGCCAAAGGAAATCCTATGTCCACATGAACTTCTTCAGCCTTCTCAACTTCCAGGCCCCCTTTCTGCCCTGGG
TGTTCATGGGGTTTTCCTTGTTGGGGAACTCAATCACTGTAGACCTTTTGGGTATTGCAGTTGGACACATATATTTTTTC
TTGGAAGATGTATTTTCTAATTAGCTTGATGGAATAAGAATTCTGAAACCACCATCTATCTTG
ORF - retro_cjac_3886 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.78 % |
| Parental protein coverage: | 76.57 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ACVLTTAAVQLELITPFQLYFNPELIFKHFQIWRLITNFLFFGPVGFNFLFNMIFLYRYCRMLEEGSFRG |
| ..V.T.....LELIT.FQLYFNPELIFKHF.I.RLITNFLFF.PVGFNFLFNMIFLY.YC.MLE.GSF.G | |
| Retrocopy | SAVPTPLPMHLELITAFQLYFNPELIFKHFKILRLITNFLFFEPVGFNFLFNMIFLYCYCPMLE-GSFWG |
| Parental | RTADFVFMFLFGGFLMTLFGLFVSLVFLGQAFTIMLVYVWSRRNPYVRMNFFGLLNFQAPFLPWVLMGFS |
| .TA..VF.FLFGGFLMTL..LF.SLVF.GQAFTIMLVYVWS.R..YV.MNFF.LLNFQAPFLPWV.MGFS | |
| Retrocopy | WTANLVFIFLFGGFLMTLLSLFLSLVFMGQAFTIMLVYVWSQRKSYVHMNFFSLLNFQAPFLPWVFMGFS |
| Parental | LLLGNSIIVDLLGIAVGHIYFFLEDVFPNQPGGIRILKTPSIL |
| .LLGNSI.VDLLGIAVGHIYFFLEDVF.N...GIRILK.PSIL | |
| Retrocopy | -LLGNSITVDLLGIAVGHIYFFLEDVFSN*LDGIRILKPPSIL |
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 | 14 .18 RPM |
| SRP051959_heart | 0 .00 RPM | 8 .54 RPM |
| SRP051959_kidney | 0 .00 RPM | 14 .18 RPM |
| SRP051959_liver | 0 .00 RPM | 23 .72 RPM |
| SRP051959_lung | 0 .00 RPM | 12 .49 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 14 .59 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 9 .65 RPM |
| SRP051959_spleen | 0 .00 RPM | 18 .21 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3886 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3886 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3886 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 10 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000011304 | 3 retrocopies |
retro_cjac_1540, retro_cjac_3886 , retro_cjac_3980,
|
| Oryctolagus cuniculus | ENSOCUG00000004811 | 2 retrocopies | |
| Tupaia belangeri | ENSTBEG00000009213 | 1 retrocopy | |
| Tarsius syrichta | ENSTSYG00000000394 | 4 retrocopies |