RetrogeneDB ID: | retro_cjac_2241 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 3:71686056..71686686(-) | ||
| Located in intron of: | ENSCJAG00000002804 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TPST1 | ||
| Ensembl ID: | ENSCJAG00000004198 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2241
CCTTATGTATGTAATAAATATCCTTTTGCCCTAAAATTCTTAACTTACCTTGCTAGGTTATTGCTCAATGCCAAATTTCT
CCTGATGGTCCCAGATGGCTGGGCATCAGTACATTCGATGATTTCTCGAAAAGTTACTATAGCTGGATTTGACCTGAACA
GCTACAGGGACTGCTTGACCAAGTGGAATCGTGCCATAGAGACCACGTATAACCAGTGTATGGAGGTTGGTTATAAAAAG
TGCATGTTGGTTCATGACAAATAGCTTGTCTTACATCCTGAATGGTGGATGAGATCACTCTTAAAGTTCTTCCATATTCC
CTGGAACCACTCGGTACTGCACCATGAAGAGATGATTGGGAAAGCTAGGGGAGTGTTTCTGTCAATAGTGGAGAGATCTA
CAGACCAAGTCATCAAGCCAGTCAGTGTAGGAGCTCTATCAAAATGGGTTGGGAAGATAGCACCAGATGTTTTGCAAGAC
ATGGCAGTGATTGCTCCTATGCTTGCCAAACTTGGATATGACCCATATGCCAACCTACCTAACTACGGAAAACCTGATCC
CCAAATTCTTGAAAACACTCGAAGCATCTGTAAGGGAAAATTCCAGCTACCTGACTTTCTTAAAGAAAAA
ORF - retro_cjac_2241 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.67 % |
| Parental protein coverage: | 56.76 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | PYLCNKDPFALKSLTYLARLFPNARFLLMVRDGRASVHSMISRKVTIAGFDLNSYRDCLTKWNRAIETMY |
| PY.CNK.PFALK.LTYLARL..NA.FLLMV.DG.ASVHSMISRKVTIAGFDLNSYRDCLTKWNRAIET.Y | |
| Retrocopy | PYVCNKYPFALKFLTYLARLLLNAKFLLMVPDGWASVHSMISRKVTIAGFDLNSYRDCLTKWNRAIETTY |
| Parental | NQCMEVGYKKCMLVHYEQLVLHPERWMRTLLKFLQIPWNHSVLHHEEMIGKAGGVSLSKVERSTDQVIKP |
| NQCMEVGYKKCMLVH...LVLHPE.WMR.LLKF..IPWNHSVLHHEEMIGKA.GV.LS.VERSTDQVIKP | |
| Retrocopy | NQCMEVGYKKCMLVHDK*LVLHPEWWMRSLLKFFHIPWNHSVLHHEEMIGKARGVFLSIVERSTDQVIKP |
| Parental | VNIGALSKWVGKIPPDVLQDMAVIAPMLAKLGYDPYANPPNYGKPDPKILENTRRVYKGEFQLPDFLKEK |
| V..GALSKWVGKI.PDVLQDMAVIAPMLAKLGYDPYAN.PNYGKPDP.ILENTR...KG.FQLPDFLKEK | |
| Retrocopy | VSVGALSKWVGKIAPDVLQDMAVIAPMLAKLGYDPYANLPNYGKPDPQILENTRSICKGKFQLPDFLKEK |
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 | 1 .93 RPM | 5 .19 RPM |
| SRP051959_heart | 1 .09 RPM | 5 .31 RPM |
| SRP051959_kidney | 1 .58 RPM | 18 .75 RPM |
| SRP051959_liver | 0 .37 RPM | 42 .24 RPM |
| SRP051959_lung | 1 .46 RPM | 4 .57 RPM |
| SRP051959_lymph_node | 2 .08 RPM | 6 .76 RPM |
| SRP051959_skeletal_muscle | 0 .37 RPM | 2 .34 RPM |
| SRP051959_spleen | 2 .06 RPM | 4 .37 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2241 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2241 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2241 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 | ENSCJAG00000004198 | 1 retrocopy |
retro_cjac_2241 ,
|
| Xiphophorus maculatus | ENSXMAG00000007886 | 1 retrocopy |