RetrogeneDB ID: | retro_cjac_2951 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 7:141379908..141380363(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CDK4 | ||
| Ensembl ID: | ENSCJAG00000006697 | ||
| Aliases: | None | ||
| Description: | cyclin-dependent kinase 4 [Source:HGNC Symbol;Acc:1773] |
Retrocopy-Parental alignment summary:
>retro_cjac_2951
GCTGAGACCATCAAGGATCTGATGCACCGGTTTTGAAGAGGTCTAGATTTTCTTCATACCCATTGCATTGTTCACTGATA
TCTGAAGCCAGAAAACATTCTGGTGACAAGTGGTGGGACAGTCAAGCTGGCTGACTTGGCCTGGCCAGAATCTATAGCTG
CTAGATGGCATTTAGACTTGTAATTGTTACATTCTTATACTGTGCTCAGTAGGTTCTTCCGCAATCTACAGAGGCAACAT
CTATGGACATGTGAAGTATTGACTGTGTCTTTGCAGAGATGTTTTCACAGAAGCCTCTCTCCTGTAGAAGCTCTAAAGAC
CATTACTTGGGCAAAATCTTTGACCTGATTGGGCTGCCTTTGTAGGATGACTGGCCCTGAGATGTGTTTCTACCGCATGG
AGCCAGTCTACACAGAAAGCCTCACCCAGTGCAGTCGGTGGTGCCTGACATGGAG
ORF - retro_cjac_2951 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.63 % |
| Parental protein coverage: | 50.33 % |
| Number of stop codons detected: | 7 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | AETIKDLMRQFLRGLDFLHANCIVHRDLKPENILVTSGGTVKLADF-GLARIYSYQMALTPVVVTLWYRA |
| AETIKDLM..F.RGLDFLH..CIVH..LKPENILVTSGGTVKLAD..GLARIYS..MA...V.VT..Y.A | |
| Retrocopy | AETIKDLMHRF*RGLDFLHTHCIVH*YLKPENILVTSGGTVKLADL<GLARIYSC*MAFRLVIVTFLYCA |
| Parental | PEVLLQSTYATPVDMWSVGCIFAEMFRRKPLFCGNSEADQLGKIFDLIGLPPEDDWPRDVSLPRGAFHPR |
| ..VL.QST.AT..DM.S..C.FAEMF..KPL.C..S....LGKIFDLIGLP..DDWP.DV.LP.GA...R | |
| Retrocopy | Q*VLPQSTEATSMDM*SIDCVFAEMFSQKPLSCRSSKDHYLGKIFDLIGLPL*DDWP*DVFLPHGASLHR |
| Parental | GPRPVQSVVPEME |
| .P.PVQSVVP.ME | |
| Retrocopy | KPHPVQSVVPDME |
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 | 16 .35 RPM |
| SRP051959_heart | 0 .00 RPM | 14 .26 RPM |
| SRP051959_kidney | 0 .00 RPM | 20 .37 RPM |
| SRP051959_liver | 0 .00 RPM | 11 .50 RPM |
| SRP051959_lung | 0 .00 RPM | 13 .76 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 15 .23 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 16 .66 RPM |
| SRP051959_spleen | 0 .00 RPM | 15 .82 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2951 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2951 was not experimentally validated.