RetrogeneDB ID: | retro_cjac_2670 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 5:134675032..134675423(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000004992 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2670
ATGCCGCCCAAAGGAAAAAGTGGTTCTGGAAAAGTGGGGAAGGGGGAGCAGCCTCTGGGAGTGGCAGTGCTGACAAGAAG
GCTCAAGGTCCCAAAGGTGGTGGCAATGCAGGAAAGGTCAGACACATTCTGTGTGAAAAACATGGCAAAACCATGGAAGC
CATGGAAAAGTCAAAGTCTGAGATGAGATTCAATGAAGTGGCCACACAATGAGTGAAGACAAAGCCAGGCAAGGGGGCGA
CTTGGGTTGGATGACCAGAGGGTCCGTGGAAGGACCGTTTCAAGAAGCAGCATTTGTCTCGTCTGTAAGTGGGATGGATA
AGCCTGTGTTTACAGACCCACCAGTTAAGACAAAATCTGGATATCATATTATTATGGTTGAAGGAAGAAAA
ORF - retro_cjac_2670 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.47 % |
| Parental protein coverage: | 85.06 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MPPKGKSGSGKAGKG-GAASGSDSAEKKAQGPKGGGNAVKVRHILCEKHSKIMEAMEKLKSGMRFNEVAA |
| MPPKGKSGSGK.GKG.GAASGS.SA.KKAQGPKGGGNA.KVRHILCEKH.K.MEAMEK.KS.MRFNEVA. | |
| Retrocopy | MPPKGKSGSGKVGKG<GAASGSGSADKKAQGPKGGGNAGKVRHILCEKHGKTMEAMEKSKSEMRFNEVAT |
| Parental | Q-YSEDKARQGGDLGWMTRGSMVGPFQEAAFALPVSGMDKPVFTDPPVKTKFGYHIIMVEGRK |
| Q..SEDKARQGGDLGWMTRGS..GPFQEAAF...VSGMDKPVFTDPPVKTK.GYHIIMVEGRK | |
| Retrocopy | Q<MSEDKARQGGDLGWMTRGSVEGPFQEAAFVSSVSGMDKPVFTDPPVKTKSGYHIIMVEGRK |
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 | 1 .31 RPM |
| SRP051959_heart | 0 .00 RPM | 1 .84 RPM |
| SRP051959_kidney | 0 .04 RPM | 3 .00 RPM |
| SRP051959_liver | 0 .00 RPM | 2 .86 RPM |
| SRP051959_lung | 0 .00 RPM | 1 .61 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 1 .71 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 1 .51 RPM |
| SRP051959_spleen | 0 .00 RPM | 1 .83 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2670 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2670 was not experimentally validated.