RetrogeneDB ID: | retro_cjac_4016 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL288442.1:8485..9232(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000035377 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000002838 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_4016
ATGGAGGACGTCTTGGCCGGGCCCCTGCACCGGGCGGCGGCGGAGGCGGCCGAGGCATGAGCGCGGCCCGGGGTGACGCT
GCTGCCCTTAGTGCCCCTCACAGGGACTGCGGAGGCGGACGAGGGCGGCGGCCACTGGAGCTTCATTGACTGCGAGATGG
AGGAGGTGGACCTGCAGGACCTGCCCAGCGCCACCATCGCCTGCCACCCGGACCCGCCCTTGTTCGTGGATGGCCTGTGC
CGGGCCAAATTTGAGTCTGTCTTTAGGACATATGGCAAGGACATCGCCTTTCAGTATTTTAAGAGTTTCAAACGAGTCAG
AATAAACTTCAGCAACCTCTTCTCCGCAGCAGATGTCAGGCTCCAGCTGCATAAGACTGAGTTTCTGGGAAAGGAAATGA
AGTTATATTTTGCTCAGACCTTACACATAGGAAGCTCGCACCTGGCTCCGCCAAACCCCGACAAGCAGTTTCTGATCTCC
CCTCCCACCTCTCCACCAGTGGGGTGGAAACAAGTGGAAGACGCAACCCCAGTCATAAACTATGATCTCTTATATGCTAT
CTCCAAGCTGGGGCCAGGGGAAAAGTATGAATTGCATGCAGCGACTGACACCACTCCCAGCGCGGTAGTCCACGTATGTG
AGAGCGATGAAGAGGAGGAGGAAGAAGAGGAGATGGAGAGAATGAAGAGACCCAAGCCAAAAATTATCCAGACCAGGAAG
CCGGAGTACACACGGATCCACCTCAGC
ORF - retro_cjac_4016 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.36 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MEDGLAGPRHGAAAEATEARARPGATLRPFAPLSGTAEADEGGGDWSFIDCEMEEVDLQDLPSATIACHL |
| MED.LAGP.H.AAAEA.EA.ARPG.TL.P..PL.GTAEADEGGG.WSFIDCEMEEVDLQDLPSATIACH. | |
| Retrocopy | MEDVLAGPLHRAAAEAAEA*ARPGVTLLPLVPLTGTAEADEGGGHWSFIDCEMEEVDLQDLPSATIACHP |
| Parental | DPRVFVDGLCRAKFESLFRTYDKDITFQYFKSFKRVRINFSNPFSAADARLQLHKTEFLGKEMKLYFAQT |
| DP..FVDGLCRAKFES.FRTY.KDI.FQYFKSFKRVRINFSN.FSAAD.RLQLHKTEFLGKEMKLYFAQT | |
| Retrocopy | DPPLFVDGLCRAKFESVFRTYGKDIAFQYFKSFKRVRINFSNLFSAADVRLQLHKTEFLGKEMKLYFAQT |
| Parental | LHIGSSHLAPPNPDKQFLISPPASPPVGWKQVEDATPVINYDLLYAISKLGPGEKYELHAATDTTPSVVV |
| LHIGSSHLAPPNPDKQFLISPP.SPPVGWKQVEDATPVINYDLLYAISKLGPGEKYELHAATDTTPS.VV | |
| Retrocopy | LHIGSSHLAPPNPDKQFLISPPTSPPVGWKQVEDATPVINYDLLYAISKLGPGEKYELHAATDTTPSAVV |
| Parental | HVCESDEEKEEEEEMERMKRPKPKIIQTRRPEYTPIHLS |
| HVCESDEE.EEEEEMERMKRPKPKIIQTR.PEYT.IHLS | |
| Retrocopy | HVCESDEEEEEEEEMERMKRPKPKIIQTRKPEYTRIHLS |
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 .04 RPM | 12 .60 RPM |
| SRP051959_heart | 0 .11 RPM | 31 .59 RPM |
| SRP051959_kidney | 0 .20 RPM | 110 .18 RPM |
| SRP051959_liver | 0 .06 RPM | 29 .11 RPM |
| SRP051959_lung | 0 .02 RPM | 14 .32 RPM |
| SRP051959_lymph_node | 0 .07 RPM | 10 .96 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 78 .01 RPM |
| SRP051959_spleen | 0 .06 RPM | 14 .12 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4016 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4016 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4016 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000002838 | 2 retrocopies |
retro_cjac_4016 , retro_cjac_437,
|
| Callithrix jacchus | ENSCJAG00000012084 | 1 retrocopy | |
| Cavia porcellus | ENSCPOG00000010683 | 1 retrocopy | |
| Tarsius syrichta | ENSTSYG00000006972 | 1 retrocopy |