RetrogeneDB ID: | retro_cjac_3644 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | ACFV01191663.1:1636..2209(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000009347 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000019358 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3644
ATGGACCCGGCTCCCGGCACCCTGATCTCCTCGCCGCCATGCCCGCGCTCCTGGGCGTCCCACAGGCGGAGGTGCTGGAG
GACGTGTTGCGGGAGCAGTTCGGGCCGCTGCCCCAGCTGGCTGCCATCTGCCGGCTCAAACGGCTGCCCTCAGGTGGCTA
CTCTTCCACCGAAGACCTCCAGTTGGTGCTGGAGTGGCGGTGCATGGCCAACACTAAGGAGCGCGAGCGGATAAAAAATC
TCAACTGTGGTTTTGCCAAATTGAAGGCACTTGTGCCATTTCTTCCCCAAAGCAGGAAGCCCAGCAAAGCTGATATTCTT
AAAGGCACAACTGAATATATATACAAGTTCTCAGTCATGTTTTGGAAGAAGCTGAAGACTCAGAGAAACAAGACCTAGAT
GAGCAGAGCTTGGTAGCAGCACTTCTGAACCACCTATATCCTCCGCTAGAGAGCTATCAAGAAACATCATCCAAGGTATA
GGCTGTGCTTTCAGCTTGAAGAATGAAGAGGAAGAGCTTTGGGCAGATGGCGGCAGTGGTGAGCCCGCACATTCTCATCA
CCAGAGTGTTGTC
ORF - retro_cjac_3644 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.08 % |
| Parental protein coverage: | 87.61 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | MDPAPGTL-DLRAATPALLGVPQAEVLEEVLREEFGPLPQLAAICRLKRLPSGGYSSTEDLQLVLERRRV |
| MDPAPGTL.DL.AA.PALLGVPQAEVLE.VLRE.FGPLPQLAAICRLKRLPSGGYSSTEDLQLVLE.R.. | |
| Retrocopy | MDPAPGTL<DLLAAMPALLGVPQAEVLEDVLREQFGPLPQLAAICRLKRLPSGGYSSTEDLQLVLEWRCM |
| Parental | ANAKEREHIKNLNRGFAKLKALVPFLPQSRKPS-KVDILKGATE-YIQVLSHVLEEAEDSEKQDPDEQS- |
| AN.KERE.IKNLN.GFAKLKALVPFLPQSRKPS.K...LK.....YIQVLSHVLEEAEDSEKQD.DEQS. | |
| Retrocopy | ANTKERERIKNLNCGFAKLKALVPFLPQSRKPS>KLIFLKAQLN>YIQVLSHVLEEAEDSEKQDLDEQS< |
| Parental | YSSSTSEPHISSTRELSRNIIQGISCAFSLKNEEEEPWADGGSGEPTHSCRQRVL |
| ..SSTSEP.ISS.RELSRNIIQGI.CAFSLKNEEEE.WADGGSGEP.HS..Q.V. | |
| Retrocopy | LGSSTSEPPISSARELSRNIIQGIGCAFSLKNEEEELWADGGSGEPAHSHHQSVV |
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 | 0 .07 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .07 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .13 RPM |
| SRP051959_lung | 0 .00 RPM | 0 .03 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .16 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .00 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .95 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3644 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3644 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3644 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000015931 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000019358 | 1 retrocopy |
retro_cjac_3644 ,
|
| Felis catus | ENSFCAG00000013444 | 1 retrocopy |