RetrogeneDB ID: | retro_cjac_4091 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:76564342..76565044(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NUF2 | ||
| Ensembl ID: | ENSCJAG00000004050 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_4091
GTTTCTCTGAAAGAAATACAAGAGAATTTGAAAACAAAAATTGTGGATTCTCCAGAGAAGCTAAAGAATTATAAAGAAAA
AGTGAAAGATAAAGTCCAGAAGCTTAAAAATGCCAGGCAAGAAGTGGTAGAGAAATATGAACTCTATGGAGATTCAGTTG
ACTGCCTACCTTCATGTCAGTTGGAAGTGCAGTTATATCGAAAGAAAATACAGGACCTTTCAGATAATAAGGAAAAATTA
GCCAGTATCTTAAAGGAGAGCCTGAACTTGGAGGACCAAATTGAGAGTGGTGAGTCAGAACTGAAGAAATTGAAGACTGA
AGAAAATTCGTTCAAAAGACTGATGATTGTGAAGAAGGAAAAACTTGCCACAGTGCAGTTCAAAATAAATAAGAAGCACG
AAGATGTTAAGCAATACAAACGCACAGTAATTGAGGATTGCAATAAAGTTCAAGAAAAAAGAGGTGCTGTCTGTAAGCAA
GTAACCACAATTAATCAAGAAATCCAGAAATACAAATTTGAAATTCAGCAACTAAAAGATGCTACGGAAAGGGAGAAGCT
GAAGTTCCAGGAAATATTTTTAAACTTGAAAACTGCTTTGGAGAAATACCACGAAGGTATTGAAAAGGCCACAGAGGACT
CTTATGCTAAGATAGATGAGAAGACAGCTGAACTGAAGAGGAAGATGTTCAAAATGTCAACC
ORF - retro_cjac_4091 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.57 % |
| Parental protein coverage: | 50.43 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VSLKEIQENLKTKIVDSPEKLKNYKEKMKDKVQKLKNARQEVVEKYELYGDSVDCLPSCQLEVQLYRKKI |
| VSLKEIQENLKTKIVDSPEKLKNYKEK.KDKVQKLKNARQEVVEKYELYGDSVDCLPSCQLEVQLYRKKI | |
| Retrocopy | VSLKEIQENLKTKIVDSPEKLKNYKEKVKDKVQKLKNARQEVVEKYELYGDSVDCLPSCQLEVQLYRKKI |
| Parental | QDLSDNKEKLASILKESLNLEDQIESGESELKKLKTEENSFKRLMIVKKEKLATVQFKINKKHEDVKQYK |
| QDLSDNKEKLASILKESLNLEDQIESGESELKKLKTEENSFKRLMIVKKEKLATVQFKINKKHEDVKQYK | |
| Retrocopy | QDLSDNKEKLASILKESLNLEDQIESGESELKKLKTEENSFKRLMIVKKEKLATVQFKINKKHEDVKQYK |
| Parental | RTVIEDCNKVQEKRGAVCKQVTTINQEIQKYKFEIQQLKDATEREKLKFQEIFLNLKTALEKYHEGIEKA |
| RTVIEDCNKVQEKRGAVCKQVTTINQEIQKYKFEIQQLKDATEREKLKFQEIFLNLKTALEKYHEGIEKA | |
| Retrocopy | RTVIEDCNKVQEKRGAVCKQVTTINQEIQKYKFEIQQLKDATEREKLKFQEIFLNLKTALEKYHEGIEKA |
| Parental | TEDSYAKIDEKTAELKRKMFKMST |
| TEDSYAKIDEKTAELKRKMFKMST | |
| Retrocopy | TEDSYAKIDEKTAELKRKMFKMST |
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 .33 RPM | 3 .22 RPM |
| SRP051959_heart | 0 .53 RPM | 0 .44 RPM |
| SRP051959_kidney | 0 .91 RPM | 0 .40 RPM |
| SRP051959_liver | 0 .32 RPM | 0 .43 RPM |
| SRP051959_lung | 0 .24 RPM | 1 .14 RPM |
| SRP051959_lymph_node | 0 .98 RPM | 2 .37 RPM |
| SRP051959_skeletal_muscle | 0 .46 RPM | 0 .15 RPM |
| SRP051959_spleen | 0 .48 RPM | 1 .55 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4091 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4091 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4091 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 | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000004050 | 1 retrocopy |
retro_cjac_4091 ,
|
| Macropus eugenii | ENSMEUG00000007093 | 1 retrocopy | |
| Tupaia belangeri | ENSTBEG00000011027 | 1 retrocopy |