RetrogeneDB ID: | retro_cjac_2080 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 22:47682192..47682786(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000023199 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000010909 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2080
AGGTTCCGGTTCTATGGTGATCTGGACTGTCCCGACTGGGTCCTGGCAGAGATCAGCACGCTGGCCAAGACGTCCTCTGT
GAAGTTGCGGCTGCTCTGCAGCCAGGTACTAAAGGGCCTGCTGGGACAGGGGACTGATTATGAGAAGATCCTGAAGCTCA
TGGCTGACACCAAGTTTGAGTCAGGCGATGTGAAGGCCACAGTGGCAGTGCTGAGCTTCATCCTCTCCAGTGCGGCCAAG
CACAGTGTTGATGGCGAATCCTTATCCAGCGAACTGCAGCAGCTGGGGCTGCCCACAGAGCACGCCGCCGGCCTGTGCCG
CTGTTACCAGGAGAAGCAAATTCCCTGGCAGAAGCACTTGTGGGTCTGCAGCCTACGCACAAACAGGTTGGCAGGTGCAG
GCTGGCGGGCAGACTACACCCTGAGCTCCAGCCTGCTGCAGTCTGTGGAAGAGCCTATGGTGCACCTGCGCCTGGAGGTG
GCAGCTGCCCCAGGTACCCCAGCCCAGCCTGTTGCCATGTCCCTCTCAGCAGACAAGTTCCAGGTCCTCCTGGCAGAGCT
GAAGCAGGCCCAGACCCTGATGAGCTCCCTGGGC
ORF - retro_cjac_2080 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.44 % |
| Parental protein coverage: | 99.5 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | RFRFCGDLDCPDWVLAEISTLAKMSSVKLRLLCSQVLKELLGQGTDYEKILKLTADTKFESGDVKATVAV |
| RFRF.GDLDCPDWVLAEISTLAK.SSVKLRLLCSQVLK.LLGQGTDYEKILKL.ADTKFESGDVKATVAV | |
| Retrocopy | RFRFYGDLDCPDWVLAEISTLAKTSSVKLRLLCSQVLKGLLGQGTDYEKILKLMADTKFESGDVKATVAV |
| Parental | LSFILSSAAKHSVDGESLSSELQQLGLPKEHAASLCRCYEEKQIPLQKHLRVCSLRTNRLAGVGWRVDYT |
| LSFILSSAAKHSVDGESLSSELQQLGLP.EHAA.LCRCY.EKQIP.QKHL.VCSLRTNRLAG.GWR.DYT | |
| Retrocopy | LSFILSSAAKHSVDGESLSSELQQLGLPTEHAAGLCRCYQEKQIPWQKHLWVCSLRTNRLAGAGWRADYT |
| Parental | LSSSLLQSVEEPMVHLRLEVAAAPGTPAQPVAMSLSADKFQVLLAELKQAQTLMSSLG |
| LSSSLLQSVEEPMVHLRLEVAAAPGTPAQPVAMSLSADKFQVLLAELKQAQTLMSSLG | |
| Retrocopy | LSSSLLQSVEEPMVHLRLEVAAAPGTPAQPVAMSLSADKFQVLLAELKQAQTLMSSLG |
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 .16 RPM | 7 .10 RPM |
| SRP051959_heart | 0 .07 RPM | 7 .07 RPM |
| SRP051959_kidney | 0 .22 RPM | 20 .94 RPM |
| SRP051959_liver | 0 .02 RPM | 6 .06 RPM |
| SRP051959_lung | 0 .08 RPM | 9 .44 RPM |
| SRP051959_lymph_node | 0 .09 RPM | 9 .59 RPM |
| SRP051959_skeletal_muscle | 0 .07 RPM | 7 .45 RPM |
| SRP051959_spleen | 0 .02 RPM | 10 .71 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2080 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2080 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2080 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 | ENSCJAG00000010909 | 1 retrocopy |
retro_cjac_2080 ,
|
| Dasypus novemcinctus | ENSDNOG00000013425 | 1 retrocopy | |
| Loxodonta africana | ENSLAFG00000006259 | 1 retrocopy |