RetrogeneDB ID: | retro_cjac_2079 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 22:44652041..44652557(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000021880 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000019139 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2079
CCCCCGCCCAGTGCTGCGGCAGCCGGCACCCCGCGGTCCCCGGCCGCCCCCGCCGCCATGTACCGCTGGCAGAAGAACAC
CAAGTTCACCAAGATCTTCGTGGGCAGCCTGCGGTACCGCACCACCGACGCCTCGCTCAGGAAGTACTTCGAGGACTTCG
GCGACATCGAGGAGGCCGTGGTCATCACCGACCCCGAGACGGGCAGGTCCCGCCGCTACGGCTTCGTGACCATGGCCACC
CGGGCGGCAGCCCAGAGGGCTTGTGAAGACCCCCACCCCGTCATCGACGGCCGCAAGACCAACGTGAACCTGGCTTACCT
GGGCGCCAAGCGGCGGAGCCTCCCGACGGGCTTTGCAACTAGGGTGCGGAAGCTGCGCCCCGCTTCGATCCAGCGAGTTT
ACCCGCCGACCCCGGACGACATCCACCCGCCAGCGACCGGGCAGCCCAGCGCGGTAATCCTGGCCGCCCCGCTCCCATCG
CTGTCCCCGCCCTACATGGGGTACGCGCCAGCCAGC
ORF - retro_cjac_2079 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.51 % |
| Parental protein coverage: | 71.97 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | PAPCAPSAGFPRPPAAPGAMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKS |
| P.P.A..AG.PR.PAAP.AM...QK.T.FTKIFVG.L.Y.TTDASLRKYFE.FGDIEEAVVITD..TG.S | |
| Retrocopy | PPPSAAAAGTPRSPAAPAAMYRWQKNTKFTKIFVGSLRYRTTDASLRKYFEDFGDIEEAVVITDPETGRS |
| Parental | RGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVQQLHPALIQRTYGLTPHY |
| R.YGFVTMA.RAAA.RAC.DP.P.IDGRK.NVNLAYLGAK.RSL.TGFA..V..L.PA.IQR.Y..TP.. | |
| Retrocopy | RRYGFVTMATRAAAQRACEDPHPVIDGRKTNVNLAYLGAKRRSLPTGFATRVRKLRPASIQRVYPPTPDD |
| Parental | IYPPAIVQPSVVIPAAPVPSLSSPYIEYTPAS |
| I.PPA..QPS.VI.AAP.PSLS.PY..Y.PAS | |
| Retrocopy | IHPPATGQPSAVILAAPLPSLSPPYMGYAPAS |
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 | 3 .02 RPM |
| SRP051959_heart | 0 .00 RPM | 11 .56 RPM |
| SRP051959_kidney | 0 .00 RPM | 2 .42 RPM |
| SRP051959_liver | 0 .13 RPM | 1 .39 RPM |
| SRP051959_lung | 0 .00 RPM | 7 .71 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 23 .42 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 11 .71 RPM |
| SRP051959_spleen | 0 .00 RPM | 6 .97 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2079 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2079 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2079 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 | ENSCJAG00000019139 | 1 retrocopy |
retro_cjac_2079 ,
|
| Macaca mulatta | ENSMMUG00000031391 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000013661 | 1 retrocopy |