RetrogeneDB ID: | retro_cjac_4056 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:43620722..43621220(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PGAP2 | ||
| Ensembl ID: | ENSCJAG00000015470 | ||
| Aliases: | None | ||
| Description: | post-GPI attachment to proteins 2 [Source:HGNC Symbol;Acc:17893] |
Retrocopy-Parental alignment summary:
>retro_cjac_4056
GCGCAGAGACTCGGGCTGCGGGAGCTTGGGCCAATCAGAGGGACAGCCCGAGAATGGCATGGTGATGGAATGCAGCTGAG
AGGTCTGACAAGATGTACCAGGTCCCACTGCCACTGGACCGGGATGGGACCCTGGTACGGCTTCACCTTGGTTGCCCTGG
TCACGATCTGCTGTCCACTTGTCGCCGCTTTCCTCTTCTGCATCCTCTTGTCCCTGATCTTCCACTTCAAGGAGACAATG
GCCACTCACTGTGGGGTGCCCTCAGTGAGCTCGGCCATCAGCGGGGAAGTGCCCCCGCACTACGTGTGGCGTTTCTGCAT
CGGCCTGCACTCAGCGCCTCACTTCTTGGTGGCCTTTGCCTATAGGAACCACTACCTCAGCTGCACCTCCCCATGTTCCT
GCTACCGCCCACTCTGCCCCACCAACTTCGGACTCAATGTCTTGGAGAACCTTGCGTTGCTAGTGCTCACTTACATCTCC
TCCTCTGAGGACTTCACT
ORF - retro_cjac_4056 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.31 % |
| Parental protein coverage: | 55.7 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | ALRLRLRELGPMRGTAPEWHGK-WNAAERSDKMYQVPLPLDRDGTLVRLR-FTLVALVTVCCPLVA-FLF |
| A.RL.LRELGP.RGTA.EWHG..WNAAERSDKMYQV..PL..D......R.FTLVALVT.CCPLVA.FLF | |
| Retrocopy | AQRLGLRELGPIRGTAREWHGD<WNAAERSDKMYQV--PLPLDRDGTLVR>FTLVALVTICCPLVAAFLF |
| Parental | CILWSLLFHFKETTATHCGVPNYLPSVSSAIGGEVPQRYVWRFCIGLHSAPRFLVAFAYWNHYLSCASPC |
| CIL.SL.FHFKET.ATHCGV....PSVSSAI.GEVP..YVWRFCIGLHSAP.FLVAFAY.NHYLSC.SPC | |
| Retrocopy | CILLSLIFHFKETMATHCGV----PSVSSAISGEVPPHYVWRFCIGLHSAPHFLVAFAYRNHYLSCTSPC |
| Parental | SCYRPLCRINFGLNVVENLALLVLTYVSSSEDFT |
| SCYRPLC..NFGLNV.ENLALLVLTY.SSSEDFT | |
| Retrocopy | SCYRPLCPTNFGLNVLENLALLVLTYISSSEDFT |
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 | 4 .30 RPM |
| SRP051959_heart | 0 .00 RPM | 5 .84 RPM |
| SRP051959_kidney | 0 .00 RPM | 7 .70 RPM |
| SRP051959_liver | 0 .00 RPM | 4 .79 RPM |
| SRP051959_lung | 0 .00 RPM | 8 .25 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 7 .85 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 6 .16 RPM |
| SRP051959_spleen | 0 .00 RPM | 7 .82 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4056 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4056 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4056 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 | ENSCJAG00000015470 | 1 retrocopy |
retro_cjac_4056 ,
|
| Macropus eugenii | ENSMEUG00000009912 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000020371 | 1 retrocopy |