RetrogeneDB ID: | retro_cjac_2061 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 22:11604572..11605166(+) | ||
| Located in intron of: | ENSCJAG00000005418 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GRAMD2 | ||
| Ensembl ID: | ENSCJAG00000018524 | ||
| Aliases: | None | ||
| Description: | GRAM domain containing 2 [Source:HGNC Symbol;Acc:27287] |
Retrocopy-Parental alignment summary:
>retro_cjac_2061
AAGTATATCTTTGTGTCACTGCTGTCCCGGGACAGTGTATATGAGCTGCTCAGGAGAGTCTGCACCCACCTATAGCCTTC
CAGCAAGAAGAGTCTAAGTGTAAGAGAATTTCCAGAGGAACCTGAGTCTCTGGAAGTCCTCATCCCTGAGATGAAGTGTA
GAAAGGTATGCCCTTCCTCCAGGTCCCTGTCTCTCCCAGACAACATGCTTCGTACTCCTCCAGCATCTGTGGACTCCACA
GACAGTTTCTTCCCCTCCAGGATGCCTCCAGGGCCTGAAAAGTCAAGAGCCCAAGTAGCCTCTGAAAATGGCAGGAGGTG
GGCATGGTCCATGCCGGGCTGGGGTCCTGCCTGCCCTAAGAAGATGCCGAACTGCTCTCCCACTGCAGAGAATGCTGTCT
GTGAGGAAGATGAGCTGGAGGAGGAGACTGGGAGCACTGGGGAGCTGAGGCTCTGGGATTACCAGCTCCTGAAGGTCTTC
TTTGTGCTGATCTGCATCCTGGTTGTGTCCTCATCTTATCTGGCGTTCCGTATTTCACAGCTAGAGCAGCAGTTATGCTC
CTTGAGTTGGGACAGCCCAGTCCCTGGGCATAGG
ORF - retro_cjac_2061 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.46 % |
| Parental protein coverage: | 56.09 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | KYIFVSLLSRDSVYELLRRVCTHLQPSSKKSLSVRQFPEEPESLEVLIPEMKWRKVCPSSRSLSLPDNMP |
| KYIFVSLLSRDSVYELLRRVCTHL.PSSKKSLSVR.FPEEPESLEVLIPEMK.RKVCPSSRSLSLPDNM. | |
| Retrocopy | KYIFVSLLSRDSVYELLRRVCTHL*PSSKKSLSVREFPEEPESLEVLIPEMKCRKVCPSSRSLSLPDNML |
| Parental | RTPAASVDSTDSFFPSRTPPGPEKSRAQVASENGRRWAWPMPGWGPACPKKMPNCSPTAENAVCEEDELE |
| RTP.ASVDSTDSFFPSR.PPGPEKSRAQVASENGRRWAW.MPGWGPACPKKMPNCSPTAENAVCEEDELE | |
| Retrocopy | RTPPASVDSTDSFFPSRMPPGPEKSRAQVASENGRRWAWSMPGWGPACPKKMPNCSPTAENAVCEEDELE |
| Parental | EETGSTGELRLWDYQLLKVFFVLICILVVSSSYLAFRISQLEQQLCSLSWDSPVPGHR |
| EETGSTGELRLWDYQLLKVFFVLICILVVSSSYLAFRISQLEQQLCSLSWDSPVPGHR | |
| Retrocopy | EETGSTGELRLWDYQLLKVFFVLICILVVSSSYLAFRISQLEQQLCSLSWDSPVPGHR |
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 .11 RPM | 0 .62 RPM |
| SRP051959_heart | 0 .28 RPM | 1 .25 RPM |
| SRP051959_kidney | 0 .18 RPM | 8 .34 RPM |
| SRP051959_liver | 0 .13 RPM | 0 .30 RPM |
| SRP051959_lung | 0 .46 RPM | 12 .85 RPM |
| SRP051959_lymph_node | 0 .43 RPM | 0 .30 RPM |
| SRP051959_skeletal_muscle | 0 .15 RPM | 0 .44 RPM |
| SRP051959_spleen | 0 .32 RPM | 0 .15 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2061 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2061 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2061 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000018524 | 3 retrocopies |
retro_cjac_1618, retro_cjac_2061 , retro_cjac_2428,
|