RetrogeneDB ID: | retro_cjac_1618 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 17:74315902..74316635(-) | ||
| Located in intron of: | None | ||
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_1618
GAATGTCTCCTTTGCAGTCTGCACTGCCCAGAAGGCTTGAAGGGTGAAGAGATAAAGAAATGTGGCCGAGAAGGGATACC
ACTGAATAAATACCACCAGCAATACCACAAGCTGTTTAAGGATGCTCCCTTGGAGGAAGTGGTTTCTCAAAGTGTGCTCC
CCTGCACTCCAGAGGGACCTCCTTCTTCAGGGCGGGCTCTGCATCTCCCCCAACTGGCTCTGCTTCCACGCCAGCCTCTT
TGGCAAGGATATCAAGGTGGTCTTCCCTGTGGTGTCTGTGCAAATGATCAAAAAACACAAGCTGGCACAGCTCCTTCCCG
ACGGAATGGCCGTCACCACCACCACCAGCCAGAAGTGTGTCTTCGTGTCACTGCTCTCCTGGGACAGTGTGTAGGGGCTG
CATAGGAGAGACTGCACCCACCTACAGCCTTCCAGCAAGAAGAGTTGAAGCATAAGAGAATTTCCAGAGGAATCTGAGTC
TCTGGAAGTCCTCATCCCTGAGATGAAGTGGAGAAAGGTATGCCCATCCTCTAGGTCCCTGTCTCTCCCGGACAACATGC
CTCGTACCCCTCCTGAATCTGTGGACTCCACAGTTTCCTTCCCCTCCAGGAAGCCTCCAGGGCCTGAAAAGTCAACAGCC
TAAGTAGCCTCTGAAAATGGCAGGAGGTGGGCATGGCCCATGCCGGGCTGGGGTCCTGCTTGCCCTAAGAAGATGCCGAA
CTGCTCTCCCACC
ORF - retro_cjac_1618 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.99 % |
| Parental protein coverage: | 69.41 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | EPLDCSLHCPEGLKGEEIKKCGREGIPLNKYNQQYHKLFKDVPLEEVV-LKVCSCALQRDLLLQGRLYIS |
| E.L.CSLHCPEGLKGEEIKKCGREGIPLNKY.QQYHKLFKD.PLEEVV.LKVCS.ALQRDLLLQG.L.IS | |
| Retrocopy | ECLLCSLHCPEGLKGEEIKKCGREGIPLNKYHQQYHKLFKDAPLEEVV>LKVCSPALQRDLLLQGGLCIS |
| Parental | PNWLCFHASLFGKDIKVVIPVVSVQMIKKHKLARLLPNGLAITTNTSQKYIFVSLLSRDSVYELLRRVCT |
| PNWLCFHASLFGKDIKVV.PVVSVQMIKKHKLA.LLP.G.A.TT.TSQK..FVSLLS.DSV..L.RR.CT | |
| Retrocopy | PNWLCFHASLFGKDIKVVFPVVSVQMIKKHKLAQLLPDGMAVTTTTSQKCVFVSLLSWDSV*GLHRRDCT |
| Parental | HLQPSSKKSLSVRQFPEEPESLEVLIPEMKWRKVCPSSRSLSLPDNMPRTPAASVDSTDSFFPSRTPPGP |
| HLQPSSKKS.S.R.FPEE.ESLEVLIPEMKWRKVCPSSRSLSLPDNMPRTP..SVDST.S.FPSR.PPGP | |
| Retrocopy | HLQPSSKKS*SIREFPEESESLEVLIPEMKWRKVCPSSRSLSLPDNMPRTPPESVDSTVS-FPSRKPPGP |
| Parental | EKSRAQVASENGRRWAWPMPGWGPACPKKMPNCSPT |
| EKS.A.VASENGRRWAWPMPGWGPACPKKMPNCSPT | |
| Retrocopy | EKSTA*VASENGRRWAWPMPGWGPACPKKMPNCSPT |
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 .04 RPM | 0 .62 RPM |
| SRP051959_heart | 0 .00 RPM | 1 .25 RPM |
| SRP051959_kidney | 0 .00 RPM | 8 .34 RPM |
| SRP051959_liver | 0 .11 RPM | 0 .30 RPM |
| SRP051959_lung | 0 .08 RPM | 12 .85 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .30 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .44 RPM |
| SRP051959_spleen | 0 .11 RPM | 0 .15 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1618 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1618 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1618 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,
|