RetrogeneDB ID: | retro_cjac_3868 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL285434.1:26435..26798(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HINT3 | ||
| Ensembl ID: | ENSCJAG00000003710 | ||
| Aliases: | None | ||
| Description: | histidine triad nucleotide binding protein 3 [Source:HGNC Symbol;Acc:18468] |
Retrocopy-Parental alignment summary:
>retro_cjac_3868
ATGGCAGATGAACGGGTGAGCAGCGCCGACCTGGCCACCGACTGTAAGGCCCCGGAGACTACAGAGTCTACGGCTTCCTC
GGTGGGGTCCTGCGAAGCCGCCACCAAGTCACCGGAGCCCAAGGACAATGACAGCACCTGCGTGTTCCGCGGGATCGCAG
GGCGGCAGGTCCCGGGCACCGAACTCCTGCACTGCGAGAATGAGGACCTGGTTTGCTTCAGAAATATCAAACCAGCAGCA
ACTCATCATTATCTTATGGTGCCAAAGAAGCATACTGGAAATTGCAGATCTCTAAGGAAAGAGCAAGTAGAACTGGCTGA
GAACATAGTAACTGTTGGAAAAACCATTCTTAGGAATAATTTC
ORF - retro_cjac_3868 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.74 % |
| Parental protein coverage: | 67.58 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MADEQVNRSAGLAPDFKAPETTECTASSVGTCEAAAKSPEPKDNDSTCVFCRIAGRQDPGTELLHCENED |
| MADE.V..SA.LA.D.KAPETTE.TASSVG.CEAA.KSPEPKDNDSTCVF..IAGRQ.PGTELLHCENED | |
| Retrocopy | MADERVS-SADLATDCKAPETTESTASSVGSCEAATKSPEPKDNDSTCVFRGIAGRQVPGTELLHCENED |
| Parental | LVCFKDIKPAATHHYLVVPKKHIGNCRSLRKDQVELVENMVTVGKTILERNNF |
| LVCF..IKPAATHHYL.VPKKH.GNCRSLRK.QVEL.EN.VTVGKTIL.RNNF | |
| Retrocopy | LVCFRNIKPAATHHYLMVPKKHTGNCRSLRKEQVELAENIVTVGKTIL-RNNF |
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 .35 RPM | 8 .61 RPM |
| SRP051959_heart | 0 .19 RPM | 15 .77 RPM |
| SRP051959_kidney | 0 .38 RPM | 32 .41 RPM |
| SRP051959_liver | 0 .19 RPM | 18 .37 RPM |
| SRP051959_lung | 0 .37 RPM | 11 .01 RPM |
| SRP051959_lymph_node | 0 .46 RPM | 6 .76 RPM |
| SRP051959_skeletal_muscle | 0 .09 RPM | 18 .47 RPM |
| SRP051959_spleen | 0 .50 RPM | 7 .56 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3868 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3868 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3868 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000001830 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000003710 | 1 retrocopy |
retro_cjac_3868 ,
|
| Cavia porcellus | ENSCPOG00000021856 | 1 retrocopy | |
| Echinops telfairi | ENSETEG00000007350 | 1 retrocopy | |
| Macropus eugenii | ENSMEUG00000007627 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000019791 | 1 retrocopy |