RetrogeneDB ID: | retro_cjac_4072 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:60239722..60240214(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NDEL1 | ||
| Ensembl ID: | ENSCJAG00000014341 | ||
| Aliases: | None | ||
| Description: | nudE nuclear distribution E homolog (A. nidulans)-like 1 [Source:HGNC Symbol;Acc:17620] |
Retrocopy-Parental alignment summary:
>retro_cjac_4072
GGCCAAGCCAGTGAAGGAGAGACAGGGGTCAAGCAATTGTGAACATGTGCTGTTGACACATTAGAGACTTTTTTCATCAT
GGATGATGAACATATACCAGATTTTTCAAGTGTAGAGGATGAAACTACTTATTGGAAGGAAATGTCCTTGAAGTATAAAC
ATATCTTCCAGGAAGCTTGACATGAGCTAGTTGAATTTCAGGAGGGAAACAGAGAATTAGAAGCAGACTTGGCAGCACAA
TTAGTACAGCCTGAACACAGAAATAGAGACTTGCAACTTGATAGCCAAAGACTGAAATATGAAGTGGAGGCATTAAAGGA
GAAACCAGAACATCAATATGCACAGAGCTACAAGCAGGTCTCAATATTAGATGATTTAAGTCAGATGTAGGCCATTAAGG
TGTGGTTGCTTAAGTATGTGAGGGAGCCAGAACAGGCCAGTGATGACCTGGAGCAAGCAAAAAGGGCAACAATCGTTTCA
CTAAAGGACTTT
ORF - retro_cjac_4072 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.94 % |
| Parental protein coverage: | 51.89 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | GAELRGWTSVERRRTCAFDTLEAFLIMDGEDIPDFSSLKEETAYWKELSLKYKQSFQEARDELVEFQEGS |
| G....G.T.V....TCA.DTLE.F.IMD.E.IPDFSS...ET.YWKE.SLKYK..FQEA..ELVEFQEG. | |
| Retrocopy | GQASEGETGVKQL*TCAVDTLETFFIMDDEHIPDFSSVEDETTYWKEMSLKYKHIFQEA*HELVEFQEGN |
| Parental | RELEAELEAQLVQAEQRNRDLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKY |
| RELEA.L.AQLVQ.E.RNRDLQ.D.QRLKYEVEALKEK.EHQYAQSYKQVS.L.DDLSQ..AIK..L.KY | |
| Retrocopy | RELEADLAAQLVQPEHRNRDLQLDSQRLKYEVEALKEKPEHQYAQSYKQVSIL-DDLSQM*AIKVWLLKY |
| Parental | VRELEQANDDLERAKRATIVSLEDF |
| VRE.EQA.DDLE.AKRATIVSL.DF | |
| Retrocopy | VREPEQASDDLEQAKRATIVSLKDF |
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 | 26 .34 RPM |
| SRP051959_heart | 0 .00 RPM | 25 .31 RPM |
| SRP051959_kidney | 0 .00 RPM | 28 .84 RPM |
| SRP051959_liver | 0 .00 RPM | 20 .79 RPM |
| SRP051959_lung | 0 .00 RPM | 39 .79 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 23 .29 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 25 .42 RPM |
| SRP051959_spleen | 0 .00 RPM | 23 .93 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4072 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4072 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4072 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000014341 | 1 retrocopy |
retro_cjac_4072 ,
|
| Cavia porcellus | ENSCPOG00000012878 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000008744 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000027930 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000006517 | 1 retrocopy |