RetrogeneDB ID: | retro_cjac_2787 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 6:16486232..16486595(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | C2orf68 | ||
| Ensembl ID: | ENSCJAG00000019632 | ||
| Aliases: | None | ||
| Description: | chromosome 2 open reading frame 68 [Source:HGNC Symbol;Acc:34353] |
Retrocopy-Parental alignment summary:
>retro_cjac_2787
CCGGGTCACTCCTGCAGGCCTCGCGGGCGGCTGGACATGAACCACGGCTTCGTGCACAATATCCGACGGAACCCGATCGC
CCGGGACGACTGCGACAAGAAGGTGAAGCAGGCGGCCAAGGAGAAGGTGAGGACGCAGCAGACGCCCGCGCCTAGGTGGC
CCCGGGAGCCAGACCTGCCGGTGTACCTAACGCGACCCTGAGTTGTCTCCGCCCACCCACGCAGCCCAGACGGTCAAGAG
TCAGGTGAAAGCAGCAGTAGTGGAGGCCCCGAGCTGGAGCCTTCTGGCTATCAGCTCTTCCACTTGGAATACCAGGCAGA
CAGTGGAGAGGTCACATCAGTTATGGTGTATCAGGTTGAGGAG
ORF - retro_cjac_2787 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.21 % |
| Parental protein coverage: | 72.89 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | PGHCCKPGGRLDMNHGFVHHIRRNQIARDDYDKKVKQAAKEKVRRRHTPAPTRPRKPDLQVYLPRHRDVS |
| PGH.C.P.GRLDMNHGFVH.IRRN.IARDD.DKKVKQAAKEKVR...TPAP..PR.PDL.VYL.R...VS | |
| Retrocopy | PGHSCRPRGRLDMNHGFVHNIRRNPIARDDCDKKVKQAAKEKVRTQQTPAPRWPREPDLPVYLTRP*VVS |
| Parental | AHPRNPDYEESSESSSSGGSELEPSGHQLFCLEYEADSGDVTSVIVYQGDD |
| AHPR.PD..ES.ESSSSGG.ELEPSG.QLF.LEY.ADSG.VTSV.VYQ... | |
| Retrocopy | AHPRSPDGQESGESSSSGGPELEPSGYQLFHLEYQADSGEVTSVMVYQVEE |
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 .07 RPM | 3 .33 RPM |
| SRP051959_heart | 0 .63 RPM | 2 .82 RPM |
| SRP051959_kidney | 0 .31 RPM | 4 .10 RPM |
| SRP051959_liver | 0 .11 RPM | 2 .56 RPM |
| SRP051959_lung | 0 .15 RPM | 6 .83 RPM |
| SRP051959_lymph_node | 0 .07 RPM | 7 .58 RPM |
| SRP051959_skeletal_muscle | 0 .22 RPM | 2 .18 RPM |
| SRP051959_spleen | 0 .02 RPM | 4 .96 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2787 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2787 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2787 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000019632 | 4 retrocopies | |
| Equus caballus | ENSECAG00000014919 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000033817 | 1 retrocopy |