RetrogeneDB ID: | retro_cjac_2519 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 5:60357606..60357869(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000019472 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2519
TTGTCTTACCTGCTGTACCCTCCCTGCATGGAGGGTGCTGTCTATTCGATCGGGAACATCAAGTGTAAGAGCTAGTACTC
CTGATTAATATCAGCTTTGTCAACAGGGTCTATGCCTTTGGCTTCCTCTTCATGCTGCTCCAGCTCTTCCTGAACTACAA
GCTGAAGTCACTGCCCGGGAAGGCCTTCACCTACAACGCTTTCAACACCTTCATTGACTATGTCTTTGCCTTCATCATCA
CCATGCCCACGTGGTGTTTCTGG
ORF - retro_cjac_2519 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.83 % |
| Parental protein coverage: | 70.68 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LSYLLYPLCIGGAAYSLLNTKYKSWYSWLIN-SFVNGVYAFGFLFMLPQLFVNCKLKSVAHLPWKAFTYK |
| LSYLLYP.C..GA.YS..N.K.KS.YS.LI..SFVN.VYAFGFLFML.QLF.N.KLKS...LP.KAFTY. | |
| Retrocopy | LSYLLYPPCMEGAVYSIGNIKCKS*YS*LIS<SFVNRVYAFGFLFMLLQLFLNYKLKS---LPGKAFTYN |
| Parental | AFNTFIEDVFAF-ITMPTSHWLACFW |
| AFNTFI..VFAF.ITMPT..W..CFW | |
| Retrocopy | AFNTFIDYVFAFIITMPT--W--CFW |
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 | 4 .04 RPM |
| SRP051959_heart | 0 .00 RPM | 2 .16 RPM |
| SRP051959_kidney | 0 .00 RPM | 6 .61 RPM |
| SRP051959_liver | 0 .00 RPM | 5 .74 RPM |
| SRP051959_lung | 0 .00 RPM | 4 .54 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 5 .07 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 2 .05 RPM |
| SRP051959_spleen | 0 .00 RPM | 6 .76 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2519 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2519 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2519 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000019472 | 1 retrocopy |
retro_cjac_2519 ,
|
| Equus caballus | ENSECAG00000013231 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000028490 | 1 retrocopy |