RetrogeneDB ID: | retro_cjac_2171 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 3:111809457..111809713(+) | ||
| Located in intron of: | ENSCJAG00000004791 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | COTL1 | ||
| Ensembl ID: | ENSCJAG00000004056 | ||
| Aliases: | None | ||
| Description: | coactosin-like 1 (Dictyostelium) [Source:HGNC Symbol;Acc:18304] |
Retrocopy-Parental alignment summary:
>retro_cjac_2171
ATCACCACCAAGATCCACAAAGAGGCTTGACCAGCGAGCGTACAATCTGTTGCGCGACGACAGCTCGGCCGTCATCTGGG
GTACTTCTAAATATAACGGCTCCACCATTGTCCCCAGCGAGCAGGGAGCGGAGTACCAGCACTTCATCCAGCAGTGCACA
GATGACGTCCGGTTGTTTGCCTTCGTGAGCTTCACCACCGGGGATGCCATGAGCAAGAGGTCCAAGTTTGCCCTCATCCC
GTGGATCGGTGATGAC
ORF - retro_cjac_2171 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.56 % |
| Parental protein coverage: | 59.86 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MATKIDKEACRA-AYNLVRDDGSAVIWVTFKYDGSTIVPGEQGAEYQHFIQQCTDDVRLFAFVRFTTGDA |
| ..TKI.KEA..A.AYNL.RDD.SAVIW.T.KY.GSTIVP.EQGAEYQHFIQQCTDDVRLFAFV.FTTGDA | |
| Retrocopy | ITTKIHKEA*PA>AYNLLRDDSSAVIWGTSKYNGSTIVPSEQGAEYQHFIQQCTDDVRLFAFVSFTTGDA |
| Parental | MSKRSKFALITWIGED |
| MSKRSKFALI.WIG.D | |
| Retrocopy | MSKRSKFALIPWIGDD |
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 | 16 .62 RPM |
| SRP051959_heart | 0 .00 RPM | 4 .79 RPM |
| SRP051959_kidney | 0 .00 RPM | 27 .87 RPM |
| SRP051959_liver | 0 .00 RPM | 8 .40 RPM |
| SRP051959_lung | 0 .00 RPM | 18 .02 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 32 .88 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 1 .29 RPM |
| SRP051959_spleen | 0 .00 RPM | 28 .34 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2171 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2171 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2171 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000004056 | 4 retrocopies | |
| Macaca mulatta | ENSMMUG00000007039 | 1 retrocopy |