RetrogeneDB ID: | retro_cjac_2172 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 3:111810672..111811099(+) | ||
| 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_2172
ATCACCACCAAGATCCACAAAGAGGCTTGCCCAGCGGCGTACAACCTGGTGCGCGACGACAGCTCGGCCGTCATCTGGGT
TACTTCTAAATATAACGGCTCCACCATTGTCCCCAGCGAGCAGGGAGCGGAGTACCAGCACTTCATCCAGCAGTGCACAG
ATGACGTCCGGTTGTTTGCCTTCGTGAGCTTCACCACCGGGGATGCCATGAGCAAGAGGTCCAAGTTTGCCCTCATCCCG
TGGATCGGTGAGGACATCAGTGGGCTGCAGGGCTCCAAAACCGGGACAGACAAGACCCTGATCAAGTAAGTCATACAGAA
TTTTGCTAAGGAGTTTGTGATCAGTGATCGGTAGGAGCTGGAGGAAGATTTCATCAAGAGTAAGCTGAAGAAGGTGGGGG
GGAGCTAATTACGACACCCAGACACAG
ORF - retro_cjac_2172 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.62 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MATKIDKEACRAAYNLVRDDGSAVIWVTFKYDGSTIVPGEQGAEYQHFIQQCTDDVRLFAFVRFTTGDAM |
| ..TKI.KEAC.AAYNLVRDD.SAVIWVT.KY.GSTIVP.EQGAEYQHFIQQCTDDVRLFAFV.FTTGDAM | |
| Retrocopy | ITTKIHKEACPAAYNLVRDDSSAVIWVTSKYNGSTIVPSEQGAEYQHFIQQCTDDVRLFAFVSFTTGDAM |
| Parental | SKRSKFALITWIGEDVSGLQRAKTGTDKTLVKEVVQNFAKEFVISDRKELEEDFIKSELKKA-GGANYDA |
| SKRSKFALI.WIGED.SGLQ..KTGTDKTL.K.V.QNFAKEFVISDR.ELEEDFIKS.LKK..GGANYD. | |
| Retrocopy | SKRSKFALIPWIGEDISGLQGSKTGTDKTLIK*VIQNFAKEFVISDR*ELEEDFIKSKLKKV>GGANYDT |
| Parental | QTE |
| QT. | |
| Retrocopy | QTQ |
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 .18 RPM | 16 .62 RPM |
| SRP051959_heart | 0 .23 RPM | 4 .79 RPM |
| SRP051959_kidney | 0 .31 RPM | 27 .87 RPM |
| SRP051959_liver | 0 .19 RPM | 8 .40 RPM |
| SRP051959_lung | 0 .36 RPM | 18 .02 RPM |
| SRP051959_lymph_node | 0 .41 RPM | 32 .88 RPM |
| SRP051959_skeletal_muscle | 0 .09 RPM | 1 .29 RPM |
| SRP051959_spleen | 0 .29 RPM | 28 .34 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2172 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2172 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2172 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 |