RetrogeneDB ID: | retro_cjac_4116 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:110617861..110618428(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TSPAN15 | ||
| Ensembl ID: | ENSCJAG00000016486 | ||
| Aliases: | None | ||
| Description: | tetraspanin 15 [Source:HGNC Symbol;Acc:23298] |
Retrocopy-Parental alignment summary:
>retro_cjac_4116
ATGCCGCGCGGGGACTCGGAGCAGGTGCGCTACTGTGCGCACTTCTCTTACCTCTGGCTCAAGTTCTCACTTATCATTTA
CTCCACCGTGTTCTGGCTGATCGGGGTCCTGGTCCTGTCCGTGGGGATCTATGCAGAGGTCGAACGGCAGAAATATAAAA
CCCTTGAAAGTGCCTTCCTGGCTCCGGTCATCATCCTCATCCTCCTGGGTGTCGTCATGTGCATGGTCTCCTTCATTGGT
GTGCTGGCATCCCTCCGTGACAACCTGTTCCTTCTCCAAGCATTCATGTACATCCTTGGGATCTGCCTCATCATGGAGCT
CATTGGTGGCGTGATGGCCTTGATCTTCCGGAACCAGACCATTGACTTCCTGAATGACAACATTCGAAGAGGAATTGAGA
ACTACTATGACGATCTGGACTTCAAAAACATCATGGACTTTGTTCAGAAAAAGTTCAAGTGCAGTGGCGGGGAGGACTAC
CGAGACTGGAGCAAGAACCAGTACCATGACTGCAGCGCTCCTGGACCCCTGGCCTGCGGGGTGCCCTACACCTGCTGCAT
CCAGAAC
ORF - retro_cjac_4116 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.83 % |
| Parental protein coverage: | 64.29 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MPRGDSEQVRYCAHFSYLWLKFSLIIYSTVFWLIGALVLSVGIYAEVERQKYKTLESAFLAPAIILILLG |
| MPRGDSEQVRYCAHFSYLWLKFSLIIYSTVFWLIG.LVLSVGIYAEVERQKYKTLESAFLAP.IILILLG | |
| Retrocopy | MPRGDSEQVRYCAHFSYLWLKFSLIIYSTVFWLIGVLVLSVGIYAEVERQKYKTLESAFLAPVIILILLG |
| Parental | VVMFMVSFIGVLASLRDNLFLLQAFMYILGICLIMELIGGVVALIFRNQTIDFLNDNIRRGIENYYDDLD |
| VVM.MVSFIGVLASLRDNLFLLQAFMYILGICLIMELIGGV.ALIFRNQTIDFLNDNIRRGIENYYDDLD | |
| Retrocopy | VVMCMVSFIGVLASLRDNLFLLQAFMYILGICLIMELIGGVMALIFRNQTIDFLNDNIRRGIENYYDDLD |
| Parental | FKNIMDFVQKKFKCCGGEDYRDWSKNQYHDCSAPGPLACGVPYTCCIRN |
| FKNIMDFVQKKFKC.GGEDYRDWSKNQYHDCSAPGPLACGVPYTCCI.N | |
| Retrocopy | FKNIMDFVQKKFKCSGGEDYRDWSKNQYHDCSAPGPLACGVPYTCCIQN |
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 .02 RPM | 44 .46 RPM |
| SRP051959_heart | 0 .00 RPM | 3 .12 RPM |
| SRP051959_kidney | 0 .02 RPM | 1 .06 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .80 RPM |
| SRP051959_lung | 0 .00 RPM | 7 .58 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 2 .81 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 2 .75 RPM |
| SRP051959_spleen | 0 .00 RPM | 5 .92 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4116 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4116 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4116 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000007278 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000016486 | 1 retrocopy |
retro_cjac_4116 ,
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