RetrogeneDB ID: | retro_cjac_450 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:95666787..95667138(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TRAPPC4 | ||
| Ensembl ID: | ENSCJAG00000013703 | ||
| Aliases: | None | ||
| Description: | trafficking protein particle complex 4 [Source:HGNC Symbol;Acc:19943] |
Retrocopy-Parental alignment summary:
>retro_cjac_450
CTCACTTCTAAAGAGAAGCTCATGCTGGCTTCCATGTTCCACTCCCCCTTTGCCATTGGCTCCCAGCTGTCTCCTGAGTA
GGGAAGCTCAGGCATTAATATGCTGGAGAAAGACACATTCAAAATGCACTGCCAGCAGACACTGATAGGGATCAAGTTTG
TGGTTCTAGCAGATCATAGGCAAGCTGGAAGAGATTCTCTTCTCCAAAAGATTTATGAGATTTACTCAGACTCTGCCCTC
AGGAATCCATTCTACTCCTTAGAAATGCCCATCGGGTGTGAGCTATTTGACCAGAATCTGAAGCTAGGCCTGGAAGTGGC
AGAGAAGGCTGGAACTTTTGGACCTGGGTCA
ORF - retro_cjac_450 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.18 % |
| Parental protein coverage: | 53.42 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LTSNEKLMLASMFHSLFAIGSQLSPEQGSSGIEMLETDTFKLHCYQTLTGIKFVVLADPRQAGIDSLLRK |
| LTS.EKLMLASMFHS.FAIGSQLSPE.GSSGI.MLE.DTFK.HC.QTL.GIKFVVLAD.RQAG.DSLL.K | |
| Retrocopy | LTSKEKLMLASMFHSPFAIGSQLSPE*GSSGINMLEKDTFKMHCQQTLIGIKFVVLADHRQAGRDSLLQK |
| Parental | IYEIYSDFALKNPFYSLEMPIRCELFDQNLKLALEVAEKAGTFGPGS |
| IYEIYSD.AL.NPFYSLEMPI.CELFDQNLKL.LEVAEKAGTFGPGS | |
| Retrocopy | IYEIYSDSALRNPFYSLEMPIGCELFDQNLKLGLEVAEKAGTFGPGS |
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 | 5 .46 RPM |
| SRP051959_heart | 0 .00 RPM | 5 .05 RPM |
| SRP051959_kidney | 0 .00 RPM | 14 .38 RPM |
| SRP051959_liver | 0 .00 RPM | 18 .30 RPM |
| SRP051959_lung | 0 .00 RPM | 8 .48 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 9 .06 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 4 .78 RPM |
| SRP051959_spleen | 0 .00 RPM | 9 .58 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_450 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_450 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_450 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000012383 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000013703 | 1 retrocopy |
retro_cjac_450 ,
|
| Dasypus novemcinctus | ENSDNOG00000007885 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000004759 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000014340 | 1 retrocopy |