RetrogeneDB ID: | retro_cjac_2314 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 4:22291298..22291529(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SNAPC5 | ||
| Ensembl ID: | ENSCJAG00000007484 | ||
| Aliases: | None | ||
| Description: | small nuclear RNA activating complex, polypeptide 5, 19kDa [Source:HGNC Symbol;Acc:15484] |
Retrocopy-Parental alignment summary:
>retro_cjac_2314
CAGGAACTGCGCAAGGAGGAGGCGATGCTGCTGCTGTTGAATGCAGCCCTGTGTGACCAGCTGAACCGTGTCAAGGTTGA
AGCCTTGGCCCTTCAATCAATGAGTGATTCTAGAAGAGGGGATGAGATGCTGTCTTCTCCAACTGCGCCTGAACAGCCAT
ATGTCATGTACGTACATGTAGACAATAAAGCATCTGTCAACCCACCTACACTGGAGTGAAGCATAGAGTCC
ORF - retro_cjac_2314 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.43 % |
| Parental protein coverage: | 78.57 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | QELRKEEETLLRLKAALHDQLNRLKVEELALQSMISSRRGDEMLSSQTVPEQSHDMLVHVDNEASINQTT |
| QELRKEE..LL.L.AAL.DQLNR.KVE.LALQSM..SRRGDEMLSS.T.PEQ...M.VHVDN.AS.N..T | |
| Retrocopy | QELRKEEAMLLLLNAALCDQLNRVKVEALALQSMSDSRRGDEMLSSPTAPEQPYVMYVHVDNKASVNPPT |
| Parental | LELSTKS |
| LE.S..S | |
| Retrocopy | LE*SIES |
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 | 2 .40 RPM |
| SRP051959_heart | 0 .00 RPM | 4 .05 RPM |
| SRP051959_kidney | 0 .00 RPM | 4 .33 RPM |
| SRP051959_liver | 0 .00 RPM | 1 .84 RPM |
| SRP051959_lung | 0 .00 RPM | 2 .88 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 3 .20 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 3 .80 RPM |
| SRP051959_spleen | 0 .00 RPM | 3 .55 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2314 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2314 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2314 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 12 parental genes, and 12 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000017304 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000007484 | 1 retrocopy |
retro_cjac_2314 ,
|
| Dasypus novemcinctus | ENSDNOG00000006689 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000003693 | 1 retrocopy | |
| Macropus eugenii | ENSMEUG00000003990 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000016841 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000032398 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000012935 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000008791 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000010156 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000009201 | 1 retrocopy | |
| Tupaia belangeri | ENSTBEG00000014333 | 1 retrocopy |