RetrogeneDB ID: | retro_cjac_403 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:68556384..68557189(+) | ||
| Located in intron of: | ENSCJAG00000009454 | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000009459 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SVOPL | ||
| Ensembl ID: | ENSCJAG00000012965 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_403
TTTTTGCCCACAAAATACCAAGGCTATATATTACCCTTGTCTCAGATGTTCTGGCTCATGGGCTCTCTGCTCATCATTGG
CCTGGCCTCTGTAATCATCCCCACCATCGGGTGGCGCTGGCTCATCCATGTCGCCTCCATCCCAGGCATCATCCTCATCA
TGGCCTTCAAGTTTATTCCTGAATCTGCCCAGTTTAATGTCTCCACTGGGAACACTCTGGCTGCCCTGGCCACTCTGGAG
TGCATCGCCAAGATGAACCACGTGGTCATGCCGGAGGGGAAGCTGGTGGAGCCTGTCCTGGAAAAAAAGAGGAACGTTTG
CAGACCTTTTGGATGCTAAATATTTACGGACCACATTACAGATCTGGGTCATATGGCTTGGAATCTCCTTTGCCTACTGC
AGGGTTATCTTGGGCAGTGCTGAGCTGCTGGAGCAGGACCTGGTCTGCGGTTCAAAGTCAGACTCTGAGGTGGTCGTGAC
TCAGGGGAACTCAGAGGAGAGCCAGAGCCCCTGCCACTGCCACATGTTTGCACCCACTGACTATCAGACCATAATCATCA
GCATTGTTAATGAAATTGCTCTGAATCCTTTAAATATCCCGGGCATCAATTTCCTGAAAAGACAGCTGAGCCTTTCCATT
ACCATGGGATGCACGGCTTTATTCTTCCTTCTCCTTAACATTTGCACATCAAGTGCCAGCCTGATTGGCTTCCCCTTTGT
GCTGAGGGCTCTGGTTTCTGCAAACTTCAACACCATCCACATTCACACAGCTGAGGTCTACCCCACCATGATGTGCACTT
TGGGG
ORF - retro_cjac_403 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.01 % |
| Parental protein coverage: | 62.76 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | FFPKEYRFWGLLSPQVFWLAGSLLIIGLASVIIPTIGWRWLIRVASIPGIILIMAFKFIPESARFNVSTG |
| F.P..Y....L...Q.FWL.GSLLIIGLASVIIPTIGWRWLI.VASIPGIILIMAFKFIPESA.FNVSTG | |
| Retrocopy | FLPTKYQGYILPLSQMFWLMGSLLIIGLASVIIPTIGWRWLIHVASIPGIILIMAFKFIPESAQFNVSTG |
| Parental | NTPAALATLEHIAKMNRAVMPEGKLVEPILEK-RGRFADLLDAKYLRTTLQIWVIWLGISFAYYGVILAS |
| NT.AALATLE.IAKMN..VMPEGKLVEP.LEK.RG.FADLLDAKYLRTTLQIWVIWLGISFAY..VIL.S | |
| Retrocopy | NTLAALATLECIAKMNHVVMPEGKLVEPVLEK>RGTFADLLDAKYLRTTLQIWVIWLGISFAYCRVILGS |
| Parental | AELLERDLVCGSKSDSEVVVTQGDSEESQSPCHCHMFAPSDYRTMIISTVGEIALNPLNILGINFLGRRL |
| AELLE.DLVCGSKSDSEVVVTQG.SEESQSPCHCHMFAP.DY.T.IIS.V.EIALNPLNI.GINFL.R.L | |
| Retrocopy | AELLEQDLVCGSKSDSEVVVTQGNSEESQSPCHCHMFAPTDYQTIIISIVNEIALNPLNIPGINFLKRQL |
| Parental | SLSITMGCTALFFLLLNICTSSAGLIGFLFLLRALVAANFNTIYIYTAEVYPTTMRALG |
| SLSITMGCTALFFLLLNICTSSA.LIGF.F.LRALV.ANFNTI.I.TAEVYPT.M..LG | |
| Retrocopy | SLSITMGCTALFFLLLNICTSSASLIGFPFVLRALVSANFNTIHIHTAEVYPTMMCTLG |
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 .09 RPM | 2 .09 RPM |
| SRP051959_heart | 0 .11 RPM | 0 .02 RPM |
| SRP051959_kidney | 0 .24 RPM | 1 .40 RPM |
| SRP051959_liver | 0 .26 RPM | 0 .02 RPM |
| SRP051959_lung | 1 .20 RPM | 0 .80 RPM |
| SRP051959_lymph_node | 1 .89 RPM | 0 .07 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 0 .00 RPM |
| SRP051959_spleen | 2 .10 RPM | 0 .13 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_403 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_403 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_403 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000012965 | 1 retrocopy |
retro_cjac_403 ,
|
| Dasypus novemcinctus | ENSDNOG00000006558 | 2 retrocopies |