RetrogeneDB ID: | retro_cjac_4213 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:107934267..107935398(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000005017 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | IFRD2 | ||
| Ensembl ID: | ENSCJAG00000004993 | ||
| Aliases: | None | ||
| Description: | interferon-related developmental regulator 2 [Source:HGNC Symbol;Acc:5457] |
Retrocopy-Parental alignment summary:
>retro_cjac_4213
CCTGACCCCGCGCCCCCTGGGCGCCCCCCGTGCCGGGTTCCCAGCATGCCTCGCTCCCGTAAGGGCAACACGCTCCGAAA
GGGTGGTCAGCGCCGTGGAGGAGGTGCCCAGAGCAGTGCCCAAGCTGACTCAGGTTCCAGTGAGGATGAGGCAGCCAGTG
AGGCCCACAGCACCGCCAGTGAATGCCCCAGCCTTCTCAGCACCACTGCAGAGGACAGCCTTGGGGGGGATGTCGTGGAT
GAGCAGAGCCAGCAAGAAGACCTTGAGGAAAAGCTGAAGGAGTATGTGGACTGCCTCATAGACAAGAGTGCCAAGACCCG
GCAGGGTGCTCTTGAGAGCCTGCGCCTGGCCCTGGCGTCCCGCCTACTCCCCGACTTCTTGCTGGAGTGCCGCCTCACAC
TAGCCGATGCCCTGGAAAAGTGCCTCAAGAAAGGGAAGGGTGAGGAACAGGCCCTGGCGGCTCCTGTGCTAGGCCTGCTC
TGCGTGCAGCTGGGCCCTGGACCCAAGGGTGAGGAGCTGTTCCACAGCCTGCAGCCCCTGCTGGTCTCTGTGCTCAGTGA
CAGCACAGCTAGCCCTGCTGCCCAGCTCCACTGCGCTTCTTCTGCTCTTGGCCTGGGCTGCTGCGTGGCTGCCGCCGACA
TCCAGGACCTGGTCTCTTGCCTTGCCTGCTTAGAAAGTGTTTTCAGCCAGTTCTATGGCTTGGGTAGCTCTGCAACTCCT
GTGGTCCCTGCCAGCCTGCACGGCCTACTCTGTGCTGCCCTGCAGGCCTGGGCATTACTGCTCACCATCTGCCCCAGCAC
CCACTTCAGCCACATCCTTGACAGGCAGCTGCCCCGGCTGCCCCAGCTCTTGTCCAGTGAAAGTGTGAACCTGCGGATTG
CTGCCGGTGAAACCATTGCCCTGCTCTTTGAGCTTGCCCGGGACCTTGAGGAGGAGTTTGTTTACAAGGACATGGAGGCC
CTCTGCAGTGCCCTGCGCACTCTGGCCACTGACAGCAACAAGTACCGTGCCAAGGCCGATCGCCGGCGCCAGCGCTCTAC
TTTCTGCGCCGTGCTGCACTCCGTGGAGAACAATGAGCTACTCCGTGACATCTTTGGGCTGGGCCCTGTGCTGGTGCTGG
ATGCTGCTGCC
ORF - retro_cjac_4213 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.06 % |
| Parental protein coverage: | 73.78 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | PRPLRPPRPPRPVPSMPRSRKGNTLRKGGQRRGGGAQSSAQADSGSSEDEAASEAHSTASECPSLLSTTA |
| P.P..P.RPP..VPSMPRSRKGNTLRKGGQRRGGGAQSSAQADSGSSEDEAASEAHSTASECPSLLSTTA | |
| Retrocopy | PDPAPPGRPPCRVPSMPRSRKGNTLRKGGQRRGGGAQSSAQADSGSSEDEAASEAHSTASECPSLLSTTA |
| Parental | EDSLGGDVVDEQSQQEDLEEKLKEYVDCLTDKSAKTRQGALESLRLALASRLLPDFLLERRLTLADALEK |
| EDSLGGDVVDEQSQQEDLEEKLKEYVDCL.DKSAKTRQGALESLRLALASRLLPDFLLE.RLTLADALEK | |
| Retrocopy | EDSLGGDVVDEQSQQEDLEEKLKEYVDCLIDKSAKTRQGALESLRLALASRLLPDFLLECRLTLADALEK |
| Parental | CLKKGKGEEQALAAAVLGLLCVQLGPGPKGEELFHSLQPLLVSVLSDSTASPAAQLHCA-SALGLGCYVA |
| CLKKGKGEEQALAA.VLGLLCVQLGPGPKGEELFHSLQPLLVSVLSDSTASPAAQLHCA.SALGLGC.VA | |
| Retrocopy | CLKKGKGEEQALAAPVLGLLCVQLGPGPKGEELFHSLQPLLVSVLSDSTASPAAQLHCASSALGLGCCVA |
| Parental | AADIQDLVSCLACLESIFSQFYGLGSSATPVVPASLHGLLCAALQAWALLLTICPSTHFSHILDRQLPRL |
| AADIQDLVSCLACLES.FSQFYGLGSSATPVVPASLHGLLCAALQAWALLLTICPSTHFSHILDRQLPRL | |
| Retrocopy | AADIQDLVSCLACLESVFSQFYGLGSSATPVVPASLHGLLCAALQAWALLLTICPSTHFSHILDRQLPRL |
| Parental | PQLLSSESVNLRIAAGETIALLFELARDLEEEFVYKDMEALCSVLRTLATDSNKYRAKADRRRQRSTFRA |
| PQLLSSESVNLRIAAGETIALLFELARDLEEEFVYKDMEALCS.LRTLATDSNKYRAKADRRRQRSTF.A | |
| Retrocopy | PQLLSSESVNLRIAAGETIALLFELARDLEEEFVYKDMEALCSALRTLATDSNKYRAKADRRRQRSTFCA |
| Parental | VLHSVEGGECEEETVRFGFEVLYMDSWA |
| VLHSVE..E........G..VL..D..A | |
| Retrocopy | VLHSVENNELLRDIFGLG-PVLVLDAAA |
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 .60 RPM | 3 .90 RPM |
| SRP051959_heart | 0 .12 RPM | 4 .98 RPM |
| SRP051959_kidney | 0 .13 RPM | 3 .26 RPM |
| SRP051959_liver | 0 .28 RPM | 8 .79 RPM |
| SRP051959_lung | 0 .37 RPM | 3 .90 RPM |
| SRP051959_lymph_node | 0 .30 RPM | 4 .31 RPM |
| SRP051959_skeletal_muscle | 0 .33 RPM | 9 .72 RPM |
| SRP051959_spleen | 0 .17 RPM | 4 .29 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4213 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4213 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4213 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000004993 | 1 retrocopy |
retro_cjac_4213 ,
|
| Macaca mulatta | ENSMMUG00000020119 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000012534 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000024363 | 1 retrocopy |