RetrogeneDB ID: | retro_tbel_4345 | ||
Retrocopy location | Organism: | Treeshrew (Tupaia belangeri) | |
| Coordinates: | scaffold_77786:7613..8405(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PSMD6 | ||
| Ensembl ID: | ENSTBEG00000008485 | ||
| Aliases: | None | ||
| Description: | proteasome (prosome, macropain) 26S subunit, non-ATPase, 6 [Source:HGNC Symbol;Acc:9564] |
Retrocopy-Parental alignment summary:
>retro_tbel_4345
ATGGCTCTGTATTACGAAGCCTTGTGCAAATCCCTCGACTGGCAGATGAACATGGACCTACTTAATAAAATGAAGGCGAA
TGAAGAAGAGTTGAAACGTTTGGATGAGGACCTGGAAGATGCTGAAAAGAATCTGGGAGAGACTGAAATTGGAGATGCGA
TGATGGCAAAGACCAAGCCCCTCAGTGGGATAGGTGAGAAGGAGGCAGCTCTGACAGCCTTTCGCAAGACATATGACAAA
ACTGAGCCCTGGGTCACCAACTGACTATTGTATTCTATCTCCTTAGAATTGTCTTATTTTATATGGATAATGATCTCATC
ACATGAAACACAGGAAAGGCCCAAAGCTTAATAGAAGGAGGAGACTGGGACAGGAGAAACCACCAAAAGGTGTATCAAGG
TCTGTATTGTGTGGCTCTTCGTGATTTCAAACAGGCAGCTGAACTCTTTCTTGGCACTGTTTCAACATTCACATCCTATG
AACTCATGGATTATAAAATGTTTGTGATTTATGCCATGTACGGCAGCATGATTGTCTAAGAAAGACCAGGGAAAATGTCA
TTAAAGGATTAGAGATTTTTGAAGTGTTGTGCAGTCTTCCAGCGGTTCAGAAGTACTATTTTCACTCTATGAATATGTTA
CTGAGTTTTATTCCAGTCATTGGCCGTCGTGGAACAGGAAATGAAAAAAGGACTGGCTTTTTCTGCCTCACTATCGATAC
TATGTGAGAGAAATGAGAATTCATGCATGCAGCCAGCTGTTGGAATCATACAGGTCATTAACTGGGCAATAT
ORF - retro_tbel_4345 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.28 % |
| Parental protein coverage: | 95.39 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MAPYYEALCKSLDWQMDMDLLNKMKKANEEELKRLDEELEDAEKNLGESEIRDAMMAKAEYLCRIGDKEG |
| MA.YYEALCKSLDWQM.MDLLNKMK.ANEEELKRLDE.LEDAEKNLGE.EI.DAMMAK...L..IG.KE. | |
| Retrocopy | MALYYEALCKSLDWQMNMDLLNKMK-ANEEELKRLDEDLEDAEKNLGETEIGDAMMAKTKPLSGIGEKEA |
| Parental | ALTAFRKTYDKTV-ALGHRLDIVFYLLRIGLFYMDNDLITRNTEKAKSLIEEGGDWDRRNRLKVYQGLYC |
| ALTAFRKTYDKT..ALGH.L.IVFYLLRI.LFYMDNDLIT.NT.KA.SLIE.GGDWDRRN..KVYQGLYC | |
| Retrocopy | ALTAFRKTYDKTE<ALGHQLTIVFYLLRIVLFYMDNDLIT*NTGKAQSLIE-GGDWDRRNHQKVYQGLYC |
| Parental | VAIRDFKQAAELFLDTVSTFTSYELMDYKTFVTYTVYVSMIALERPDLREKVIKGAEILEVLHSLPAVRQ |
| VA.RDFKQAAELFL.TVSTFTSYELMDYK.FV.Y..Y.SMI..ERP.......K....L.........R. | |
| Retrocopy | VALRDFKQAAELFLGTVSTFTSYELMDYKMFVIYAMYGSMIV*ERPG--KMSLKD*RFLKCCAVFQRFRS |
| Parental | YLFSLYECRYSVFFQSLAVVEQEM-KKDWLFAPHYRYYVREMRIHAYSQLLESYRSLTLGY |
| ..F.L..C.Y.V.FQSLAVVEQEM.KKDWLF.PHYRYYVREMRIHA.SQLLESYRSLT..Y | |
| Retrocopy | TIFTL*IC-Y*VLFQSLAVVEQEM>KKDWLFLPHYRYYVREMRIHACSQLLESYRSLTGQY |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Tupaia belangeri was not studied using RNA-Seq expression data.
Tupaia belangeri was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_tbel_4345 retrocopy.
Tupaia belangeri was not studied using FANTOM5 data.
retro_tbel_4345 was not experimentally validated.
Retrocopy orthology:
Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000005852 | 1 retrocopy | |
| Tupaia belangeri | ENSTBEG00000008485 | 2 retrocopies |
retro_tbel_1619, retro_tbel_4345 ,
|