RetrogeneDB ID: retro_tbel_1619

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5267:364946..365737(-)
• Located in intron of: ENSTBEG00000011495

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PSMD6
• Ensembl ID: ENSTBEG00000008485
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 6 [Source:HGNC Symbol;Acc:9564]

Sequence

>retro_tbel_1619
ATGGCTCTGTATTACGAAGCCTTGTGCAAATCCCTCGACTGGCAGATGAACATGGACCTACTTAATAAAATGAAGGTGAA
TGAAGAAGAGTTGAAACGTTTGGATGAGGACCTGGAAGATGCTGAAAAGAATCTGGGAGAGACTGAAATTGGAGATGTGA
TGATGGCAAAGACCAAGCCCCTCAGTGGGATAGGTGAGAAGGAGGCAGCTCTGACCGCCTTTCGCAAGACATATGACACA
ACTGAGCCCTGGGTCACCAACTGACTATTGTATTCTATCTCCTTAGAATTGTCTTATTTTATATGGATAATGATCTCATC
ACACGAAACACAGAAAAGGCCCAAAGCTTAATAGAAGGAGGAGACTGGGACAGGAGAAACTGCCAAAATGTGTATCAAGG
TCTGTATTGTGTGGCTCTTCGTGATTTCAAACAGGCAGCTGAACTCTTTCTTGGCACTGTTTCAACATTCACATCCCATG
AACTCATGGATTATAAAATGTTTGTAATTTATGCCATGTATAGCAGCATGATTGTCTAAGAAAGACCAGGGAAAATGTCA
TTAAAGGATTAGAGATTTTTGAAGTGTTGTGCAGTCTTCCAGCGGTTCAGAAGTACTATTTTCACTCTATGAATATGTTA
CTCAGTTTTATTCCAGTCATTGGCCATCGTGGAACAGGAAATGAAAAAGGACTGGCTTTTTCTGCCTCACTATCGATACT
ATGTGAGAGAAATGAGAATTCATGCATGCAGCCAGCTGTTGGAATCATACAGGTCATTAACTGGGCAATAT

Alignment

ORF - retro_tbel_1619 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.44 %
• Parental protein coverage: 95.39 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPYYEALCKSLDWQMDMDLLNKMKKANEEELKRLDEELEDAEKNLGESEIRDAMMAKAEYLCRIGDKEG
          MA.YYEALCKSLDWQM.MDLLNKMK..NEEELKRLDE.LEDAEKNLGE.EI.D.MMAK...L..IG.KE.
Retrocopy MALYYEALCKSLDWQMNMDLLNKMK-VNEEELKRLDEDLEDAEKNLGETEIGDVMMAKTKPLSGIGEKEA

Parental  ALTAFRKTYDKTV-ALGHRLDIVFYLLRIGLFYMDNDLITRNTEKAKSLIEEGGDWDRRNRLKVYQGLYC
          ALTAFRKTYD.T..ALGH.L.IVFYLLRI.LFYMDNDLITRNTEKA.SLIE.GGDWDRRN...VYQGLYC
Retrocopy ALTAFRKTYDTTE<ALGHQLTIVFYLLRIVLFYMDNDLITRNTEKAQSLIE-GGDWDRRNCQNVYQGLYC

Parental  VAIRDFKQAAELFLDTVSTFTSYELMDYKTFVTYTVYVSMIALERPDLREKVIKGAEILEVLHSLPAVRQ
          VA.RDFKQAAELFL.TVSTFTS.ELMDYK.FV.Y..Y.SMI..ERP.......K....L.........R.
Retrocopy VALRDFKQAAELFLGTVSTFTSHELMDYKMFVIYAMYSSMIV*ERPG--KMSLKD*RFLKCCAVFQRFRS

Parental  YLFSLYECRYSVFFQSLAVVEQEMKKDWLFAPHYRYYVREMRIHAYSQLLESYRSLTLGY
          ..F.L..C.YSV.FQSLA.VEQEMKKDWLF.PHYRYYVREMRIHA.SQLLESYRSLT..Y
Retrocopy TIFTL*IC-YSVLFQSLAIVEQEMKKDWLFLPHYRYYVREMRIHACSQLLESYRSLTGQY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_1619 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1619 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000005852	1 retrocopy	retro_dnov_672,
Tupaia belangeri	ENSTBEG00000008485	2 retrocopies	retro_tbel_1619 , retro_tbel_4345,