RetrogeneDB ID: retro_tbel_3091

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_129719:73377..74102(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2Q1
• Ensembl ID: ENSTBEG00000013007
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2Q family member 1 [Source:HGNC Symbol;Acc:15698]

Sequence

>retro_tbel_3091
ACGGAGGAAGCGACCTCAGAAGAGGAGGAGGAGGAAGAGATGGCTGACGATGCAGAGGACTTGGATCACTCTGAGATGAA
GGAAGAAGAGCCTACCAGTGGGGAAAAGTCAGAGGATGAAGGGCTTGCAAGAGAAAATTTGGCAATATTAGACAAAATTA
GTAAGACACAAAGGGGAAGATCATTTAAATGATGCCGAGGCTGGGTCAGTGCAAGCTTCAGACAGACTGATGAAAGAACT
CAGGGCCATATACAAACTGCAGAGTTATAAAACAGGGATTTACTCCACTGAGCTCATAAGCAACAGTCTATATGACTGGC
ATGTTAAACTGCAGAAGCCTGGCCCTGATAGTCCTTTGGGCAGGGATCTTCAGATCTTAAAAGAAAAAGAAGGCATAGAA
TATATTTTGCTTAACTTCTCTTTTAAGGATAACTTTCCATTCTCTCCTCCCTTTGTTCGAGTGGCGTCACTGACCTCTCA
GGAGGGTGTGTGCCGGATGGTGGAGCACTGTGTGTGTACTTCTCACTACACAGGGCTGGAGTAGAGCCTACTCGATAGAC
TCGGTCATCGTGCAGACAAATGCCACCCCAGTCAAAGGCAAAGCCACAGTGCAGTTTGGAGCAAGTAAGAGTCAGTATGA
CCTAGCAAGAGCCCAAGAGTCCTCTAAGTCCATGGTACAGATCCATGAGAAGAATGGCTGGTACCCCCCTCCAAAGGAAG
ATGGC

Alignment

ORF - retro_tbel_3091 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.98 %
• Parental protein coverage: 76.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TQEDVSSEDEDEEMPEDTEDLDHYEMKEEEPAEGKKSEDDGIGKENLAILEKIKKNQR-QDYLNGAVSGS
          T.E..S.E.E.EEM..D.EDLDH.EMKEEEP..G.KSED.G...ENLAIL.KI.K.QR..D.LN.A..GS
Retrocopy TEEATSEEEEEEEMADDAEDLDHSEMKEEEPTSGEKSEDEGLARENLAILDKISKTQR>EDHLNDAEAGS

Parental  VQATDRLMKELRDIYRSQSFKGGNYAVELVNDSLYDWNVKLLKVDQDSALHNDLQILKEKEGADFILLNF
          VQA.DRLMKELR.IY..QS.K.G.Y..EL...SLYDW.VKL.K...DS.L..DLQILKEKEG...ILLNF
Retrocopy VQASDRLMKELRAIYKLQSYKTGIYSTELISNSLYDWHVKLQKPGPDSPLGRDLQILKEKEGIEYILLNF

Parental  SFKDNFPFDPPFVRVVSPV-LSGGYVLGGGAICM-ELLTKQGWSSAYSIESVIMQISATLVKGKARVQFG
          SFKDNFPF.PPFVRV.S...LSGG.V..GGA.C...LLT.QGWS.AYSI.SVI.Q..AT.VKGKA.VQFG
Retrocopy SFKDNFPFSPPFVRVASLT<LSGGCVPDGGALCV<VLLTTQGWSRAYSIDSVIVQTNATPVKGKATVQFG

Parental  ANKSQYSLTRAQQSYKSLVQIHEKNGWYTPPKEDG
          A.KSQY.L.RAQ.S.KS.VQIHEKNGWY.PPKEDG
Retrocopy ASKSQYDLARAQESSKSMVQIHEKNGWYPPPKEDG

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_3091 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3091 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000008889	1 retrocopy	retro_dnov_449,
Macropus eugenii	ENSMEUG00000003718	2 retrocopies	retro_meug_1816, retro_meug_358,
Microcebus murinus	ENSMICG00000001427	1 retrocopy	retro_mmur_339,
Rattus norvegicus	ENSRNOG00000020791	1 retrocopy	retro_rnor_297,
Tupaia belangeri	ENSTBEG00000013007	1 retrocopy	retro_tbel_3091 ,
Tursiops truncatus	ENSTTRG00000013998	1 retrocopy	retro_ttru_975,