RetrogeneDB ID: retro_tbel_963

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3445:41..678(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000013038
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: U2AF1
• Ensembl ID: ENSTBEG00000000453
• Aliases: None
• Description: U2 small nuclear RNA auxiliary factor 1 [Source:HGNC Symbol;Acc:12453]

Sequence

>retro_tbel_963
GTCAACTGTTCGTCTTATTTCAAACTTGGAGCATGTCGTCATGGAGACAGATGCTCTGGGTTGCACAATAAACCGACCTT
TAGCCAGACCATCGTGCTCCTGAACATTTACCGTAACCTCCATAACTCCTCCCCGTCTGCCGGCGGTTTGCACGGTGCTG
TGAGCGATGCTGAAATGCAGCAACACTATGATGAGTTTTTCAAGGAAGTGTTTACAGAAATGGAGGAGAAGTACGGGGAA
GTGGAAGAGATGAACGTCTGCGACAACGCGGGAGACCACCTGGCGGGGAACGTCTACGTCAAGTTTCGCCGCGAAGAAGA
TGCGGAAAAGGCTGTGATGGACTTGAATAACCGCTGGTTTAACCGGCAGCCGATCCGCGCTGAGCTCTCGCCTGTGACCG
ATTTCCGAGAAGCCTGCTGCCGCCAGTATGAAATGGGAGAGTGCACCCAAGGCGGCTTCTGCAACCTCATGCACCTGAAG
CCCATTTCCAGAGAGCTGCGGCGGGAGCTGTACGTACGCCGGCGCCGGCGCAGATCGGGGTCCGGGTCGGGAGAGGGGCG
CTCGGGGTCTAGAGACGGAGGTCCTGGCAGCTGCCCGCGGCGGTGGACCGGAGCGTGACAGGAGGCAGTCGAGAGAC

Alignment

ORF - retro_tbel_963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.72 %
• Parental protein coverage: 96.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VNCSFYFKIGACRHGDRCSRLHNKPTFSQTILIQNIYRNPQNSAQTADGSHCAVSDVEMQEHYDEFFEEV
          VNCS.YFK.GACRHGDRCS.LHNKPTFSQTI...NIYRN..NS...A.G.H.AVSD.EMQ.HYDEFF.EV
Retrocopy VNCSSYFKLGACRHGDRCSGLHNKPTFSQTIVLLNIYRNLHNSSPSAGGLHGAVSDAEMQQHYDEFFKEV

Parental  FTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSPVTDFREACC
          FTEMEEKYGEVEEMNVCDN.GDHL.GNVYVKFRREEDAEKAV.DLNNRWFN.QPI.AELSPVTDFREACC
Retrocopy FTEMEEKYGEVEEMNVCDNAGDHLAGNVYVKFRREEDAEKAVMDLNNRWFNRQPIRAELSPVTDFREACC

Parental  RQYEMGECTRGGFCNFMHLKPISRELRRELYGRRRKKHRSRSRSRERRSRSRDRGRG-GGGGGGGGGRER
          RQYEMGECT.GGFCN.MHLKPISRELRRELY.RRR...RS.S.S.E.RS.SRD.G.G....GGG....ER
Retrocopy RQYEMGECTQGGFCNLMHLKPISRELRRELYVRRRRR-RSGSGSGEGRSGSRDGGPG>AARGGG---PER

Parental  DRRRSRD
          DRR.SRD
Retrocopy DRRQSRD

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_963 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_963 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000013835	1 retrocopy	retro_mmur_614,
Otolemur garnettii	ENSOGAG00000016504	1 retrocopy	retro_ogar_241,
Pan troglodytes	ENSPTRG00000013952	2 retrocopies	retro_ptro_1000, retro_ptro_549,
Tupaia belangeri	ENSTBEG00000000453	2 retrocopies	retro_tbel_2115, retro_tbel_963 ,
Vicugna pacos	ENSVPAG00000002856	1 retrocopy	retro_vpac_489,