RetrogeneDB ID: retro_tbel_2115

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_100860:1952..2618(-)
• Located in intron of: None

Retrocopy information

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

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_2115
GTCAACTGCTCGTTTTATTTCAAAATTGGAGCATGTCGCCATGGAGACAGATGCTCTCGACTGCACAACAGGCCGACGTT
TAGCCAGACCATCGTCTCCGGCACATGTACCGCAACCCTCAGAACCCTGCCCAGTCTGCTGACGCTGTGCGCGGTGCCCT
GAGCGAGGCCGAGATGCAGCAGCACTATGAGGAGTTCTTCCAGGAGGTGTTTACAGAGATGGAGGAGTACGGGGAAGTGG
AAGAGATGAACGTCTGCGACAAACCTGGGGGACCACCTGGTGGGGAACGTCTATGTCAAGTTTGGCCGTGAGGAAGATGC
GGAAAAGGCCCTGGTGGCCGTGAACAGCCGCTGGTTTCATGGGCAGCTGATCCACGCCGAGCTGTCCCCTGTGACGGATT
TCAGAGAGGCCTGCTGCCGCCAGTACGAAATGGGAGCGTGCGCGCGAGGAGGCTTCTGCAACTTCATGCACCTGAAGCCC
ATCTCCAGGGAGCTGCGGCGGGAGCTGTATGGGCGCCGGCGCAGGAAGCACAGATCCAGGTCCCGGTCGGGGGCGCGGCG
TTCTCGGTCTAGAGACCCTGGTGGTGGCGGCAATGGAGGTGGAGGTGGCGGTAGACGGGAGTGTGACAGGAGGCCGTGGA
GAGGCCGTGAAAGATCTAGGCGATTC

Alignment

ORF - retro_tbel_2115 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VNCSFYFKIGACRHGDRCSRLHNKPTFSQTIL-IQNIYRNPQNSAQTADGSHCAVSDVEMQEHYDEFFEE
          VNCSFYFKIGACRHGDRCSRLHN.PTFSQTI......YRNPQN.AQ.AD....A.S..EMQ.HY.EFF.E
Retrocopy VNCSFYFKIGACRHGDRCSRLHNRPTFSQTIV<LRHMYRNPQNPAQSADAVRGALSEAEMQQHYEEFFQE

Parental  VFTEMEEKYGEVEEMNVCD-NLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSPVTDFREA
          VFTEMEE.YGEVEEMNVCD.NLGDHLVGNVYVKF.REEDAEKA....N.RWF.GQ.IHAELSPVTDFREA
Retrocopy VFTEMEE-YGEVEEMNVCD>NLGDHLVGNVYVKFGREEDAEKALVAVNSRWFHGQLIHAELSPVTDFREA

Parental  CCRQYEMGECTRGGFCNFMHLKPISRELRRELYGRRRKKHRSRSRSRERRSRSRDRGRGGGGGGGGGGRE
          CCRQYEMG.C.RGGFCNFMHLKPISRELRRELYGRRR.KHRSRSRS..RRSRSRD.G.GG.GGGGGG.RE
Retrocopy CCRQYEMGACARGGFCNFMHLKPISRELRRELYGRRRRKHRSRSRSGARRSRSRDPGGGGNGGGGGGRRE

Parental  RDRRRSRDRERSGRF
          .DRR..R.RERS.RF
Retrocopy CDRRPWRGRERSRRF

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_2115 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2115 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,