RetrogeneDB ID: retro_tbel_1482

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4859:508146..508730(-)
• Located in intron of: ENSTBEG00000007345

Retrocopy information

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

Parental gene information

• Parental gene symbol: XRCC4
• Ensembl ID: ENSTBEG00000002518
• Aliases: None
• Description: X-ray repair complementing defective repair in Chinese hamster cells 4 [Source:HGNC Symbol;Acc:12831]

Sequence

>retro_tbel_1482
GAGAAAAACCTGAAAGATATTTCATTCAGACTTGGTTCCTTCAACCTAGAGAAAGTTGAAATCCCAGCTGAGGTCATTAG
AGAATTTATTTTTTACTGCCTGGACACCATTACAGAAAACCAAGCCAAAAATGAGCACCTGCAGAAAGAAAACGAAAAGC
TTCTGAGAGATTGGAATGATATTGAAGGACGGTTTGAAAAATGTGTGAGTGCGAAGGAAGCTTTGGAGATGGATCTTTAT
GAACGGTTTATTTTGGTGTTGAATGAGAAGAAAACAAAGATTCGAACCTTACAGAAATCATTACATGAAGTTCAAGAACT
ACAAAAGAACACTGAATGTGAAAAGGAAACGGCAACCTGTTCTGAAATGACTGTTGACAGAGATGCAATCTATGATGAAA
GTACTGATGAGGAAAGTGAAAATCTGGTCTCTCTGTGTTGGCTGCAGCCACTGAAAGAAAAGAAGATTCTATTATTTCAA
GTCCTGATGTCATCGATATTGCACCAAGTAGAAAGAGGAGGCAGCAAATGCTAAAAAATCTTGGGACAGAATCTAAAATT
GCTCCTCAGGAACCTCAACTGCAA

Alignment

ORF - retro_tbel_1482 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.37 %
• Parental protein coverage: 58.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKNLKDVSFRLGSFNLEKVASPAEVIRELICYCLDTITENQAKNEHLQKENERLLRDWNDIEGRFEKCVS
          EKNLKD.SFRLGSFNLEKV..PAEVIRE.I.YCLDTITENQAKNEHLQKENE.LLRDWNDIEGRFEKCVS
Retrocopy EKNLKDISFRLGSFNLEKVEIPAEVIREFIFYCLDTITENQAKNEHLQKENEKLLRDWNDIEGRFEKCVS

Parental  AKEALEMDLYERFILVLNEKKTKIRTLQKSLNEVQELQKNTECERETATCSEMTVDRDAIYDESTDEESE
          AKEALEMDLYERFILVLNEKKTKIRTLQKSL.EVQELQKNTECE.ETATCSEMTVDRDAIYDESTDEESE
Retrocopy AKEALEMDLYERFILVLNEKKTKIRTLQKSLHEVQELQKNTECEKETATCSEMTVDRDAIYDESTDEESE

Parental  NLSGLSVL-AAATERKEDSIISSPDVIDIAPSRKRRQRMLKNLGTEPKIAPQESQLQ
          NL..L..L.AA.TERKEDSIISSPDVIDIAPSRKRRQ.MLKNLGTE.KIAPQE.QLQ
Retrocopy NLVSLCWL<AA-TERKEDSIISSPDVIDIAPSRKRRQQMLKNLGTESKIAPQEPQLQ

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_1482 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1482 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 1 parental gene, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Tupaia belangeri	ENSTBEG00000002518	7 retrocopies	retro_tbel_1160, retro_tbel_1481, retro_tbel_1482 , retro_tbel_1586, retro_tbel_2351, retro_tbel_4287, retro_tbel_4542,