RetrogeneDB ID: retro_tbel_2351

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_109346:122735..123305(-)
• Located in intron of: None

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_2351
ATAGAGAGAAAAGTAAGCAGAACCTGTCTTGCTTCTGAACCCAATATTATTTATTTTCTACAAGTATCTTGGGAGAAAAC
ACTAGGATCTGGTTTTGTTATTACATTTACTGATGATAAGTCTGTATTGATTGGGACAGTTTCAGAATCAGAGATTTACC
CGGAAGCTGATTACATGGTAATGGAAAAAGAGAAATGCGTTGATGAGCTGAGAAAAGCATCAGTGTCAGAAACAGGACCA
GCTGATGCATACAACTTTAATTTTTCTAAAGTCTTGTCACTTCTCCTTTGAGAAAAATCTGAAAGATATTTCATTCAGAC
TTGGTTTGTTCAACCTATAGAAAGTTGCAAGCCCAGCTGAGGTCATTAGAGAACTTACTTGTTACTGCCTGGACAATTAA
CAGAAAACCAAGCCAAACATGAGCACTTACAGAAAGAAAATGAAAGGCTTCTGAGAGAGTGGAATGATATTGAAGGACGC
TTTGAAAAATGTGTGAGAGCTAAAGAAACTTTTGAGATAGATCTTTATGAACAGTTTATTTTAGTGTTGAATGAGAAGAA
AACAAAGATT

Alignment

ORF - retro_tbel_2351 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.9 %
• Parental protein coverage: 57.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MERKVRRICLASEPNIIHFLQVSWEKTLGSGFIITLTDGQSAWIGTVSESEISQEADDMAMEKEKYVDEL
          .ERKV.R.CLASEPNII.FLQVSWEKTLGSGF.IT.TD..S..IGTVSESEI..EAD.M.MEKEK.VDEL
Retrocopy IERKVSRTCLASEPNIIYFLQVSWEKTLGSGFVITFTDDKSVLIGTVSESEIYPEADYMVMEKEKCVDEL

Parental  RKALVSETGPADAYNFN-FSKESCHFSFEKNLKDVSFRLGSFNLEKVASPAEVIRELICYCLDT-ITENQ
          RKA.VSETGPADAYNFN.F.K.SCHFSFEKNLKD.SFRLG.FNL.KVASPAEVIREL.CYCLD...TENQ
Retrocopy RKASVSETGPADAYNFN>FLK-SCHFSFEKNLKDISFRLGLFNL*KVASPAEVIRELTCYCLDN<LTENQ

Parental  AKNEHLQKENERLLRDWNDIEGRFEKCVSAKEALEMDLYERFILVLNEKKTKI
          AK.EHLQKENERLLR.WNDIEGRFEKCV.AKE..E.DLYE.FILVLNEKKTKI
Retrocopy AKHEHLQKENERLLREWNDIEGRFEKCVRAKETFEIDLYEQFILVLNEKKTKI

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_2351 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2351 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,