RetrogeneDB ID: retro_tbel_4287

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_75384:3005..3893(-)
• 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_4287
ATGGAGAGAAAAGTAAGAAGAATCTACCTTGCTTCTGAACCCAATATAATTCATTTTCTACAAGTATCTTGGGAGAAAAC
ACTAGGATCTGGTTTTGTTATTACACTTACTGATGGTCAGTCTGCATGGATTGGGACAGTTTCCGAATCAGAGATTTCCC
AAGAAGCTGATGACATGGCAATGGAAAAAGAGAAATATGTTGATGAGCTGAGAAAAGCATTGGTATCAGAAACAGGACCA
GCTGATGCATACAACTTTAATTTTTCTAAAGAGTCTTGTCACTTCTCCTTCGAGAAAAACCTGAAAGATGTTTCATTCAG
ACTTGGTTCCTTCAACCTAGAGAAAGTTGCAAGCCCAGCTGAGGTCATTAGAGAACTTATTTGTTACTGCCTGGACACCA
TCACAGAAAACCAAGCCAAAAATGAGCACCTGCAGAAAGAAAATGAAAGGCTTCTGAGAGATTGGAATGATATTGAAGGA
CGGTTTGAAAAATGTGTGAGTGCAAAGGAAGCTTTGGAGATGGATCTTTATGAACGATTTATTTTGGTGTTGAATGAGAA
GAAAACGAAGATTCGAACCTTACAGAAATCATTAAATGAAGTTCAAGAACTACAAAAGAACACTGAATGTGAAAGGGAAA
CTGCAACCTGTTCTGAAATGACTGTTGACAGAGATGCAATCCATGATGAAAGTACTGATGAGGAAAGTGAAAATCTGTCT
GGTCTCTCTGAGTTGGCTGCAGCCACGGAAAGAAAAGAAGATTCCATTATTTCAAGTCCTGATGTCATCGATATTGCACC
AAGTAGAAAGAGGAGGCAGCGAATGCTAAAAAATCTTGGGACAGAACCTAAAATTGCTCCTCAGGAATCTCAACTGCAAG
AAAAGGAA

Alignment

ORF - retro_tbel_4287 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.65 %
• Parental protein coverage: 88.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MERKVRRICLASEPNIIHFLQVSWEKTLGSGFIITLTDGQSAWIGTVSESEISQEADDMAMEKEKYVDEL
          MERKVRRI.LASEPNIIHFLQVSWEKTLGSGF.ITLTDGQSAWIGTVSESEISQEADDMAMEKEKYVDEL
Retrocopy MERKVRRIYLASEPNIIHFLQVSWEKTLGSGFVITLTDGQSAWIGTVSESEISQEADDMAMEKEKYVDEL

Parental  RKALVSETGPADAYNFNFSKESCHFSFEKNLKDVSFRLGSFNLEKVASPAEVIRELICYCLDTITENQAK
          RKALVSETGPADAYNFNFSKESCHFSFEKNLKDVSFRLGSFNLEKVASPAEVIRELICYCLDTITENQAK
Retrocopy RKALVSETGPADAYNFNFSKESCHFSFEKNLKDVSFRLGSFNLEKVASPAEVIRELICYCLDTITENQAK

Parental  NEHLQKENERLLRDWNDIEGRFEKCVSAKEALEMDLYERFILVLNEKKTKIRTLQKSLNEVQELQKNTEC
          NEHLQKENERLLRDWNDIEGRFEKCVSAKEALEMDLYERFILVLNEKKTKIRTLQKSLNEVQELQKNTEC
Retrocopy NEHLQKENERLLRDWNDIEGRFEKCVSAKEALEMDLYERFILVLNEKKTKIRTLQKSLNEVQELQKNTEC

Parental  ERETATCSEMTVDRDAIYDESTDEESENLSGLSVLAAATERKEDSIISSPDVIDIAPSRKRRQRMLKNLG
          ERETATCSEMTVDRDAI.DESTDEESENLSGLS.LAAATERKEDSIISSPDVIDIAPSRKRRQRMLKNLG
Retrocopy ERETATCSEMTVDRDAIHDESTDEESENLSGLSELAAATERKEDSIISSPDVIDIAPSRKRRQRMLKNLG

Parental  TEPKIAPQESQLQEKE
          TEPKIAPQESQLQEKE
Retrocopy TEPKIAPQESQLQEKE

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_4287 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4287 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,