RetrogeneDB ID: retro_tbel_1160

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3970:3854..4480(+)
• 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_1160
ATGGAGAGAAAAGTAAGCAGAATCTACCTTGCTTCTGAACCCAGTATTATTCATTTTCTACAAGTATCTTGGGAGAAAAC
ACTAGGATCTGGTTTAGTTATTACACTTAACTGATGGTCAGTCTGCATGGATTGGGACAGTTTCTGAATCAGAGATTTCC
CAAGAAGCTGATGACATGGCAATGGAAAAAAGAGGAATACGTTGATGAGCTGAGAAAAGTGTTGGTGTCAGAAACAGGAC
CAGCTGATGCATACAACTTGAATTTTTCTAAAGAGTCTTGTCACTTCTCCTTTGAGAAAAACCTGAAAGATGTTTCATTC
AGACTTGGTTCCTTCAACCTAGAGAAAGTTGCAAGCCCAGCTGAGGTCATTAGAGAACTTATTTGTTACTGCCTGGACAC
CATCACAGAAAACCAAGCCAAAAATGAGCACGTGCAGAAGGAAAATGAAAGGCTTCTGAGAGATTGGAACGATATTGGAG
GACAGTTTGAAAAATGTGTGAGTGCGAAGAAAGCTTTGGAGATGGATTTTTATGAACAGTTTATTTTGGTGTTGAATGAG
AAGAAAACAAAGATTCGAACCTTACAGAAATCATTAAATGAAGTTCAAGAACTACAAAAGAACACT

Alignment

ORF - retro_tbel_1160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.38 %
• Parental protein coverage: 62.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MERKVRRICLASEPNIIHFLQVSWEKTLGSGFIITL-TDGQSAWIGTVSESEISQEADDMAMEK-EKYVD
          MERKV.RI.LASEP.IIHFLQVSWEKTLGSG..ITL.TDGQSAWIGTVSESEISQEADDMAMEK.E.YVD
Retrocopy MERKVSRIYLASEPSIIHFLQVSWEKTLGSGLVITL>TDGQSAWIGTVSESEISQEADDMAMEK>EEYVD

Parental  ELRKALVSETGPADAYNFNFSKESCHFSFEKNLKDVSFRLGSFNLEKVASPAEVIRELICYCLDTITENQ
          ELRK.LVSETGPADAYN.NFSKESCHFSFEKNLKDVSFRLGSFNLEKVASPAEVIRELICYCLDTITENQ
Retrocopy ELRKVLVSETGPADAYNLNFSKESCHFSFEKNLKDVSFRLGSFNLEKVASPAEVIRELICYCLDTITENQ

Parental  AKNEHLQKENERLLRDWNDIEGRFEKCVSAKEALEMDLYERFILVLNEKKTKIRTLQKSLNEVQELQKNT
          AKNEH.QKENERLLRDWNDI.G.FEKCVSAK.ALEMD.YE.FILVLNEKKTKIRTLQKSLNEVQELQKNT
Retrocopy AKNEHVQKENERLLRDWNDIGGQFEKCVSAKKALEMDFYEQFILVLNEKKTKIRTLQKSLNEVQELQKNT

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_1160 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1160 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,