RetrogeneDB ID: retro_tbel_1523

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_499:37937..39038(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: XRCC6
• Ensembl ID: ENSTBEG00000011736
• Aliases: None
• Description: X-ray repair complementing defective repair in Chinese hamster cells 6 [Source:HGNC Symbol;Acc:4055]

Sequence

>retro_tbel_1523
GAATATAAACATTCAGGAGGATGTAATTTGATATTTTTGACTGATTCCTCAGGGTCATGTTTAACCATCAGGATGAACAG
GAATTGTCTTCTTTTGACATGAACATCTAGTGTATCCAGAGTGGTGTACACCAATATGCTCATAAGCAGTGATAGTGATC
TTTTGGCAGACGTATTCTATCGTACTGAGAAAGACAAAATTCAGTGAATTTCAAAAATATTTACATCTTACAAGAGTGGA
TAGTCCAAGTGCTAAACAAATACTAGAGCTTGATGAGTTTAAGGTACAACAGGGCAAGAAATGGTTCCAAGACCAGATGG
GCAGTGGATCTGATTACTCATTCGGTGAAGTGTTGTGGGTCTGTGCCAATCTCTTTAGTGATGTCCAGGTCAAAATGGGT
CATAAGAGAATCATGCTGTTAACCAACGAAGATGACCTCTACTGCAACGACAGCACCAAGGCCAGCCAGGCCAAGACCAA
AGCCAGTGATCTTAGTGACAAGGATATCTTCCTTGAGTTGATGCACCTGAAGAAACCCGGGGCCTTTGATATATCCTTGT
TCTACAGAGATTTCATTAGTGTAGCAGAGAATGAGGACCTCAGAGCTCACTTAGAGGTGCTGAGCAGACTGGAAGGTCTG
ATGAGGAAGGGTCATGCCAAGGAAACAAAGAAGAGACCACTCTACAGGTTAAAGTTTAAGCTCAGCAAAGATACAGTACT
CCCAGTGGGCATTTATAGTTTGTTCCAGAAGACTTTCAAATCTTCTTCAATAAGGCCGTATCGGGAAACAAATGAACCAG
TGAAAGTCAAGACCCGGATATTTAGTATAAATACAGGCAGTTTGCTCCTGCCTAGTTACACCAAGAGGTCTCAGATCTAT
GGGAACCATCAGATTCTACTGGAGAAAGTGGAAACAGAGGAGCTGGAACAGTTTGATGAGCCAGGTTTGATTCTTATCAG
TTTCAAGCCCTTAGTAATGTTGAAAAAGCACCATTACCAGGGTCCTCCATGTTTGTGTATGCCGAGGAGACCCTGGTAAA
TGGGAGTTCGACCTTGTTCAGTGCTCTCCTCAGCACTTCTGGAGAGGAGGTCGTAGCAGTT

Alignment

ORF - retro_tbel_1523 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.95 %
• Parental protein coverage: 63.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EYKCSGRDSLIFLVDASSA-MFEYQDEEELSPFDMSIQCIQS-VYTNKLISSDRDLLAVVFYGTEKDK-N
          EYK.SG...LIFL.D.S...MF..QDE.ELS.FDM.I.CIQS.VYTN.LISSD.DLLA.VFY.TEKDK.N
Retrocopy EYKHSGGCNLIFLTDSSGS<MFNHQDEQELSSFDMNI*CIQS>VYTNMLISSDSDLLADVFYRTEKDK<N

Parental  SVNFKNIYVLQE-LDSPGAKRVLELDQFKGQQGKKRFQDQMGHGSDYSFSEVLWVCANLFSDVQVKMSHK
          SVNFKNIY.LQE..DSP.AK..LELD.FK.QQGKK.FQDQMG.GSDYSF.EVLWVCANLFSDVQVKM.HK
Retrocopy SVNFKNIYILQE<VDSPSAKQILELDEFKVQQGKKWFQDQMGSGSDYSFGEVLWVCANLFSDVQVKMGHK

Parental  RIMLFTNEDDPHRNDSAKASRARTKASDLRDTGIFLELMHLKKPGGFDISLFYRDIISVAEDEDLGVHLE
          RIML.TNEDD...NDS.KAS.A.TKASDL.D..IFLELMHLKKPG.FDISLFYRD.ISVAE.EDL..HLE
Retrocopy RIMLLTNEDDLYCNDSTKASQAKTKASDLSDKDIFLELMHLKKPGAFDISLFYRDFISVAENEDLRAHLE

Parental  VSSKLEDLMRKVRAKETKKRPLYRLKFKLSKDIALTVGIYNLLQKAFKSSAIRLYRETNEPVKVKTRIFS
          V.S.LE.LMRK..AKETKKRPLYRLKFKLSKD..L.VGIY.L.QK.FKSS.IR.YRETNEPVKVKTRIFS
Retrocopy VLSRLEGLMRKGHAKETKKRPLYRLKFKLSKDTVLPVGIYSLFQKTFKSSSIRPYRETNEPVKVKTRIFS

Parental  INTGSLLLPSDTKRSQIYGNRQILLEKEETEELKRFDEPGLILIGFKPLVMLKKHHYLRP-SMFVYPEET
          INTGSLLLPS.TKRSQIYGN.QILLEK.ETEEL..FDEPGLILI.FKPLVMLKKHHY..P.SMFVY.EET
Retrocopy INTGSLLLPSYTKRSQIYGNHQILLEKVETEELEQFDEPGLILISFKPLVMLKKHHYQGP<SMFVYAEET

Parental  LVNGSSTLFSALLSKCLEKEVVAV
          LVNGSSTLFSALLS...E.EVVAV
Retrocopy LVNGSSTLFSALLSTSGE-EVVAV

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_1523 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1523 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 7 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000196419	4 retrocopies	retro_hsap_4066, retro_hsap_4880, retro_hsap_4913, retro_hsap_511,
Gorilla gorilla	ENSGGOG00000015885	2 retrocopies	retro_ggor_3067, retro_ggor_471,
Macaca mulatta	ENSMMUG00000001856	2 retrocopies	retro_mmul_2346, retro_mmul_430,
Nomascus leucogenys	ENSNLEG00000015610	3 retrocopies	retro_nleu_1552, retro_nleu_2287, retro_nleu_2676,
Pongo abelii	ENSPPYG00000011876	1 retrocopy	retro_pabe_3821,
Tupaia belangeri	ENSTBEG00000011736	3 retrocopies	retro_tbel_1474, retro_tbel_1523 , retro_tbel_3859,
Tursiops truncatus	ENSTTRG00000006749	1 retrocopy	retro_ttru_289,