RetrogeneDB ID: retro_tbel_1474

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4838:250424..251757(+)
• 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_1474
GAATATAAATGTTCAGGAAGAGATAGTTTGATTTTTTTGGTTGATACCTCCATGGCCATGTTTGGATATCAAGATGAAGA
AGAATTGTCTCCTTTTGACATGAACATCCAGTATATCCAGAGTATGTACACTAAGCTCATAAGCAGTGGTTGAGATCTCT
TGGCAGTGGTGTTCTATGGTACTGAGAAACACAAAAATTCAGTGAATTTCAAATTTTTTTACATCTTACAAGAGTTGGAT
AGTCCAGGTGCTTAACGAGTGCTAGAGCTTGACCAGTTTAAGGGCAACAGGGCAAGAAACGATTCCAAGACCAGATGGAC
CATGGATCTGACCATTCATTCAGTGAAGTGCTGTGGGTCTGTGTCAACCTCTTTAGTGATGTCCAGGTCAAAATGAGTCA
TAAGATAATCATGCTGTTCACCAACGAAGATGACCCCCACCGCAATGACAGCACCAAAGCCAGCCAGGCCAGGACCAAAG
CTAGTGATCTTTGTGACACGGGTATCTTCCTTGAGTTGATGCACCTGAAGAAACCTGGGGGCTTTGACATATCCTTGTTC
TACAGAGATATCATTAGTGTAGCAGAGGATAAGGACCTCGGGGTTCACTTAGAGGTGTCGAGCAAACTAGAAGACCTAAT
GAGGAAGGTACGTGCCAAGGAAACCAAAAAGAGACCATTCTACAGGTTAAAGTTTAAGTTCAGCAAAGATACAGCATTCA
CTGTGGGCATTTATAATTTGCTCCAGAAGGCTTTCAAGTCTTCTGCAATAAGACTGTATTGGGAAACAAATGAACCAGTG
AAAGTCAAGACCCAGATATTTAGTATAAATACAGGCAGTTTGCTCCTGCCTAGCGACACCAAGAGGTCTCAGACCTATGG
GAACCATCAGATTCTAATGGAGAAAGAGGAAACAGAAGAGCTGAAATGGTTTGATGAGCCAGGTTTGATTTTCATCGGTT
TCAAGCCCTTAGTAATGTTGAAAAAGCACCATTACCTGTAGCCCTCCATGTTCATGTATCCCAAGGAGACCCTGGTAAAC
AGGAGCTCAACCTTGTTTAGTTCTCTCCTCAGCGAGTGTCTGGAGAAGGTGGTCATAGCAGTGTGCAGGTACACGCCCCA
CCAGAACACCCCACCATATTTTGTGGCTCTGGTGCCACAAAGGAAGAGGAACTGGATGACCAGAACATTCAGGTGACTCC
TCCAGGTTTACAGCTGTTTTACCTACTCTTTGCTGATGACAAACGGAAGGTGCCCATTACTGAGAAAGTCAAGGCAAGCC
CAGAGCAAGTGGACAAGATGAAGGCTATTATTCAGAAACTCCGCTTCAAGTAC

Alignment

ORF - retro_tbel_1474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.39 %
• Parental protein coverage: 76.46 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EYKCSGRDSLIFLVDASSAMFEYQDEEELSPFDMSIQCIQSVYTNKLISSDRDLLAVVFYGTEKDKNSVN
          EYKCSGRDSLIFLVD.S.AMF.YQDEEELSPFDM.IQ.IQS.YT.KLISS..DLLAVVFYGTEK.KNSVN
Retrocopy EYKCSGRDSLIFLVDTSMAMFGYQDEEELSPFDMNIQYIQSMYT-KLISSG*DLLAVVFYGTEKHKNSVN

Parental  FKNIYVLQELDSPGAKRVLELDQFKG-QQGKKRFQDQMGHGSDYSFSEVLWVCANLFSDVQVKMSHKRIM
          FK..Y.LQELDSPGA.RVLELDQFKG.QQGKKRFQDQM.HGSD.SFSEVLWVC.NLFSDVQVKMSHK.IM
Retrocopy FKFFYILQELDSPGA*RVLELDQFKG<QQGKKRFQDQMDHGSDHSFSEVLWVCVNLFSDVQVKMSHKIIM

Parental  LFTNEDDPHRNDSAKASRARTKASDLRDTGIFLELMHLKKPGGFDISLFYRDIISVAEDEDLGVHLEVSS
          LFTNEDDPHRNDS.KAS.ARTKASDL.DTGIFLELMHLKKPGGFDISLFYRDIISVAED.DLGVHLEVSS
Retrocopy LFTNEDDPHRNDSTKASQARTKASDLCDTGIFLELMHLKKPGGFDISLFYRDIISVAEDKDLGVHLEVSS

Parental  KLEDLMRKVRAKETKKRPLYRLKFKLSKDIALTVGIYNLLQKAFKSSAIRLYRETNEPVKVKTRIFSINT
          KLEDLMRKVRAKETKKRP.YRLKFK.SKD.A.TVGIYNLLQKAFKSSAIRLY.ETNEPVKVKT.IFSINT
Retrocopy KLEDLMRKVRAKETKKRPFYRLKFKFSKDTAFTVGIYNLLQKAFKSSAIRLYWETNEPVKVKTQIFSINT

Parental  GSLLLPSDTKRSQIYGNRQILLEKEETEELKRFDEPGLILIGFKPLVMLKKHHYLRPSMFVYPEETLVNG
          GSLLLPSDTKRSQ.YGN.QIL.EKEETEELK.FDEPGLI.IGFKPLVMLKKHHYL.PSMF.YP.ETLVN.
Retrocopy GSLLLPSDTKRSQTYGNHQILMEKEETEELKWFDEPGLIFIGFKPLVMLKKHHYL*PSMFMYPKETLVNR

Parental  SSTLFSALLSKCLEKEVVAVCRYTPRKNTPPYFVALVPQ-EEE-LDDQKIQVTPPGFQLFYLPYADDKRK
          SSTLFS.LLS.CLEK.V.AVCRYTP..NTPPYFVALVPQ..EE.LDDQ.IQVTPPG.QLFYL..ADDKRK
Retrocopy SSTLFSSLLSECLEKVVIAVCRYTPHQNTPPYFVALVPQ<KEEELDDQNIQVTPPGLQLFYLLFADDKRK

Parental  VPITEKVKANPEQVDKMKAIIQKLRFKY
          VPITEKVKA.PEQVDKMKAIIQKLRFKY
Retrocopy VPITEKVKASPEQVDKMKAIIQKLRFKY

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_1474 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1474 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,