RetrogeneDB ID: retro_pabe_3821

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:150278456..150279530(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: XRCC6
• Ensembl ID: ENSPPYG00000011876
• Aliases: None
• Description: X-ray repair complementing defective repair in Chinese hamster cells 6 [Source:HGNC Symbol;Acc:4055]

Sequence

>retro_pabe_3821
TTGTCAGGGCGGGAGTCATATTACAAAACCAAGGGCGATGAAGAAGTTGAAGAAGAACAGGAAGAGAACCTTGAAGCAAG
AGGAGACTACAAATATTCAGAAAGAGATAGTTTGATTTTTTTGGTTGATGCCTCCAAGGCTATGTTTGAATCTCCTAGTG
AAGATGAGTTGACACCTTTTGACATGAGCATCCAGTGTATTCAAAGTGTGTACATCAGTAAGATCATAAGCAGTGATCGA
GATCTCTTGACTGTGGTGTTCTATGGTACTGAGAAAGACAAAAATTCAGTGAATTTTAAAAATATTTATATCTTACAGGA
GCTGGATAATCCAGGTGCAAAATGAATTCTAGAGCTTGACCACTTTAAGGGGCAGCAGGGACAAAAACGTTTCCAAGACC
TGATGGGCCATGCATCTGACTACTCACTCAGTGAAGTGCTGTGGGTCCGTGCCAACCTCTTTAGTGATGTCCAATTCAAG
ATGAGTCATAAGAAGATCATGCTCTTCACCAATAAAGACAACCCCCATGGCAATGAGAGTGCCAAAGCCAGCCAGGCCAG
GACCAAAGCCGGTGATCTCCAAGATACAGGCATCTTCCTTGACTTGATGCATCTGAAGAAACCTGGAGGCTTTGACATAT
CCTTGTTCTACAGAGATATCATCAGCATAGCAGAGGATGAGGACCTCAAGGTTCACTTTGAGGAATCCAGCAAGCTAGAA
GACCTGTTGCGGAAGGTTCACGCCAAAGAGACCAGGAAGCGAGCACTCAGCAGGTTAAAGCTGAAGCTCAACAAAGATAT
AGTGATCTCTGTGGGCATTTATAATCTGGTCCAGAAGGCTGTCAAGCCTCCTCCAATAAAGCCCTATGGGGAAATAAATG
AACCAGTGAAAACCAAGACCGGGACCTTTAATACAAGTACAGATGGTTTGCTTCTGCCTAGCGATACCAAGAGGTCTCAG
ATCTATGGGAGTCATCAGATTATACTGGAGAAAGAGGAAACAGAAGAGCTAAAACGGTTTGATGATCCAGGTTTGATGCT
CATGGGTTTCAAGCCATTGGTGCTGCTGAAGAAA

Alignment

ORF - retro_pabe_3821 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.9 %
• Parental protein coverage: 64.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSENELTPFDMSIQCIQSV
          .SG.ESYYKT.GDEE.EEEQEENLEA.GDYKYS.RDSLIFLVDASKAMFES.SE.ELTPFDMSIQCIQSV
Retrocopy LSGRESYYKTKGDEEVEEEQEENLEARGDYKYSERDSLIFLVDASKAMFESPSEDELTPFDMSIQCIQSV

Parental  YISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELDQFKGQQGQKRFQELMGHGSD
          YISKIISSDRDLL.VVFYGTEKDKNSVNFKNIY.LQELDNPGAK.ILELD.FKGQQGQKRFQ.LMGH.SD
Retrocopy YISKIISSDRDLLTVVFYGTEKDKNSVNFKNIYILQELDNPGAK*ILELDHFKGQQGQKRFQDLMGHASD

Parental  YSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDSAKASRARTKAGDLRDTGIFLDLMHLKKPGG
          YSLSEVLWV.ANLFSDVQFKMSHK.IMLFTN.DNPHGN.SAKAS.ARTKAGDL.DTGIFLDLMHLKKPGG
Retrocopy YSLSEVLWVRANLFSDVQFKMSHKKIMLFTNKDNPHGNESAKASQARTKAGDLQDTGIFLDLMHLKKPGG

Parental  FDISLFYRDIISIAEDEDLRVHFEESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKA
          FDISLFYRDIISIAEDEDL.VHFEESSKLEDLLRKV.AKETRKRALSRLKLKLNKDIVISVGIYNLVQKA
Retrocopy FDISLFYRDIISIAEDEDLKVHFEESSKLEDLLRKVHAKETRKRALSRLKLKLNKDIVISVGIYNLVQKA

Parental  LKPPPIKLYRETNEPVKTKTRTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGF
          .KPPPIK.Y.E.NEPVKTKT.TFNTST.GLLLPSDTKRSQIYGS.QIILEKEETEELKRFDDPGLMLMGF
Retrocopy VKPPPIKPYGEINEPVKTKTGTFNTSTDGLLLPSDTKRSQIYGSHQIILEKEETEELKRFDDPGLMLMGF

Parental  KPLVLLKK
          KPLVLLKK
Retrocopy KPLVLLKK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	131.76 RPM
SRP007412_cerebellum	0.12 RPM	110.17 RPM
SRP007412_heart	0.00 RPM	63.43 RPM
SRP007412_kidney	0.03 RPM	91.58 RPM
SRP007412_liver	0.03 RPM	100.25 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3821 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3821 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3821 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4913
Gorilla gorilla	retro_ggor_3067

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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,