RetrogeneDB ID: retro_hsap_4913

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:149399293..149401120(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000234825
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: XRCC6
• Ensembl ID: ENSG00000196419
• Aliases: XRCC6, CTC75, CTCBF, G22P1, KU70, ML8, TLAA
• Description: X-ray repair complementing defective repair in Chinese hamster cells 6 [Source:HGNC Symbol;Acc:4055]

Sequence

>retro_hsap_4913
TTGTCAGGGTGGGAGTCATATTACAAAACCGAGGGCAGTGAAGAAGCTGAAGAAGAACAAGAAGAGAACCTTGAAGCAAG
AGGAGACTATAAATATTCAGAAAGAGATAGTTTGATTTTTTTGGTTGATGCCTCCAAGGCTATGTTTGAATCTCCTAGTG
AAGATGAATTGACACCTTTTGACATGAGCATCCAGTGTATTCAAAGTGTGTACATCAGTAAGATCATAAGCAGTGATCGA
GATCTCTTGGCTGTGGTGTTCTACGGTACCGAGAAAGACAAAAATTCAGTGAATTTTAAAAATATTTATGTCTTATAGGA
GCTGGATAATCCAGGTGCAAAATGAATTCTAGAGCTTGACCAGTTTAAGGGGCAGCAGGGACAAAAACGTTTCCAAGACC
TGATGGGCCATGGATCTGACTACTCACTCAGTGAAGTGCTGTGGGTCCGTGCCAACCTCTTTAGTGATGTCCAATTCAAG
ATGAGTCATACGAAGATCACGCTCTTCACCAATGAAGACAACCCCCATGGCAATGAGAGTGCCAAAGCCAGCCAGGCCAG
GACCAAAGCCGGTGATCTCCGAGATACAGGCATCTTCCTTGACTTGATGCATCTGAAGAAACCTGGAGGCTTTGACATAT
CCTTGTTCTACAGAGATATCATCAGCATAGCAGAGGATGAGGACCTCAGGGTTCACTTTGAGGAATCCAGCAAGCTAGAA
GACCTGTTGCAGAAGGTTCACGCCAAAGAGACCAGGAAGCGAGCACTCAGCAGGTTAAAGCTGAAGCTCAACAAAGATAT
AGTGATCTCTGTGGGCATTTATAATCTGGTCCAGAAGGCTCTCAAGCCTCCTCCAATAAAGCTCTATAGGGAAATAAATG
AACCAGTGAAAACCAAGACCCGGACCTTTAATACAAGTACAGACGATTTGCTTCTGCCTAGCGATACCAAGTGGTCTCAG
ATCTATGGGAGTCGTCAGATTATACTGGAGAAAGAGGAAACAGAAGAGCTAAAACGGTTTGATGATCCAGGTTTGATGCT
CATGGGTTTCAAGCCATTGGTACTGCTGAAGAAACGCCATTACCTGAGGCCCTCCCTGTCTGTGTACCCAGAGGAGTCGC
TGGTGATTGGGAGCTCAACCCTGTTCAGTGCTCTGCTCATCAAGTGTCTGGAGAAGGAGGTTGCAGCATTGTGCAGATAC
ACACCCCGCAGGAACATCCCCCCTTATTTTGTGGCTTTGGTGACACAGGAAGAAGTGTTGGATGACCAGAAAATTCAGGT
GACTCCTCCGGGCTTCCAGCTGGTCTTTTTACCCTTTGCTGATGATAAAAGGAAGATGCCCTTTACTGAAAAAGTCACGG
CAACTCCAGAGCAGGTGGACAAGATGAAGGCTATCATTGAGAAGCTTCGCTTCACGTACAGAAGTGACAGCTTTGAGAAC
CCCGTGCTGCAGCAGCACTTCAGGAACCTGGAGGCCTTGGCCTTGGATTTGATGGAGCCAGAACAAGCAGTGGACCTGAC
ATTGCCCAAGGTTGAAGCAATAAATAGAAGACTGGGCTCCCTGGTGGATGAGTTTAAGGAGCTTGTTCACCCACCAGATT
ACAATCCTGAAGGGAAAGTTACCAAGAGAAAACATGATAATGAAGGTTCTGGAAGCAAAAGGCCCAAGGTGGAGTATTCA
GAAGAGGAGCTGAAGACCCACATTAGCAAGGGCACGCTGGGCAAGTTCACTGTGCCCATGTTGAAAGAGGCCTGCCGGGC
TTACGGGCTGAAGAGTGGGCTGAAGAAGCAGGAGCTGCTGGAAGCCCTCACCAAGCACTTCCAGGAT

Alignment

ORF - retro_hsap_4913 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPFDMSIQCIQSV
          .SGWESYYKTEG.EEAEEEQEENLEA.GDYKYS.RDSLIFLVDASKAMFES.SEDELTPFDMSIQCIQSV
Retrocopy LSGWESYYKTEGSEEAEEEQEENLEARGDYKYSERDSLIFLVDASKAMFESPSEDELTPFDMSIQCIQSV

Parental  YISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELDQFKGQQGQKRFQDMMGHGSD
          YISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVL.ELDNPGAK.ILELDQFKGQQGQKRFQD.MGHGSD
Retrocopy YISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVL*ELDNPGAK*ILELDQFKGQQGQKRFQDLMGHGSD

Parental  YSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDSAKASRARTKAGDLRDTGIFLDLMHLKKPGG
          YSLSEVLWV.ANLFSDVQFKMSH..I.LFTNEDNPHGN.SAKAS.ARTKAGDLRDTGIFLDLMHLKKPGG
Retrocopy YSLSEVLWVRANLFSDVQFKMSHTKITLFTNEDNPHGNESAKASQARTKAGDLRDTGIFLDLMHLKKPGG

Parental  FDISLFYRDIISIAEDEDLRVHFEESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKA
          FDISLFYRDIISIAEDEDLRVHFEESSKLEDLL.KV.AKETRKRALSRLKLKLNKDIVISVGIYNLVQKA
Retrocopy FDISLFYRDIISIAEDEDLRVHFEESSKLEDLLQKVHAKETRKRALSRLKLKLNKDIVISVGIYNLVQKA

Parental  LKPPPIKLYRETNEPVKTKTRTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGF
          LKPPPIKLYRE.NEPVKTKTRTFNTST..LLLPSDTK.SQIYGSRQIILEKEETEELKRFDDPGLMLMGF
Retrocopy LKPPPIKLYREINEPVKTKTRTFNTSTDDLLLPSDTKWSQIYGSRQIILEKEETEELKRFDDPGLMLMGF

Parental  KPLVLLKKHHYLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEEL
          KPLVLLKK.HYLRPSL.VYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALV.QEE.L
Retrocopy KPLVLLKKRHYLRPSLSVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVTQEEVL

Parental  DDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFENPVLQQHFRNL
          DDQKIQVTPPGFQLVFLPFADDKRKMPFTEK..ATPEQV.KMKAI.EKLRFTYRSDSFENPVLQQHFRNL
Retrocopy DDQKIQVTPPGFQLVFLPFADDKRKMPFTEKVTATPEQVDKMKAIIEKLRFTYRSDSFENPVLQQHFRNL

Parental  EALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKVTKRKHDNEGSGSKRPKVEYS
          EALALDLMEPEQAVDLTLPKVEA.N.RLGSLVDEFKELV.PPDYNPEGKVTKRKHDNEGSGSKRPKVEYS
Retrocopy EALALDLMEPEQAVDLTLPKVEAINRRLGSLVDEFKELVHPPDYNPEGKVTKRKHDNEGSGSKRPKVEYS

Parental  EEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELLEALTKHFQD
          EEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELLEALTKHFQD
Retrocopy EEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELLEALTKHFQD

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
bodymap2_adipose	0.14 RPM	245.15 RPM
bodymap2_adrenal	0.12 RPM	255.25 RPM
bodymap2_brain	0.12 RPM	212.81 RPM
bodymap2_breast	0.12 RPM	184.01 RPM
bodymap2_colon	0.06 RPM	240.15 RPM
bodymap2_heart	0.00 RPM	143.28 RPM
bodymap2_kidney	0.29 RPM	191.36 RPM
bodymap2_liver	0.08 RPM	96.11 RPM
bodymap2_lung	0.09 RPM	250.97 RPM
bodymap2_lymph_node	0.05 RPM	168.12 RPM
bodymap2_ovary	0.25 RPM	310.45 RPM
bodymap2_prostate	0.10 RPM	240.75 RPM
bodymap2_skeletal_muscle	0.20 RPM	237.61 RPM
bodymap2_testis	0.32 RPM	484.43 RPM
bodymap2_thyroid	0.23 RPM	315.37 RPM
bodymap2_white_blood_cells	0.16 RPM	276.65 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4913 was not detected

EST

No EST(s) were mapped for retro_hsap_4913 retrocopy.

TSS

No TSS is located nearby retro_hsap_4913 retrocopy 5' end.

Lab

retro_hsap_4913 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4913 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_3067
Pongo abelii	retro_pabe_3821

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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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.13 RPM
CEU_NA11843	0.09 RPM
CEU_NA11930	0.33 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.15 RPM
CEU_NA12760	0.31 RPM
CEU_NA12827	0.33 RPM
CEU_NA12872	0.05 RPM
CEU_NA12873	0.29 RPM
FIN_HG00183	0.22 RPM
FIN_HG00277	0.30 RPM
FIN_HG00315	0.19 RPM
FIN_HG00321	0.09 RPM
FIN_HG00328	0.21 RPM
FIN_HG00338	0.13 RPM
FIN_HG00349	0.34 RPM
FIN_HG00375	0.24 RPM
FIN_HG00377	0.23 RPM
FIN_HG00378	0.11 RPM
GBR_HG00099	0.49 RPM
GBR_HG00111	0.15 RPM
GBR_HG00114	0.18 RPM
GBR_HG00119	0.12 RPM
GBR_HG00131	0.11 RPM
GBR_HG00133	0.14 RPM
GBR_HG00134	0.11 RPM
GBR_HG00137	0.19 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.31 RPM
TSI_NA20513	0.17 RPM
TSI_NA20518	1.03 RPM
TSI_NA20532	0.31 RPM
TSI_NA20538	0.37 RPM
TSI_NA20756	0.32 RPM
TSI_NA20765	0.19 RPM
TSI_NA20771	0.23 RPM
TSI_NA20786	0.29 RPM
TSI_NA20798	0.19 RPM
YRI_NA18870	0.20 RPM
YRI_NA18907	0.21 RPM
YRI_NA18916	0.19 RPM
YRI_NA19093	0.13 RPM
YRI_NA19099	0.24 RPM
YRI_NA19114	0.21 RPM
YRI_NA19118	0.15 RPM
YRI_NA19213	0.19 RPM
YRI_NA19214	0.07 RPM
YRI_NA19223	0.04 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).