RetrogeneDB ID:

retro_hsap_4880

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:98974355..98975476(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000215070
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
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]


Retrocopy-Parental alignment summary:






>retro_hsap_4880
GTTCACTTTGAGGAATCCAGCAATCTAGAAGACCTGTTGCAGAAGGTTCGTGCCAAGGAGACCAGGAAATGGGCACTCAG
CAGGTTAAAGCTGAAGCTCAACAAAGACATAGTGATCTCTGTGGGCATTTACAGTCTCGTCCAGAAGGCTCTCAAGCCTC
CTTCAATAAAACTCTATCGGAAAACAAATGAACCAGTGAAAACCAAGTCCCGGAAATTTAATATTAATACCGGCAGTTTG
CTTCTGCCTAGCGATACCAAGCGGTCTCAGATCTATGGGAGTCATCAGATTATACTGGAGAAAGAGGAAACAGAAGAGCT
AAAATGGTTTGATGAACCAGCTTTGATGCTCATGGTTTTCAAGCCCTTGGTAATGCTGAAGGAGCACCATTACCCGAGGC
CCTCCTTGTTCACGTACCCTGAGGAGTCGCCGGTGAATGGGAGTTCAACCCTGTTCAGTGCTCTGCTCATTAAGTGTCTG
GAGAAGGTGGTCATAGCATTGTGCAGATACACACCCCGCAGGAACATCCCCCCTTATTTGGTGGCTTTGGTGTCACAGGA
AGAGGAGTTGGATGACCAGAAAATTCAGGTGACTACTCCAGGTTTCCAGCTGGTCTTTTTACCCTTTGCTGATGATAAAA
GGAAGGTGCCCTTTACTGAAAAAGTCATGGCAACTCCAGAGCAGGTGGACAACATGAAGGCTATCATTCAGAAGCTCTGC
TTCACATACAGAAGTGACAGCTTTGAGAACCCCGTGCTGCAGCAGCACTTCGGGAACCTGGAGCCCTTGATCTTGTATTT
GATGGAGGAACAAGCAGTGGACCTTATATTACCCAAGGTTGAAGAAATGAATAAAAGACTGGGCTCCATGGTGAATGAGT
TTAAGGAACTTGTCTACTCACCAGATTATAATCCTGAAGGGAAAATTACCAAGAGAAAATGCAATAATGAAGGTTCCAGA
AGCAAAAGGCCCAAGCGGAGTATTCAGAAGAGGAGCTGAAGACCCACATCAGCAAGGGCACATTGGGAAAGTTCACTGTG
CCAATGATGAAAGAGGCCTGCCTGGAGTACTGGCTGAAGAAGCAGGAGCTGCTAGAAGCCCTCACCAAGCACTTCCAGGA
C

ORF - retro_hsap_4880 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.74 %
Parental protein coverage: 79.62 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVHFEESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKT
VHFEESS.LEDLL.KVRAKETRK.ALSRLKLKLNKDIVISVGIY.LVQKALKPP.IKLYR.TNEPVKTK.
RetrocopyVHFEESSNLEDLLQKVRAKETRKWALSRLKLKLNKDIVISVGIYSLVQKALKPPSIKLYRKTNEPVKTKS
ParentalRTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYP
R.FN..TG.LLLPSDTKRSQIYGS.QIILEKEETEELK.FD.P.LMLM.FKPLV.LK.HHY.RPSLF.YP
RetrocopyRKFNINTGSLLLPSDTKRSQIYGSHQIILEKEETEELKWFDEPALMLMVFKPLVMLKEHHYPRPSLFTYP
ParentalEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQLVFLPFA
EES.V.GSSTLFSALLIKCLEK.V.ALCRYTPRRNIPPY.VALV.QEEELDDQKIQVT.PGFQLVFLPFA
RetrocopyEESPVNGSSTLFSALLIKCLEKVVIALCRYTPRRNIPPYLVALVSQEEELDDQKIQVTTPGFQLVFLPFA
ParentalDDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFENPVLQQHFRNLEALALDLMEPEQAVDLTLPK
DDKRK.PFTEK.MATPEQV..MKAI..KL.FTYRSDSFENPVLQQHF.NLE.L.L.LME.EQAVDL.LPK
RetrocopyDDKRKVPFTEKVMATPEQVDNMKAIIQKLCFTYRSDSFENPVLQQHFGNLEPLILYLME-EQAVDLILPK
ParentalVEAMNKRLGSLVDEFKELVYPPDYNPEGKVTKRKHDNEGSGSKRPK-VEYSEEELKTHISKGTLGKFTVP
VE.MNKRLGS.V.EFKELVY.PDYNPEGK.TKRK..NEGS.SKRPK..EYSEEELKTHISKGTLGKFTVP
RetrocopyVEEMNKRLGSMVNEFKELVYSPDYNPEGKITKRKCNNEGSRSKRPK<AEYSEEELKTHISKGTLGKFTVP
ParentalMLKEACRAYGLKSGLKKQELLEALTKHFQD
M.KEAC..Y.LK....KQELLEALTKHFQD
RetrocopyMMKEACLEYWLK----KQELLEALTKHFQD

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
bodymap2_adipose 0 .00 RPM 245 .15 RPM
bodymap2_adrenal 0 .00 RPM 255 .25 RPM
bodymap2_brain 0 .00 RPM 212 .81 RPM
bodymap2_breast 0 .04 RPM 184 .01 RPM
bodymap2_colon 0 .00 RPM 240 .15 RPM
bodymap2_heart 0 .00 RPM 143 .28 RPM
bodymap2_kidney 0 .00 RPM 191 .36 RPM
bodymap2_liver 0 .00 RPM 96 .11 RPM
bodymap2_lung 0 .00 RPM 250 .97 RPM
bodymap2_lymph_node 0 .00 RPM 168 .12 RPM
bodymap2_ovary 0 .00 RPM 310 .45 RPM
bodymap2_prostate 0 .00 RPM 240 .75 RPM
bodymap2_skeletal_muscle 0 .00 RPM 237 .61 RPM
bodymap2_testis 0 .00 RPM 484 .43 RPM
bodymap2_thyroid 0 .00 RPM 315 .37 RPM
bodymap2_white_blood_cells 0 .00 RPM 276 .65 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4880 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4880 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4880 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4880 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4880 has 0 orthologous retrocopies within eutheria group .

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 ENSGGOG000000158852 retrocopies
retro_ggor_3067, retro_ggor_471,
Macaca mulatta ENSMMUG000000018562 retrocopies
retro_mmul_2346, retro_mmul_430,
Nomascus leucogenys ENSNLEG000000156103 retrocopies
retro_nleu_1552, retro_nleu_2287, retro_nleu_2676,
Pongo abelii ENSPPYG000000118761 retrocopy
retro_pabe_3821,
Tupaia belangeri ENSTBEG000000117363 retrocopies
retro_tbel_1474, retro_tbel_1523, retro_tbel_3859,
Tursiops truncatus ENSTTRG000000067491 retrocopy
retro_ttru_289,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.03 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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





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