RetrogeneDB ID:

retro_hsap_4869

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:86053603..86054229(-)
Located in intron of:ENSG00000126733
Retrocopy
information
Ensembl ID:ENSG00000271290
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:COPS8
Ensembl ID:ENSG00000198612
Aliases:None
Description:COP9 signalosome subunit 8 [Source:HGNC Symbol;Acc:24335]


Retrocopy-Parental alignment summary:






>retro_hsap_4869
ATGCCAGTGGCAATGATGAAGGAAAGTGCCTTCAGTTTCAAAAAGTTGTTGGATCAGTGCGAGAACCAAGAGTTCCAGGG
TCTTGGAGGAACTGCTGCACCCCCAGTGAATGGTCAGCTTCTAGCTTTTTATTTGCTCCATAACGACATGAATAATCCAA
GATATCTTTGGGAAAGAATACCACCTGCTATAAAATCTGCAAATTCTGAACTTGGGAGAATTTGCTCAGTAGGAAAAAAA
TTCTGACATAGAGATTTCTTTGGGATGTATACAACCCTCCGTGCTTACCAGTAGCCTAAGATGTTCCAGTCAATTATGGA
AGCACTTAGAGATACAACAAGGAGATGAGCCTTTGCCCTGCCCTCTCAAGTGTATATCTCAATAATCGTTGATGATTTTG
AAGCCTTTTTTGGATGTCCTGTAGAAGAGGCTGTGAAAGGTATATTAAAACAAGAATGGCAAGCTGACCCAACCATAAGA
ACGGTTATGCCCAGAAAGCCAATTGCAAGGGCCCTGGATGTTTCTTTTAACAAGTTTATTCCCTTGCCAGAGCCAATTCC
AGTTCACCCATCCCCAGTGAATAGCAGTTATCCAGACTGACGGGTTATGTGGCTTTCCTTGATAAC

ORF - retro_hsap_4869 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.33 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMPVAVMAESAFSFKKLLDQCENQELEAPGGIATPPVYGQLLALYLLHNDMNNARYLWKRIPPAIKSANSE
MPVA.M.ESAFSFKKLLDQCENQE....GG.A.PPV.GQLLA.YLLHNDMNN.RYLW.RIPPAIKSANSE
RetrocopyMPVAMMKESAFSFKKLLDQCENQEFQGLGGTAAPPVNGQLLAFYLLHNDMNNPRYLWERIPPAIKSANSE
ParentalLGGIWSVGQRIWQRDFPGIYTTINAHQWSETVQPIMEALRDATRRRAFALVSQAYTSIIADDFAAFVGLP
LG.I.SVG.....RDF.G.YTT..A.Q.....Q.IMEALRD.TRR.AFAL.SQ.Y.SII.DDF.AF.G.P
RetrocopyLGRICSVGKKF*HRDFFGMYTTLRAYQ*PKMFQSIMEALRDTTRR*AFALPSQVYISIIVDDFEAFFGCP
ParentalVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDVSFNKFIPLSEPAPV-PPIPNEQQLARLTDYVAFLEN
VEEAVKGIL.Q.WQAD.T.R.V.PRKP.A.ALDVSFNKFIPL.EP.PV..PIP.E.QL.RLT.YVAFL.N
RetrocopyVEEAVKGILKQEWQADPTIRTVMPRKPIARALDVSFNKFIPLPEPIPV<SPIPSE*QLSRLTGYVAFLDN

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 37 .39 RPM
bodymap2_adrenal 0 .00 RPM 36 .52 RPM
bodymap2_brain 0 .00 RPM 88 .35 RPM
bodymap2_breast 0 .00 RPM 43 .44 RPM
bodymap2_colon 0 .00 RPM 55 .30 RPM
bodymap2_heart 0 .00 RPM 58 .95 RPM
bodymap2_kidney 0 .00 RPM 57 .06 RPM
bodymap2_liver 0 .00 RPM 18 .34 RPM
bodymap2_lung 0 .00 RPM 44 .62 RPM
bodymap2_lymph_node 0 .00 RPM 43 .75 RPM
bodymap2_ovary 0 .00 RPM 56 .52 RPM
bodymap2_prostate 0 .00 RPM 62 .82 RPM
bodymap2_skeletal_muscle 0 .00 RPM 94 .32 RPM
bodymap2_testis 0 .00 RPM 79 .33 RPM
bodymap2_thyroid 0 .00 RPM 57 .94 RPM
bodymap2_white_blood_cells 0 .00 RPM 36 .15 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4869 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4869 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4869 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4869 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4869 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_3787
Macaca mulatta retro_mmul_2610
Callithrix jacchus retro_cjac_4193
Parental genes homology:
Parental genes homology involve 18 parental genes, and 42 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000058543 retrocopies
retro_btau_1315, retro_btau_1401, retro_btau_1402,
Canis familiaris ENSCAFG000000301681 retrocopy
retro_cfam_1327,
Callithrix jacchus ENSCJAG000000022671 retrocopy
retro_cjac_4193,
Dasypus novemcinctus ENSDNOG000000153095 retrocopies
retro_dnov_1157, retro_dnov_1306, retro_dnov_149, retro_dnov_1701, retro_dnov_527,
Homo sapiens ENSG00000198612 2 retrocopies
retro_hsap_2657, retro_hsap_4869 ,
Macropus eugenii ENSMEUG000000081893 retrocopies
retro_meug_583, retro_meug_609, retro_meug_701,
Macaca mulatta ENSMMUG000000216051 retrocopy
retro_mmul_2610,
Monodelphis domestica ENSMODG000000074741 retrocopy
retro_mdom_1295,
Mustela putorius furoENSMPUG000000000681 retrocopy
retro_mputfur_176,
Mus musculus ENSMUSG000000344321 retrocopy
retro_mmus_1812,
Nomascus leucogenys ENSNLEG000000107062 retrocopies
retro_nleu_1528, retro_nleu_2002,
Oryctolagus cuniculus ENSOCUG000000073414 retrocopies
retro_ocun_1549, retro_ocun_1579, retro_ocun_428, retro_ocun_550,
Pongo abelii ENSPPYG000000133081 retrocopy
retro_pabe_3787,
Rattus norvegicus ENSRNOG000000196353 retrocopies
retro_rnor_1005, retro_rnor_1078, retro_rnor_975,
Ictidomys tridecemlineatus ENSSTOG000000226624 retrocopies
retro_itri_1065, retro_itri_1383, retro_itri_1737, retro_itri_296,
Tupaia belangeri ENSTBEG000000159441 retrocopy
retro_tbel_4315,
Tarsius syrichta ENSTSYG000000021967 retrocopies
retro_tsyr_1053, retro_tsyr_1559, retro_tsyr_165, retro_tsyr_1695, retro_tsyr_1874, retro_tsyr_448, retro_tsyr_943,
Tursiops truncatus ENSTTRG000000136141 retrocopy
retro_ttru_1448,

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 = 0.02 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 .00 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 .00 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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