RetrogeneDB ID:

retro_hsap_1762

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:17:46791091..46791307(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000241788
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:COX6B1
Ensembl ID:ENSG00000126267
Aliases:COX6B1, COX6B, COXG, COXVIb1
Description:cytochrome c oxidase subunit VIb polypeptide 1 (ubiquitous) [Source:HGNC Symbol;Acc:2280]


Retrocopy-Parental alignment summary:






>retro_hsap_1762
TACAAGACCGCTCTTTTTGACAGCAGCTTCCCCAACCAGAACCAGCCCAGGAACTGCTTGCAGGACTACCTGGACTTCCA
CCTCTGTGAGAAGGCAGTGATTGCTAAAGGGGACAATGTCTTTGTATGTGAATGGTACCAGCCTGTGTACAAGTCCCTCA
TTCCCATATCCTGGATCTCAGCCTGGGACGACCACTGGGCAGAAGCCACATTTCCC

ORF - retro_hsap_1762 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.67 %
Parental protein coverage: 83.72 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalYKTAPFDSRFPNQNQTRNCWQNYLDFHRCQKAMTAKGGDISVCEWYQRVYQSLCPTSWVTDWDEQRAEGT
YKTA.FDS.FPNQNQ.RNC.Q.YLDFH.C.KA..AKG....VCEWYQ.VY.SL.P.SW...WD...AE.T
RetrocopyYKTALFDSSFPNQNQPRNCLQDYLDFHLCEKAVIAKGDNVFVCEWYQPVYKSLIPISWISAWDDHWAEAT
ParentalFP
FP
RetrocopyFP

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 .29 RPM
bodymap2_adrenal 0 .00 RPM 65 .09 RPM
bodymap2_brain 0 .00 RPM 42 .71 RPM
bodymap2_breast 0 .00 RPM 62 .49 RPM
bodymap2_colon 0 .00 RPM 61 .43 RPM
bodymap2_heart 0 .00 RPM 181 .38 RPM
bodymap2_kidney 0 .00 RPM 92 .44 RPM
bodymap2_liver 0 .00 RPM 92 .99 RPM
bodymap2_lung 0 .00 RPM 80 .43 RPM
bodymap2_lymph_node 0 .00 RPM 76 .40 RPM
bodymap2_ovary 0 .00 RPM 35 .37 RPM
bodymap2_prostate 0 .07 RPM 83 .86 RPM
bodymap2_skeletal_muscle 0 .00 RPM 120 .44 RPM
bodymap2_testis 0 .00 RPM 38 .88 RPM
bodymap2_thyroid 0 .00 RPM 50 .73 RPM
bodymap2_white_blood_cells 0 .00 RPM 92 .67 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1762 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1762 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1762 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1762 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1762 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1209
Macaca mulatta retro_mmul_1227
Parental genes homology:
Parental genes homology involve 22 parental genes, and 79 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000005633 retrocopies
retro_amel_1653, retro_amel_581, retro_amel_775,
Canis familiaris ENSCAFG000000069137 retrocopies
retro_cfam_1614, retro_cfam_1760, retro_cfam_517, retro_cfam_6, retro_cfam_775, retro_cfam_830, retro_cfam_929,
Callithrix jacchus ENSCJAG000000102115 retrocopies
retro_cjac_1513, retro_cjac_2007, retro_cjac_268, retro_cjac_2870, retro_cjac_2924,
Equus caballus ENSECAG000000123173 retrocopies
retro_ecab_1051, retro_ecab_190, retro_ecab_719,
Felis catus ENSFCAG000000063785 retrocopies
retro_fcat_107, retro_fcat_2017, retro_fcat_293, retro_fcat_758, retro_fcat_783,
Homo sapiens ENSG00000126267 5 retrocopies
retro_hsap_1762 , retro_hsap_2906, retro_hsap_3807, retro_hsap_4032, retro_hsap_4089,
Microcebus murinus ENSMICG000000099025 retrocopies
retro_mmur_1099, retro_mmur_1413, retro_mmur_1588, retro_mmur_77, retro_mmur_809,
Myotis lucifugus ENSMLUG000000113654 retrocopies
retro_mluc_2244, retro_mluc_2455, retro_mluc_55, retro_mluc_933,
Macaca mulatta ENSMMUG000000167655 retrocopies
retro_mmul_1212, retro_mmul_1227, retro_mmul_1655, retro_mmul_1989, retro_mmul_2327,
Monodelphis domestica ENSMODG000000139621 retrocopy
retro_mdom_1046,
Mustela putorius furoENSMPUG000000062581 retrocopy
retro_mputfur_998,
Mus musculus ENSMUSG000000367511 retrocopy
retro_mmus_2498,
Nomascus leucogenys ENSNLEG000000112835 retrocopies
retro_nleu_1914, retro_nleu_2396, retro_nleu_2829, retro_nleu_2845, retro_nleu_978,
Oryctolagus cuniculus ENSOCUG000000096062 retrocopies
retro_ocun_1797, retro_ocun_840,
Oryzias latipes ENSORLG000000060701 retrocopy
retro_olat_4,
Pan troglodytes ENSPTRG000000108544 retrocopies
retro_ptro_1209, retro_ptro_1964, retro_ptro_2583, retro_ptro_2733,
Pteropus vampyrus ENSPVAG000000128218 retrocopies
retro_pvam_1031, retro_pvam_1044, retro_pvam_1331, retro_pvam_303, retro_pvam_336, retro_pvam_576, retro_pvam_717, retro_pvam_757,
Rattus norvegicus ENSRNOG000000243091 retrocopy
retro_rnor_201,
Sorex araneus ENSSARG000000107711 retrocopy
retro_sara_51,
Sus scrofa ENSSSCG000000029072 retrocopies
retro_sscr_780, retro_sscr_89,
Tarsius syrichta ENSTSYG000000145638 retrocopies
retro_tsyr_1179, retro_tsyr_1257, retro_tsyr_1260, retro_tsyr_1897, retro_tsyr_44, retro_tsyr_486, retro_tsyr_78, retro_tsyr_80,
Tursiops truncatus ENSTTRG000000022412 retrocopies
retro_ttru_619, retro_ttru_94,

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 ) 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 .00 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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