RetrogeneDB ID:

retro_hsap_3667

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:136355781..136356024(-)
Located in intron of:ENSG00000171408
Retrocopy
information
Ensembl ID:ENSG00000213111
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:COX5B
Ensembl ID:ENSG00000135940
Aliases:None
Description:cytochrome c oxidase subunit Vb [Source:HGNC Symbol;Acc:2269]


Retrocopy-Parental alignment summary:






>retro_hsap_3667
ATGGCTTCGAGGTTACTTTGAGGAGCTGGGGTGCCGGCTGTGCGGGCCCTGAGGGCCCAGGGTCCCTGAGGGGTGGTTGA
AGTGCACTCCAATGCATCTGGAGGTGATGTTCTTACTGACAATGAGCAGGTGACTGGGTTGGAGAGGGATATCATGATGG
CTGCACGGAAGGGACTGGACCCATATAATATACTACCCCCAAAGGCAGCTTCAGGTACCAAAGAGGACCTTAATTTAGCC
CCC

ORF - retro_hsap_3667 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.9 %
Parental protein coverage: 62.79 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMASRLLRGAGTLAAQALRARGPSGAAAMRSMASGGGVPTDEEQATGLEREIMLAAKKGLDPYNVLAPKGA
MASRLL.GAG..A..ALRA.GP.G.....S.ASGG.V.TD.EQ.TGLER.IM.AA.KGLDPYN.L.PK.A
RetrocopyMASRLL*GAGVPAVRALRAQGP*GVVEVHSNASGGDVLTDNEQVTGLERDIMMAARKGLDPYNILPPKAA
ParentalSGTREDPNLVP
SGT.ED.NL.P
RetrocopySGTKEDLNLAP

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 48 .20 RPM
bodymap2_adrenal 0 .02 RPM 69 .06 RPM
bodymap2_brain 0 .00 RPM 88 .88 RPM
bodymap2_breast 0 .00 RPM 78 .93 RPM
bodymap2_colon 0 .00 RPM 76 .51 RPM
bodymap2_heart 0 .00 RPM 197 .09 RPM
bodymap2_kidney 0 .08 RPM 112 .75 RPM
bodymap2_liver 0 .04 RPM 71 .19 RPM
bodymap2_lung 0 .00 RPM 52 .71 RPM
bodymap2_lymph_node 0 .00 RPM 47 .68 RPM
bodymap2_ovary 0 .10 RPM 40 .15 RPM
bodymap2_prostate 0 .00 RPM 88 .40 RPM
bodymap2_skeletal_muscle 0 .00 RPM 137 .48 RPM
bodymap2_testis 0 .00 RPM 61 .14 RPM
bodymap2_thyroid 0 .00 RPM 83 .10 RPM
bodymap2_white_blood_cells 0 .00 RPM 47 .53 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3667 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3667 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3667 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3667 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3667 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2488
Gorilla gorilla retro_ggor_2479
Parental genes homology:
Parental genes homology involve 29 parental genes, and 113 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000052427 retrocopies
retro_amel_1546, retro_amel_1583, retro_amel_1744, retro_amel_1867, retro_amel_536, retro_amel_65, retro_amel_746,
Bos taurus ENSBTAG000000185422 retrocopies
retro_btau_1018, retro_btau_1651,
Canis familiaris ENSCAFG000000023878 retrocopies
retro_cfam_1231, retro_cfam_1284, retro_cfam_1307, retro_cfam_1494, retro_cfam_1779, retro_cfam_2130, retro_cfam_398, retro_cfam_712,
Callithrix jacchus ENSCJAG000000169116 retrocopies
retro_cjac_1679, retro_cjac_2119, retro_cjac_2477, retro_cjac_3096, retro_cjac_495, retro_cjac_505,
Dipodomys ordii ENSDORG000000149943 retrocopies
retro_dord_246, retro_dord_360, retro_dord_72,
Equus caballus ENSECAG000000079683 retrocopies
retro_ecab_189, retro_ecab_674, retro_ecab_762,
Erinaceus europaeus ENSEEUG000000002581 retrocopy
retro_eeur_402,
Felis catus ENSFCAG000000017047 retrocopies
retro_fcat_1572, retro_fcat_1795, retro_fcat_1961, retro_fcat_331, retro_fcat_568, retro_fcat_600, retro_fcat_776,
Homo sapiens ENSG00000135940 7 retrocopies
retro_hsap_1295, retro_hsap_270, retro_hsap_3058, retro_hsap_3667 , retro_hsap_3908, retro_hsap_903, retro_hsap_997,
Gorilla gorilla ENSGGOG000000011426 retrocopies
retro_ggor_2101, retro_ggor_2479, retro_ggor_2635, retro_ggor_317, retro_ggor_730, retro_ggor_796,
Loxodonta africana ENSLAFG000000093862 retrocopies
retro_lafr_605, retro_lafr_696,
Macropus eugenii ENSMEUG000000058552 retrocopies
retro_meug_1202, retro_meug_1712,
Myotis lucifugus ENSMLUG000000145121 retrocopy
retro_mluc_336,
Mustela putorius furoENSMPUG000000113278 retrocopies
retro_mputfur_1412, retro_mputfur_1528, retro_mputfur_1559, retro_mputfur_367, retro_mputfur_811, retro_mputfur_851, retro_mputfur_871, retro_mputfur_983,
Mus musculus ENSMUSG000000615181 retrocopy
retro_mmus_59,
Nomascus leucogenys ENSNLEG000000116685 retrocopies
retro_nleu_114, retro_nleu_1143, retro_nleu_1652, retro_nleu_380, retro_nleu_871,
Oryctolagus cuniculus ENSOCUG000000170852 retrocopies
retro_ocun_1639, retro_ocun_508,
Otolemur garnettii ENSOGAG000000168403 retrocopies
retro_ogar_1136, retro_ogar_1365, retro_ogar_2269,
Ochotona princeps ENSOPRG000000020303 retrocopies
retro_opri_1128, retro_opri_334, retro_opri_568,
Pongo abelii ENSPPYG000000120786 retrocopies
retro_pabe_1074, retro_pabe_1907, retro_pabe_2532, retro_pabe_3184, retro_pabe_399, retro_pabe_778,
Pan troglodytes ENSPTRG000000122577 retrocopies
retro_ptro_1983, retro_ptro_226, retro_ptro_2488, retro_ptro_2658, retro_ptro_623, retro_ptro_754, retro_ptro_887,
Rattus norvegicus ENSRNOG000000166602 retrocopies
retro_rnor_2740, retro_rnor_2741,
Sorex araneus ENSSARG000000112751 retrocopy
retro_sara_579,
Sarcophilus harrisii ENSSHAG000000173583 retrocopies
retro_shar_656, retro_shar_793, retro_shar_797,
Sus scrofa ENSSSCG000000081954 retrocopies
retro_sscr_306, retro_sscr_562, retro_sscr_757, retro_sscr_893,
Ictidomys tridecemlineatus ENSSTOG000000109803 retrocopies
retro_itri_1185, retro_itri_848, retro_itri_94,
Tupaia belangeri ENSTBEG000000121304 retrocopies
retro_tbel_1170, retro_tbel_2821, retro_tbel_3647, retro_tbel_3684,
Tursiops truncatus ENSTTRG000000134905 retrocopies
retro_ttru_1438, retro_ttru_253, retro_ttru_270, retro_ttru_596, retro_ttru_790,
Vicugna pacos ENSVPAG000000065601 retrocopy
retro_vpac_249,

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 .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 .03 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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