RetrogeneDB ID:

retro_hsap_3261

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:159685259..159685592(+)
Located in intron of:ENSG00000135083
Retrocopy
information
Ensembl ID:ENSG00000254373
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:UQCRB
Ensembl ID:ENSG00000156467
Aliases:UQCRB, MC3DN3, QCR7, QP-C, QPC, UQBC, UQBP, UQCR6, UQPC
Description:ubiquinol-cytochrome c reductase binding protein [Source:HGNC Symbol;Acc:12582]


Retrocopy-Parental alignment summary:






>retro_hsap_3261
ATGGCTGGCAAGAAGGCTGTTGCAGCATCAGGCAAGTGGCTGGATGGTATTCGAAAATGGTATTACAACGCCACAGGATT
CAATAAACTGGGGTTAATGAAAGATGATACAATATATGAGAATGAAGATGTGAAAGAAGCCATAAGAAGGCTTCCTGAGA
ACCTTTATAATGACAGGATGTTTCACATGAAGAGGGCACTGGACCTGTCCATGAAGCATCAGATCTTGCCTAAAGAGCAG
TGGACCAAATATGAAGAGGAAAATTTCTACCTTGAACCGTATCTGAAAGAGGTTATTCGGGAAAGAAAAGAAAGAGCAGA
ATGGGCAAAGAGG

ORF - retro_hsap_3261 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.09 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAGKQAVSASGKWLDGIRKWYYNAAGFNKLGLMRDDTIYEDEDVKEAIRRLPENLYNDRMFRIKRALDLN
MAGK.AV.ASGKWLDGIRKWYYNA.GFNKLGLM.DDTIYE.EDVKEAIRRLPENLYNDRMF..KRALDL.
RetrocopyMAGKKAVAASGKWLDGIRKWYYNATGFNKLGLMKDDTIYENEDVKEAIRRLPENLYNDRMFHMKRALDLS
ParentalLKHQILPKEQWTKYEEENFYLEPYLKEVIRERKEREEWAKK
.KHQILPKEQWTKYEEENFYLEPYLKEVIRERKER.EWAK.
RetrocopyMKHQILPKEQWTKYEEENFYLEPYLKEVIRERKERAEWAKR

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 150 .22 RPM
bodymap2_adrenal 0 .02 RPM 188 .79 RPM
bodymap2_brain 0 .00 RPM 299 .42 RPM
bodymap2_breast 0 .00 RPM 231 .62 RPM
bodymap2_colon 0 .00 RPM 375 .79 RPM
bodymap2_heart 0 .00 RPM 447 .22 RPM
bodymap2_kidney 0 .00 RPM 205 .30 RPM
bodymap2_liver 0 .00 RPM 88 .30 RPM
bodymap2_lung 0 .00 RPM 139 .31 RPM
bodymap2_lymph_node 0 .00 RPM 151 .32 RPM
bodymap2_ovary 0 .02 RPM 255 .09 RPM
bodymap2_prostate 0 .00 RPM 251 .96 RPM
bodymap2_skeletal_muscle 0 .00 RPM 152 .05 RPM
bodymap2_testis 0 .26 RPM 200 .33 RPM
bodymap2_thyroid 0 .13 RPM 213 .75 RPM
bodymap2_white_blood_cells 0 .00 RPM 145 .77 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3261 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3261 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_151549267 libraries168 libraries778 libraries352 libraries264 libraries

The graphical summary, for retro_hsap_3261 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_3261 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3261 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_2703
Macaca mulatta retro_mmul_2053
Parental genes homology:
Parental genes homology involve 23 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000072871 retrocopy
retro_amel_985,
Canis familiaris ENSCAFG000000094494 retrocopies
retro_cfam_1504, retro_cfam_1509, retro_cfam_1531, retro_cfam_792,
Callithrix jacchus ENSCJAG000000205602 retrocopies
retro_cjac_2206, retro_cjac_894,
Cavia porcellus ENSCPOG000000121492 retrocopies
retro_cpor_1086, retro_cpor_866,
Erinaceus europaeus ENSEEUG000000013121 retrocopy
retro_eeur_224,
Felis catus ENSFCAG000000263025 retrocopies
retro_fcat_1292, retro_fcat_178, retro_fcat_1780, retro_fcat_378, retro_fcat_558,
Homo sapiens ENSG00000156467 2 retrocopies
retro_hsap_3261 , retro_hsap_4838,
Gorilla gorilla ENSGGOG000000265281 retrocopy
retro_ggor_3017,
Latimeria chalumnae ENSLACG000000044651 retrocopy
retro_lcha_127,
Loxodonta africana ENSLAFG000000025421 retrocopy
retro_lafr_727,
Myotis lucifugus ENSMLUG000000071821 retrocopy
retro_mluc_1601,
Macaca mulatta ENSMMUG000000088043 retrocopies
retro_mmul_2053, retro_mmul_2065, retro_mmul_2581,
Mus musculus ENSMUSG000000215204 retrocopies
retro_mmus_1175, retro_mmus_1628, retro_mmus_2610, retro_mmus_514,
Nomascus leucogenys ENSNLEG000000266701 retrocopy
retro_nleu_1357,
Oryctolagus cuniculus ENSOCUG000000081133 retrocopies
retro_ocun_1149, retro_ocun_345, retro_ocun_570,
Otolemur garnettii ENSOGAG000000043021 retrocopy
retro_ogar_1451,
Ochotona princeps ENSOPRG000000088922 retrocopies
retro_opri_109, retro_opri_688,
Pongo abelii ENSPPYG000000187632 retrocopies
retro_pabe_2703, retro_pabe_3762,
Rattus norvegicus ENSRNOG000000249671 retrocopy
retro_rnor_290,
Sorex araneus ENSSARG000000029993 retrocopies
retro_sara_460, retro_sara_52, retro_sara_704,
Ictidomys tridecemlineatus ENSSTOG000000080171 retrocopy
retro_itri_46,
Tarsius syrichta ENSTSYG000000105022 retrocopies
retro_tsyr_1114, retro_tsyr_898,
Drosophila melanogaster FBgn00307331 retrocopy
retro_dmel_22,

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 = 0.11 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 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .02 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 .03 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .06 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .11 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .08 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .02 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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