RetrogeneDB ID: retro_hsap_564

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:44227781..44228054(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000224162
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UQCRH
• Ensembl ID: ENSG00000173660
• Aliases: UQCRH, QCR6, UQCR8
• Description: ubiquinol-cytochrome c reductase hinge protein [Source:HGNC Symbol;Acc:12590]

Sequence

>retro_hsap_564
ATGGGACTGGAGGATGAGCAAAAGATGCTGAGCAGGTCCTGAGATCCTAAGGAGGAGGAAGAGGAAGAGGAGGAATGAGT
GAATCCCCTAACAACCGTGAGATAGCAATGTGAGCAGTTGGAGAAATGTGTAAAGGCCTGGAAGCAGCTAGAGCTCTGTG
ACAAGCGTGTTATCCTCTCGATCACATACAGAAGAGGATTGCAAGAGGAGCTCTTTGACTTCTTGCATGCAAGGGACCAT
TGCTTTGCCCACAAACTCCTTAACAACTTGAAA

Alignment

ORF - retro_hsap_564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGLEDEQKMLTESGDPEEEEEEEEELVDPLTTVREQCEQLEKCVKARERLELCDERV-SSRSHTEEDCT-
          MGLEDEQKML..S.DP.EEEEEEEE.V.PLTTVR.QCEQLEKCVKA...LELCD.RV.SSRSHTEEDC..
Retrocopy MGLEDEQKMLSRS*DPKEEEEEEEE*VNPLTTVR*QCEQLEKCVKAWKQLELCDKRV>SSRSHTEEDCK<

Parental  EELFDFLHARDHCVAHKLFNNLK
          EELFDFLHARDHC.AHKL.NNLK
Retrocopy EELFDFLHARDHCFAHKLLNNLK

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	0.00 RPM	56.91 RPM
bodymap2_adrenal	0.00 RPM	78.46 RPM
bodymap2_brain	0.00 RPM	97.00 RPM
bodymap2_breast	0.00 RPM	96.81 RPM
bodymap2_colon	0.00 RPM	107.60 RPM
bodymap2_heart	0.00 RPM	255.57 RPM
bodymap2_kidney	0.00 RPM	92.61 RPM
bodymap2_liver	0.00 RPM	50.44 RPM
bodymap2_lung	0.00 RPM	67.60 RPM
bodymap2_lymph_node	0.00 RPM	88.10 RPM
bodymap2_ovary	0.00 RPM	62.03 RPM
bodymap2_prostate	0.00 RPM	103.11 RPM
bodymap2_skeletal_muscle	0.00 RPM	57.95 RPM
bodymap2_testis	0.00 RPM	64.82 RPM
bodymap2_thyroid	0.00 RPM	65.29 RPM
bodymap2_white_blood_cells	0.00 RPM	65.36 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_564 was not detected

EST

No EST(s) were mapped for retro_hsap_564 retrocopy.

TSS

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_4796	1752 libraries	75 libraries	0 libraries	1 library	1 library

The graphical summary, for retro_hsap_564 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)

Lab

retro_hsap_564 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_564 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_422
Pongo abelii	retro_pabe_516
Callithrix jacchus	retro_cjac_962

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009603	3 retrocopies	retro_btau_1247, retro_btau_691, retro_btau_732,
Callithrix jacchus	ENSCJAG00000021126	5 retrocopies	retro_cjac_1303, retro_cjac_1337, retro_cjac_2726, retro_cjac_3338, retro_cjac_962,
Homo sapiens	ENSG00000173660	5 retrocopies	retro_hsap_2085, retro_hsap_2659, retro_hsap_3200, retro_hsap_348, retro_hsap_564 ,
Gorilla gorilla	ENSGGOG00000010631	1 retrocopy	retro_ggor_1855,
Macropus eugenii	ENSMEUG00000006850	1 retrocopy	retro_meug_1932,
Mus musculus	ENSMUSG00000063882	4 retrocopies	retro_mmus_1426, retro_mmus_1965, retro_mmus_2126, retro_mmus_894,
Nomascus leucogenys	ENSNLEG00000016523	4 retrocopies	retro_nleu_1152, retro_nleu_1529, retro_nleu_2134, retro_nleu_2212,
Oryctolagus cuniculus	ENSOCUG00000007600	1 retrocopy	retro_ocun_1410,
Otolemur garnettii	ENSOGAG00000001134	2 retrocopies	retro_ogar_487, retro_ogar_763,
Ochotona princeps	ENSOPRG00000016059	1 retrocopy	retro_opri_489,
Pongo abelii	ENSPPYG00000025831	4 retrocopies	retro_pabe_2314, retro_pabe_2653, retro_pabe_516, retro_pabe_7,
Pan troglodytes	ENSPTRG00000000691	4 retrocopies	retro_ptro_1534, retro_ptro_1792, retro_ptro_2246, retro_ptro_422,
Rattus norvegicus	ENSRNOG00000012550	1 retrocopy	retro_rnor_1227,
Sorex araneus	ENSSARG00000006763	1 retrocopy	retro_sara_110,
Tupaia belangeri	ENSTBEG00000011608	2 retrocopies	retro_tbel_1692, retro_tbel_2458,
Tarsius syrichta	ENSTSYG00000006572	2 retrocopies	retro_tsyr_1821, retro_tsyr_2156,
Tursiops truncatus	ENSTTRG00000006326	1 retrocopy	retro_ttru_622,

Population studies

Expression level across human populations :

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	0.02 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

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Indel association:

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