RetrogeneDB ID: retro_hsap_3349

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:82575955..82576438(-)
• Located in intron of: ENSG00000152422

Retrocopy information

• Ensembl ID: ENSG00000251552
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: COQ10B
• Ensembl ID: ENSG00000115520
• Aliases: None
• Description: coenzyme Q10 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:25819]

Sequence

>retro_hsap_3349
GCCTTGAGAAGGGTGGTCTTGGGATGCCATCTGAAGTCGGCTACAGTGGTCGGAGTGTGGGCTCCAGTGCAGGGGCCTGT
GCAGAATGTCAGATATTTAGCTTCCTGTGGTATACTGATGAGCAGAACTCTTCTACTACATACCTCAATTTTGCCTAAGG
AGATATGTGCAAGAACTTTCTTCAAAATTGCGGCACCATTAATAAACAAAAGGAAAGAATATTCAGAGAGAAGAATTTTA
AGACATTCAAGAAACATGAAGGAAATGCATGATCTAGTATCAGGAATAGAGGATTACAAGCATTTCATTCCTTGGTGTAA
AACATCAAATGTAGTATCAAAGACATCCGGATATTGTAAAACACAATTAGAAATTGGGTTTCCACCTGTGTTGGGGCAAT
ATACATCAGTAGTAACCTTGGTGAAACCTCATTTTGGAAAGGCATCCTGTATTGATGGGAAACTTCTCGATCATTTGGAG
ACT

Alignment

ORF - retro_hsap_3349 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.02 %
• Parental protein coverage: 65.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALRRVVSGCRPKSATAAGA----QAPVRNGRYLASCGILMSRTLPLHTSILPKEICARTFFKITAPLINK
          ALRRVV.GC..KSAT..G.....Q.PV.N.RYLASCGILMSRTL.LHTSILPKEICARTFFKI.APLINK
Retrocopy ALRRVVLGCHLKSATVVGVWAPVQGPVQNVRYLASCGILMSRTLLLHTSILPKEICARTFFKIAAPLINK

Parental  RKEYSERRILGYS--MQEMYDVVSGVEDYKHFVPWCKKSDVISKRSGYCKTRLEIGFPPVLERYTSVVTL
          RKEYSERRIL..S..M.EM.D.VSG.EDYKHF.PWCK.S.V.SK.SGYCKT.LEIGFPPVL..YTSVVTL
Retrocopy RKEYSERRILRHSRNMKEMHDLVSGIEDYKHFIPWCKTSNVVSKTSGYCKTQLEIGFPPVLGQYTSVVTL

Parental  VKPHLVKASCTDGRLFNHLET
          VKPH..KASC.DG.L..HLET
Retrocopy VKPHFGKASCIDGKLLDHLET

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	0.04 RPM	32.52 RPM
bodymap2_adrenal	0.00 RPM	34.63 RPM
bodymap2_brain	0.07 RPM	34.03 RPM
bodymap2_breast	0.00 RPM	31.30 RPM
bodymap2_colon	0.00 RPM	30.98 RPM
bodymap2_heart	0.02 RPM	32.92 RPM
bodymap2_kidney	0.02 RPM	44.92 RPM
bodymap2_liver	0.00 RPM	26.04 RPM
bodymap2_lung	0.00 RPM	42.35 RPM
bodymap2_lymph_node	0.00 RPM	37.59 RPM
bodymap2_ovary	0.04 RPM	27.57 RPM
bodymap2_prostate	0.00 RPM	38.26 RPM
bodymap2_skeletal_muscle	0.00 RPM	13.44 RPM
bodymap2_testis	0.11 RPM	31.41 RPM
bodymap2_thyroid	0.08 RPM	26.82 RPM
bodymap2_white_blood_cells	0.00 RPM	50.83 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3349 was not detected

EST

No EST(s) were mapped for retro_hsap_3349 retrocopy.

TSS

No TSS is located nearby retro_hsap_3349 retrocopy 5' end.

Lab

retro_hsap_3349 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3349 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2137

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004659	2 retrocopies	retro_btau_1595, retro_btau_1832,
Choloepus hoffmanni	ENSCHOG00000005807	1 retrocopy	retro_chof_1504,
Callithrix jacchus	ENSCJAG00000003971	1 retrocopy	retro_cjac_1836,
Dasypus novemcinctus	ENSDNOG00000003229	2 retrocopies	retro_dnov_1571, retro_dnov_2203,
Dipodomys ordii	ENSDORG00000004090	1 retrocopy	retro_dord_508,
Erinaceus europaeus	ENSEEUG00000001626	1 retrocopy	retro_eeur_401,
Felis catus	ENSFCAG00000022385	1 retrocopy	retro_fcat_1487,
Homo sapiens	ENSG00000115520	1 retrocopy	retro_hsap_3349 ,
Gorilla gorilla	ENSGGOG00000023373	2 retrocopies	retro_ggor_2270, retro_ggor_569,
Myotis lucifugus	ENSMLUG00000000865	1 retrocopy	retro_mluc_1236,
Macaca mulatta	ENSMMUG00000010488	1 retrocopy	retro_mmul_2434,
Monodelphis domestica	ENSMODG00000012281	1 retrocopy	retro_mdom_600,
Mus musculus	ENSMUSG00000025981	1 retrocopy	retro_mmus_3224,
Nomascus leucogenys	ENSNLEG00000006871	1 retrocopy	retro_nleu_1172,
Ochotona princeps	ENSOPRG00000010091	3 retrocopies	retro_opri_1020, retro_opri_173, retro_opri_664,
Pongo abelii	ENSPPYG00000013045	2 retrocopies	retro_pabe_2758, retro_pabe_576,
Pan troglodytes	ENSPTRG00000012772	1 retrocopy	retro_ptro_2137,
Rattus norvegicus	ENSRNOG00000014456	1 retrocopy	retro_rnor_1620,
Tarsius syrichta	ENSTSYG00000012642	2 retrocopies	retro_tsyr_1213, retro_tsyr_1666,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.15 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.07 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.06 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	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.05 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.07 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.08 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.05 RPM
YRI_NA19223	0.12 RPM

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Indel association:

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