RetrogeneDB ID: retro_hsap_587

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:70392127..70392481(+)
• Located in intron of: ENSG00000138336

Retrocopy information

• Ensembl ID: ENSG00000213025
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: COX20
• Ensembl ID: ENSG00000203667
• Aliases: COX20, FAM36A
• Description: COX20 cytochrome C oxidase assembly factor [Source:HGNC Symbol;Acc:26970]

Sequence

>retro_hsap_587
ATGGCCTCCACGCCGGAGCCCGGTGAGCCCGAGGAGAGGAAGTCCCTTAAGCTCCTAGGATTTTTAGATGTTGAAAATAC
TCCCTGCGCCCGGCATTCAATATTGTATGGTTCATTAGGATCTGTTGTGGCTGGCTTTGGACATTTTTTGTTCACTAGTA
GAATTAGAAGATCATGTGATGTTGGAGTAGGGGGGTTTATCTTGGTGACTTTGGGATGCTGGTTTCACTGTAGGTATAAT
TATGCAAGGCAAAGAATCCAGGAAAGAATTGCCAGAGAAGAAATTAAAAAGAAGATATTATATGAAGGTACCCACCTCGA
TCCTGAAAGAAAACACAACGGCGGCAGCAGCAAT

Alignment

ORF - retro_hsap_587 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAPPEPGEPEERKSLKLLGFLDVENTPCARHSILYGSLGSVVAGFGHFLFTSRIRRSCDVGVGGFILVT
          MA..PEPGEPEERKSLKLLGFLDVENTPCARHSILYGSLGSVVAGFGHFLFTSRIRRSCDVGVGGFILVT
Retrocopy MASTPEPGEPEERKSLKLLGFLDVENTPCARHSILYGSLGSVVAGFGHFLFTSRIRRSCDVGVGGFILVT

Parental  LGCWFHCRYNYAKQRIQERIAREEIKKKILYEGTHLDPERKHNGSSSN
          LGCWFHCRYNYA.QRIQERIAREEIKKKILYEGTHLDPERKHNG.SSN
Retrocopy LGCWFHCRYNYARQRIQERIAREEIKKKILYEGTHLDPERKHNGGSSN

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	0.93 RPM	1.81 RPM
bodymap2_adrenal	0.10 RPM	4.61 RPM
bodymap2_brain	0.02 RPM	2.48 RPM
bodymap2_breast	1.19 RPM	2.28 RPM
bodymap2_colon	0.06 RPM	5.96 RPM
bodymap2_heart	0.02 RPM	2.12 RPM
bodymap2_kidney	0.35 RPM	4.36 RPM
bodymap2_liver	0.00 RPM	0.47 RPM
bodymap2_lung	0.19 RPM	1.07 RPM
bodymap2_lymph_node	0.00 RPM	3.33 RPM
bodymap2_ovary	1.14 RPM	4.26 RPM
bodymap2_prostate	0.87 RPM	4.33 RPM
bodymap2_skeletal_muscle	0.35 RPM	1.31 RPM
bodymap2_testis	0.06 RPM	3.94 RPM
bodymap2_thyroid	0.00 RPM	5.52 RPM
bodymap2_white_blood_cells	0.93 RPM	0.83 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_587 was not detected

EST

No EST(s) were mapped for retro_hsap_587 retrocopy.

TSS

No TSS is located nearby retro_hsap_587 retrocopy 5' end.

Lab

retro_hsap_587 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_587 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001381	4 retrocopies	retro_chof_1820, retro_chof_207, retro_chof_299, retro_chof_825,
Erinaceus europaeus	ENSEEUG00000012147	1 retrocopy	retro_eeur_104,
Homo sapiens	ENSG00000203667	1 retrocopy	retro_hsap_587 ,
Myotis lucifugus	ENSMLUG00000026132	7 retrocopies	retro_mluc_1273, retro_mluc_1505, retro_mluc_1863, retro_mluc_1954, retro_mluc_2343, retro_mluc_792, retro_mluc_958,
Monodelphis domestica	ENSMODG00000024669	1 retrocopy	retro_mdom_2014,
Mus musculus	ENSMUSG00000026500	1 retrocopy	retro_mmus_2957,
Nomascus leucogenys	ENSNLEG00000004027	1 retrocopy	retro_nleu_2518,
Ochotona princeps	ENSOPRG00000004534	6 retrocopies	retro_opri_1072, retro_opri_287, retro_opri_31, retro_opri_585, retro_opri_676, retro_opri_720,
Pongo abelii	ENSPPYG00000000053	1 retrocopy	retro_pabe_2090,
Pteropus vampyrus	ENSPVAG00000002577	1 retrocopy	retro_pvam_945,
Rattus norvegicus	ENSRNOG00000004553	2 retrocopies	retro_rnor_1033, retro_rnor_2184,
Sorex araneus	ENSSARG00000004625	2 retrocopies	retro_sara_167, retro_sara_470,
Tupaia belangeri	ENSTBEG00000015272	4 retrocopies	retro_tbel_1186, retro_tbel_3207, retro_tbel_3838, retro_tbel_3926,
Tarsius syrichta	ENSTSYG00000005644	1 retrocopy	retro_tsyr_100,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.04 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.13 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.10 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	2.78 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	3.10 RPM
FIN_HG00277	6.91 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.12 RPM
FIN_HG00328	0.07 RPM
FIN_HG00338	0.06 RPM
FIN_HG00349	3.53 RPM
FIN_HG00375	0.07 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.13 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.13 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.07 RPM
GBR_HG00134	0.09 RPM
GBR_HG00137	1.95 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.08 RPM
TSI_NA20513	4.45 RPM
TSI_NA20518	3.50 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	3.82 RPM
TSI_NA20756	0.06 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	2.89 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	2.62 RPM
YRI_NA18870	1.83 RPM
YRI_NA18907	1.98 RPM
YRI_NA18916	2.23 RPM
YRI_NA19093	3.57 RPM
YRI_NA19099	2.40 RPM
YRI_NA19114	0.10 RPM
YRI_NA19118	0.08 RPM
YRI_NA19213	3.47 RPM
YRI_NA19214	4.70 RPM
YRI_NA19223	0.02 RPM

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Indel association:

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