RetrogeneDB ID: retro_pcap_461

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_97911:2544..2991(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000015342
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMD10
• Ensembl ID: ENSPCAG00000005221
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 10 [Source:HGNC Symbol;Acc:9555]

Sequence

>retro_pcap_461
ATGGCGGGGTCTGTGTCAAACCTAATGGTCTGCAACCTGGCCTACAATGGAAAGCTGAAGGAGCTGAAAGAAAGGATCCT
GGCCGATAAGTCTTTGGCTACTACAACTGACCAGGACAGCAGAACTGTACTGCATTGGGCATGCTCTGCAGGACATACAG
AAATAGTTGAATTCTTGCTGCAACTTGGAGTGTCAGTGAATGATAAAGATGATGCAGGTTGGTCTCCTCTTCATATTGCT
GCTTCCGCTGGCCGGGATGAGATTGTAAAAGCCCTTCTAGGAAAAGGTGCTCAGGTGAATGCTGTCAATCAGAATGGCTG
TACTCCTCTGCATTATGCAGCTTCCAAAAACAGGCATGAGATTGCTGTCATGTTATTAGAAGGTGGGGCTAATCCAGATG
CTAAGGACGATTTCGAGGCTACAGCACTGCACTGGGCAGCAGCCAAG

Alignment

ORF - retro_pcap_461 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.64 %
• Parental protein coverage: 66.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEGSVSNLMVCNLAYNGKLEELKERILADKSLATTTDQYSRTVLHWACSAGHTEIVEFLLQLGVSVNDKD
          M.GSVSNLMVCNLAYNGKL.ELKERILADKSLATTTDQ.SRTVLHWACSAGHTEIVEFLLQLGVSVNDKD
Retrocopy MAGSVSNLMVCNLAYNGKLKELKERILADKSLATTTDQDSRTVLHWACSAGHTEIVEFLLQLGVSVNDKD

Parental  DAGWSPLHIAASAGRDEIVKALLGKGAQVNAVNQNGCTPLHYAASKNRHEIAVMLLEGGANPDAKDHFEA
          DAGWSPLHIAASAGRDEIVKALLGKGAQVNAVNQNGCTPLHYAASKNRHEIAVMLLEGGANPDAKD.FEA
Retrocopy DAGWSPLHIAASAGRDEIVKALLGKGAQVNAVNQNGCTPLHYAASKNRHEIAVMLLEGGANPDAKDDFEA

Parental  TALHRAAAK
          TALH.AAAK
Retrocopy TALHWAAAK

Legend:

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

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_461 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012006	1 retrocopy	retro_acar_134,
Callithrix jacchus	ENSCJAG00000007717	1 retrocopy	retro_cjac_2515,
Cavia porcellus	ENSCPOG00000015068	1 retrocopy	retro_cpor_358,
Dasypus novemcinctus	ENSDNOG00000001902	5 retrocopies	retro_dnov_1194, retro_dnov_208, retro_dnov_705, retro_dnov_824, retro_dnov_835,
Homo sapiens	ENSG00000101843	3 retrocopies	retro_hsap_1214, retro_hsap_2435, retro_hsap_2737,
Gorilla gorilla	ENSGGOG00000002969	3 retrocopies	retro_ggor_1515, retro_ggor_1906, retro_ggor_945,
Microcebus murinus	ENSMICG00000002059	1 retrocopy	retro_mmur_550,
Myotis lucifugus	ENSMLUG00000014534	1 retrocopy	retro_mluc_2008,
Macaca mulatta	ENSMMUG00000016981	1 retrocopy	retro_mmul_1290,
Nomascus leucogenys	ENSNLEG00000014001	2 retrocopies	retro_nleu_243, retro_nleu_690,
Oryctolagus cuniculus	ENSOCUG00000010837	1 retrocopy	retro_ocun_793,
Otolemur garnettii	ENSOGAG00000006419	1 retrocopy	retro_ogar_213,
Procavia capensis	ENSPCAG00000005221	1 retrocopy	retro_pcap_461 ,
Pongo abelii	ENSPPYG00000020618	3 retrocopies	retro_pabe_1010, retro_pabe_1793, retro_pabe_2275,
Pan troglodytes	ENSPTRG00000022169	3 retrocopies	retro_ptro_1407, retro_ptro_1851, retro_ptro_831,
Ictidomys tridecemlineatus	ENSSTOG00000003783	3 retrocopies	retro_itri_1684, retro_itri_312, retro_itri_676,
Tarsius syrichta	ENSTSYG00000009920	13 retrocopies	retro_tsyr_1160, retro_tsyr_1674, retro_tsyr_1684, retro_tsyr_1741, retro_tsyr_1830, retro_tsyr_1968, retro_tsyr_1989, retro_tsyr_2010, retro_tsyr_2138, retro_tsyr_2151, retro_tsyr_2167, retro_tsyr_674, retro_tsyr_803,