RetrogeneDB ID: retro_pabe_2275

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:190550607..190551227(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PSMD10
• Ensembl ID: ENSPPYG00000020618
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 10 [Source:HGNC Symbol;Acc:9555]

Sequence

>retro_pabe_2275
ATGGAGGGGTGTGTGTCTAACCTAATGGTCTGCAACCTGGCCTACAGAGGAAGCTGGAAGAGTTGAAGGAGAGTATTCTG
GCCGATAAATTCCTGTCTAGTAGAACTGACTAGAACAGCAGAACTGCATTGCACTGGGCATGCTCAGCCAGACATGCAGA
AATTGTTGAATTTTTGTTGCAACTTGGAGTGCCAGTGAGTGATAAAGGCAATGCAGGTTGGTCTCCTCTTCATACTGCAG
CTTCCGCTGGGCGGGATGAGATTGTAAAAGCCCTTCTGGTAAAATGTGCTCAAATAAATGCTGTCAGTCAAAATGGCTGT
ACTCCCCTACATTATACAGTTTCCAAAAACAGACATGAGATTGCTGTCATGTTACTAGAAGGCAGGGCTGATCCACATGC
TGAGGACCATTGTGAGGCTATGGCAATGCACCGGGCAGCAGCCAAAGGTCACTTGAAGATGATTCCTATATTTCTGTACT
ACAGAACATCCACGAACATCCAAGACACTGAGGGTAACACTCCTCTACACTTAGCCTGTGATGAGGAGAGAGTGGAAGAA
GGAGCAAGTGTCCCAAGGAGCAAGGATTTACATTGAGAATAAAGAAGAAAAGACACGCCT

Alignment

ORF - retro_pabe_2275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.51 %
• Parental protein coverage: 92.04 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEGCVSNLMVCNLAYSG-KLEELKESILADKSLATRTDQDSRTALHWACSAGHTEIVEFLLQLGVPVNDK
          MEGCVSNLMVCNLAY.G.KLEELKESILADK.L..RTD..SRTALHWACSA.H.EIVEFLLQLGVPV.DK
Retrocopy MEGCVSNLMVCNLAYRG<KLEELKESILADKFLSSRTD*NSRTALHWACSARHAEIVEFLLQLGVPVSDK

Parental  DDAGWSPLHIAASAGRDEIVKALLGKGAQVNAVNQNGCTPLHYAASKNRHEIAVMLLEGGANPDAKDHYE
          ..AGWSPLH.AASAGRDEIVKALL.K.AQ.NAV.QNGCTPLHY..SKNRHEIAVMLLEG.A.P.A.DH.E
Retrocopy GNAGWSPLHTAASAGRDEIVKALLVKCAQINAVSQNGCTPLHYTVSKNRHEIAVMLLEGRADPHAEDHCE

Parental  ATAMHRAAAKGNLKMIHILLYYKASTNIQDTEGNTPLHLACDEERVEEAKLLVSQGASIYIENKEEKTP
          A.AMHRAAAKG.LKMI.I.LYY..STNIQDTEGNTPLHLACDEERVEE....V........E.....TP
Retrocopy AMAMHRAAAKGHLKMIPIFLYYRTSTNIQDTEGNTPLHLACDEERVEEG-ASVPRSKDLH*E*RRKDTP

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	31.02 RPM
SRP007412_cerebellum	0.00 RPM	33.08 RPM
SRP007412_heart	0.00 RPM	9.51 RPM
SRP007412_kidney	0.00 RPM	17.57 RPM
SRP007412_liver	0.00 RPM	11.26 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2275 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2275 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2275 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2737
Pan troglodytes	retro_ptro_1851
Gorilla gorilla	retro_ggor_1906

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 42 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,
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,