RetrogeneDB ID: retro_ptro_831

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:72914769..72915212(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD10
• Ensembl ID: ENSPTRG00000022169
• Aliases: None
• Description: None

Sequence

>retro_ptro_831
ATGGAGGGGTGTGTGTCTAACCTAATGGTCTGCAATCTGGCCTACAGCAGGAAGCTGGAAGAGTTCAAAGAGGGTATTCT
GGCCGATAAATCCCTAGCTACTAGAACTGACCAGGACAGCAGAACAGCATTGCACTAGGCATGCTCAGCTGGACATAAAG
GAATTGATGAATTTTTGTTGCAACTTGGAGTGCCAGTGAATGATAAAGACGATGCAAGTTGGTCTCCTCTCAAATTGCGG
CTTCTGCTGGCTGGGATGAGATTGTAAAAGCCCTTCTGGGAAAAGGTGCTCAAGTGAATGCTGTCCATCAAAATGACTGT
ACTCCCTTACATTATGCAGCTTCCAAAAATAGGCATGAGATTGCTGTCATGTTACTAGAAGGCAGGGCTAATCCTCATGC
TAAGGACCATTATGAGGCTACAGCATTGCACTAGGCAGCAGCC

Alignment

ORF - retro_ptro_831 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.59 %
• Parental protein coverage: 65.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEGCVSNLMVCNLAYSGKLEELKESILADKSLATRTDQDSRTALHWACSAGHTEIVEFLLQLGVPVNDKD
          MEGCVSNLMVCNLAYS.KLEE.KE.ILADKSLATRTDQDSRTALH.ACSAGH..I.EFLLQLGVPVNDKD
Retrocopy MEGCVSNLMVCNLAYSRKLEEFKEGILADKSLATRTDQDSRTALH*ACSAGHKGIDEFLLQLGVPVNDKD

Parental  DAGWSPL-HIAASAGRDEIVKALLGKGAQVNAVNQNGCTPLHYAASKNRHEIAVMLLEGGANPDAKDHYE
          DA.WSPL..IAASAG.DEIVKALLGKGAQVNAV.QN.CTPLHYAASKNRHEIAVMLLEG.ANP.AKDHYE
Retrocopy DASWSPL<QIAASAGWDEIVKALLGKGAQVNAVHQNDCTPLHYAASKNRHEIAVMLLEGRANPHAKDHYE

Parental  ATAMHRAAA
          ATA.H.AAA
Retrocopy ATALH*AAA

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	21.68 RPM
SRP007412_cerebellum	0.07 RPM	29.54 RPM
SRP007412_heart	0.00 RPM	10.14 RPM
SRP007412_kidney	0.03 RPM	20.48 RPM
SRP007412_liver	0.07 RPM	15.02 RPM
SRP007412_testis	0.00 RPM	21.81 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_831 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_831 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_831 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1214
Gorilla gorilla	retro_ggor_945
Pongo abelii	retro_pabe_1010
Macaca mulatta	retro_mmul_1290

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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,