RetrogeneDB ID: retro_ptro_2159

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:71830448..71830748(+)
• Located in intron of: ENSPTRG00000016843

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFA12
• Ensembl ID: ENSPTRG00000005306
• Aliases: None
• Description: Pan troglodytes NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 12 (NDUFA12), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001071784]

Sequence

>retro_ptro_2159
GAAGACAAATAAGGAAGCAAATACTATGAAGATAACAAGCAGTTTTCTGGCCATCACAGAGAGGTTATATACGCTACTGA
AATGAATGGCAGAAGCACATCCTGGGATGTGGATGGAAGCCTGGTGCCTCTTGAGTGGCTTCATTGGCTTCACTGTATGA
CTGAAGATCCTCCTATAAAATCACCTATTGCTAGTAAATTTATTTGGACAAGCCATAAATTCACTGTGAGTAGCACCCCA
GAATATGTACTTTATTCAACCACTAGAAAGATTCAGAAGAAGGTCCCACCTTCAAAACCT

Alignment

ORF - retro_ptro_2159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.96 %
• Parental protein coverage: 71.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EDKYGNKYYEDNKQFFGRHRWVVYTTEMNGKNTFWDVDGSMVPPEWHRWLHSMTDDPPTTKPLTARKFIW
          EDK.G.KYYEDNKQF.G.HR.V.Y.TEMNG..T.WDVDGS.VP.EW..WLH.MT.DPP...P..A.KFIW
Retrocopy EDK*GSKYYEDNKQFSGHHREVIYATEMNGRSTSWDVDGSLVPLEWLHWLHCMTEDPPIKSPI-ASKFIW

Parental  TNHKFNVTGTPEQYVPYSTTRKKIQEWIPPSTP
          T.HKF.V..TPE.YV.YSTTR.KIQ...PPS.P
Retrocopy TSHKFTVSSTPE-YVLYSTTR-KIQKKVPPSKP

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	0.02 RPM	37.46 RPM
SRP007412_cerebellum	0.00 RPM	33.88 RPM
SRP007412_heart	0.00 RPM	121.10 RPM
SRP007412_kidney	0.03 RPM	46.13 RPM
SRP007412_liver	0.00 RPM	30.61 RPM
SRP007412_testis	0.00 RPM	67.66 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2159 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2159 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2159 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3312

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Parental genes homology:

Parental genes homology involve 28 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002294	2 retrocopies	retro_amel_1069, retro_amel_1414,
Bos taurus	ENSBTAG00000014669	4 retrocopies	retro_btau_1294, retro_btau_1377, retro_btau_1449, retro_btau_869,
Choloepus hoffmanni	ENSCHOG00000007134	2 retrocopies	retro_chof_2234, retro_chof_2322,
Callithrix jacchus	ENSCJAG00000002846	2 retrocopies	retro_cjac_1796, retro_cjac_1862,
Cavia porcellus	ENSCPOG00000010154	2 retrocopies	retro_cpor_1326, retro_cpor_650,
Dasypus novemcinctus	ENSDNOG00000009192	1 retrocopy	retro_dnov_1859,
Equus caballus	ENSECAG00000015836	1 retrocopy	retro_ecab_910,
Echinops telfairi	ENSETEG00000010118	2 retrocopies	retro_etel_1401, retro_etel_787,
Felis catus	ENSFCAG00000023050	3 retrocopies	retro_fcat_1283, retro_fcat_1483, retro_fcat_362,
Homo sapiens	ENSG00000184752	3 retrocopies	retro_hsap_1293, retro_hsap_3199, retro_hsap_3312,
Gorilla gorilla	ENSGGOG00000012880	1 retrocopy	retro_ggor_1015,
Loxodonta africana	ENSLAFG00000030887	1 retrocopy	retro_lafr_671,
Microcebus murinus	ENSMICG00000008634	3 retrocopies	retro_mmur_1630, retro_mmur_224, retro_mmur_544,
Myotis lucifugus	ENSMLUG00000027131	1 retrocopy	retro_mluc_908,
Macaca mulatta	ENSMMUG00000018897	1 retrocopy	retro_mmul_1321,
Mustela putorius furo	ENSMPUG00000007354	1 retrocopy	retro_mputfur_1257,
Mus musculus	ENSMUSG00000020022	1 retrocopy	retro_mmus_2605,
Nomascus leucogenys	ENSNLEG00000005766	2 retrocopies	retro_nleu_2105, retro_nleu_2756,
Otolemur garnettii	ENSOGAG00000010853	5 retrocopies	retro_ogar_1158, retro_ogar_1310, retro_ogar_2943, retro_ogar_455, retro_ogar_896,
Pongo abelii	ENSPPYG00000004839	2 retrocopies	retro_pabe_1071, retro_pabe_2652,
Pan troglodytes	ENSPTRG00000005306	2 retrocopies	retro_ptro_2159 , retro_ptro_885,
Pteropus vampyrus	ENSPVAG00000007564	5 retrocopies	retro_pvam_1141, retro_pvam_1457, retro_pvam_33, retro_pvam_375, retro_pvam_661,
Rattus norvegicus	ENSRNOG00000007407	1 retrocopy	retro_rnor_874,
Sorex araneus	ENSSARG00000013220	1 retrocopy	retro_sara_442,
Sus scrofa	ENSSSCG00000000905	1 retrocopy	retro_sscr_802,
Tupaia belangeri	ENSTBEG00000013724	8 retrocopies	retro_tbel_1707, retro_tbel_2577, retro_tbel_2822, retro_tbel_2888, retro_tbel_3320, retro_tbel_3566, retro_tbel_4553, retro_tbel_4577,
Tursiops truncatus	ENSTTRG00000015720	2 retrocopies	retro_ttru_1607, retro_ttru_1880,
Vicugna pacos	ENSVPAG00000008508	1 retrocopy	retro_vpac_332,