RetrogeneDB ID: retro_pabe_2565

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:145736744..145737173(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB4
• Ensembl ID: ENSPPYG00000013503
• Aliases: None
• Description: NADH dehydrogenase [Source:RefSeq peptide;Acc:NP_001126504]

Sequence

>retro_pabe_2565
CCAACAGAACACAAAGGATGAGATCTGGGCTGGGTCGCCAAGATGTAACTCCCAAAGTATACTCCATCACGCCTGGCCAC
TCTGCCCTCAACCCTCGACCCAGCTGAATACGATATATCTCTGGAGACCCAGTGGGCACAAGCTGAGCGATTGGCCATAA
GGGCCTGGCCTAAACAGGAATACCTGCTTCAGTACAACAACCCTAACCGCCAAGGGCTCATCCAAGGTATTACCTTGATT
TGTTGGACCTATGCAAGATCAGCAAGTGTTTATCTCAATTTCAGACCCGCTCCCAAAAACCCTCTCTTGGGAGCTCTCTG
TGGAATTGGGCCCCTCTTCTTCTAGTATTATGTTTTCAAAACTGACAGGGATAGAAAAGAAAAATTTATCCAGGAAGCAA
AATTGGGTTGAACATTTAACATCTCATGG

Alignment

ORF - retro_pabe_2565 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.34 %
• Parental protein coverage: 75.66 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PQNRAGAIVAWVAKMSFPKYKPSRLSPLPETLDPAEYNISPETRRAQAERLAIRAQLKREYLLQYNDPNR
          P....G....WVAKM..PKY.PSRL..LP.TLDPAEY.IS.ET..AQAERLAIRA..K.EYLLQYN.PNR
Retrocopy PTEHKG*DLGWVAKM*LPKYTPSRLATLPSTLDPAEYDISLETQWAQAERLAIRAWPKQEYLLQYNNPNR

Parental  RGLIENPALLRWAYARTTNVYPNFRPTPKNSLMGALYGFGPLIFIYYIIKTERDRKEKLIQEGKLDRTFQ
          .GLI....L..W.YAR...VY.NFRP.PKN.L.GAL.G.GPL.F.YY..KT.RDRKEK.IQE.KL..TF.
Retrocopy QGLIQGITLICWTYARSASVYLNFRPAPKNPLLGALCGIGPLFF*YYVFKTDRDRKEKFIQEAKLG*TFN

Parental  LSY
          .S.
Retrocopy ISW

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	24.49 RPM
SRP007412_cerebellum	0.00 RPM	53.75 RPM
SRP007412_heart	0.00 RPM	52.86 RPM
SRP007412_kidney	0.00 RPM	21.28 RPM
SRP007412_liver	0.03 RPM	16.28 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2565 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2565 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2565 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3103
Pan troglodytes	retro_ptro_2099
Callithrix jacchus	retro_cjac_2140

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 76 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011462	1 retrocopy	retro_acar_74,
Ailuropoda melanoleuca	ENSAMEG00000004761	2 retrocopies	retro_amel_1289, retro_amel_1491,
Bos taurus	ENSBTAG00000015892	2 retrocopies	retro_btau_184, retro_btau_995,
Choloepus hoffmanni	ENSCHOG00000000006	2 retrocopies	retro_chof_188, retro_chof_777,
Callithrix jacchus	ENSCJAG00000008695	4 retrocopies	retro_cjac_1290, retro_cjac_2140, retro_cjac_302, retro_cjac_3251,
Danio rerio	ENSDARG00000019332	1 retrocopy	retro_drer_32,
Dasypus novemcinctus	ENSDNOG00000024123	4 retrocopies	retro_dnov_1290, retro_dnov_1833, retro_dnov_394, retro_dnov_486,
Homo sapiens	ENSG00000065518	6 retrocopies	retro_hsap_1378, retro_hsap_1729, retro_hsap_2238, retro_hsap_2656, retro_hsap_2926, retro_hsap_3103,
Gorilla gorilla	ENSGGOG00000013923	2 retrocopies	retro_ggor_1853, retro_ggor_2265,
Loxodonta africana	ENSLAFG00000021459	1 retrocopy	retro_lafr_1078,
Microcebus murinus	ENSMICG00000005226	4 retrocopies	retro_mmur_1409, retro_mmur_1415, retro_mmur_882, retro_mmur_915,
Myotis lucifugus	ENSMLUG00000027951	3 retrocopies	retro_mluc_1433, retro_mluc_2010, retro_mluc_489,
Macaca mulatta	ENSMMUG00000001592	4 retrocopies	retro_mmul_1217, retro_mmul_1514, retro_mmul_1979, retro_mmul_356,
Monodelphis domestica	ENSMODG00000018229	1 retrocopy	retro_mdom_1658,
Mustela putorius furo	ENSMPUG00000008272	1 retrocopy	retro_mputfur_81,
Mus musculus	ENSMUSG00000022820	4 retrocopies	retro_mmus_1075, retro_mmus_1077, retro_mmus_1405, retro_mmus_1820,
Nomascus leucogenys	ENSNLEG00000007706	4 retrocopies	retro_nleu_134, retro_nleu_2889, retro_nleu_2989, retro_nleu_762,
Otolemur garnettii	ENSOGAG00000005956	5 retrocopies	retro_ogar_1454, retro_ogar_1917, retro_ogar_1922, retro_ogar_2874, retro_ogar_3091,
Pongo abelii	ENSPPYG00000013503	3 retrocopies	retro_pabe_1526, retro_pabe_2500, retro_pabe_2565 ,
Pan troglodytes	ENSPTRG00000015270	6 retrocopies	retro_ptro_1226, retro_ptro_1582, retro_ptro_1791, retro_ptro_1980, retro_ptro_2099, retro_ptro_947,
Rattus norvegicus	ENSRNOG00000002721	3 retrocopies	retro_rnor_275, retro_rnor_291, retro_rnor_99,
Sorex araneus	ENSSARG00000012482	1 retrocopy	retro_sara_600,
Ictidomys tridecemlineatus	ENSSTOG00000020092	3 retrocopies	retro_itri_3, retro_itri_666, retro_itri_786,
Tarsius syrichta	ENSTSYG00000006456	7 retrocopies	retro_tsyr_1062, retro_tsyr_109, retro_tsyr_1617, retro_tsyr_1635, retro_tsyr_410, retro_tsyr_627, retro_tsyr_736,
Tursiops truncatus	ENSTTRG00000016658	1 retrocopy	retro_ttru_625,
Vicugna pacos	ENSVPAG00000003774	1 retrocopy	retro_vpac_251,