RetrogeneDB ID: retro_pabe_2350

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:138408792..138409153(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFS6
• Ensembl ID: ENSPPYG00000015323
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) Fe-S protein 6, 13kDa (NADH-coenzyme Q reductase) [Source:HGNC Symbol;Acc:7713]

Sequence

>retro_pabe_2350
ATGGCAGCAGCAATGATTTACCAGCTGCTGGGCTGGAGCAGCATAGTGGCGTTGAACCTGCCCTCAGGTGCCAGGTGTTT
TGGGGTATGAGCCTTGCCAACTGGAGAGAAGGTCCTGCATGCCAGCCAGGTTGATAATAAAGACTCCAGAAAAATTCAGT
TTGTGGGTTGTCAGAAAGAGGTGAATATAAACTTTGCCACTGATTTGATAACAGAGCAACCTATGAGTGAAGTAGAGAGT
TGGGTAATATTGTGTAACTGGTTGGGGAGCTCTTGGCTACCCAAAAGTGTGTGTAAACATAGACAAAGAAACAAAAACTG
GGATATGTGGTTATTGTGGACTATAGTTCAAAAAACACCAT

Alignment

ORF - retro_pabe_2350 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.52 %
• Parental protein coverage: 99.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAMTFYRLLNRWGEAARSLHLGARCFGVRVSPTGEKVTHTGQVYDDKDYRRIRFVGRQKEVNENFAID
          MAAAM..Y.LL......A..L..GARCFGV...PTGEKV.H..QV.D.KD.R.I.FVG.QKEVN.NFA.D
Retrocopy MAAAM-IYQLLGWSSIVALNLPSGARCFGV*ALPTGEKVLHASQV-DNKDSRKIQFVGCQKEVNINFATD

Parental  LIAEQPVSEVETRVIACD-GGGGALGHPKVYINLDKETKTGTCGYCGLQFRQHH
          LI.EQP.SEVE..VI.C..G.G.ALG.PKV..N.DKETKTG.CGYCGL.F..HH
Retrocopy LITEQPMSEVESWVILCN>GWG-ALGYPKVCVNIDKETKTGICGYCGL*FKKHH

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	30.47 RPM
SRP007412_cerebellum	0.00 RPM	14.23 RPM
SRP007412_heart	0.00 RPM	59.57 RPM
SRP007412_kidney	0.00 RPM	51.34 RPM
SRP007412_liver	0.00 RPM	23.87 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2350 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2350 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2350 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2838
Pan troglodytes	retro_ptro_1924
Macaca mulatta	retro_mmul_1473
Callithrix jacchus	retro_cjac_1552

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010930	2 retrocopies	retro_amel_213, retro_amel_228,
Bos taurus	ENSBTAG00000009914	2 retrocopies	retro_btau_302, retro_btau_333,
Callithrix jacchus	ENSCJAG00000019382	1 retrocopy	retro_cjac_1552,
Equus caballus	ENSECAG00000021690	3 retrocopies	retro_ecab_701, retro_ecab_838, retro_ecab_917,
Homo sapiens	ENSG00000145494	1 retrocopy	retro_hsap_2838,
Latimeria chalumnae	ENSLACG00000004625	1 retrocopy	retro_lcha_95,
Loxodonta africana	ENSLAFG00000005708	1 retrocopy	retro_lafr_5,
Myotis lucifugus	ENSMLUG00000016888	1 retrocopy	retro_mluc_1750,
Macaca mulatta	ENSMMUG00000004447	1 retrocopy	retro_mmul_1473,
Monodelphis domestica	ENSMODG00000001425	1 retrocopy	retro_mdom_207,
Mus musculus	ENSMUSG00000021606	1 retrocopy	retro_mmus_3044,
Nomascus leucogenys	ENSNLEG00000011199	1 retrocopy	retro_nleu_1593,
Oryctolagus cuniculus	ENSOCUG00000004581	2 retrocopies	retro_ocun_1011, retro_ocun_1624,
Pongo abelii	ENSPPYG00000015323	1 retrocopy	retro_pabe_2350 ,
Pan troglodytes	ENSPTRG00000016706	1 retrocopy	retro_ptro_1924,
Rattus norvegicus	ENSRNOG00000023387	1 retrocopy	retro_rnor_1619,
Rattus norvegicus	ENSRNOG00000049394	1 retrocopy	retro_rnor_1618,
Sarcophilus harrisii	ENSSHAG00000017779	1 retrocopy	retro_shar_176,
Ictidomys tridecemlineatus	ENSSTOG00000003715	1 retrocopy	retro_itri_496,