RetrogeneDB ID: retro_pabe_2241

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:108927181..108927705(+)
• Located in intron of: ENSPPYG00000014017

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFAF4
• Ensembl ID: ENSPPYG00000016857
• Aliases: NDUFAF4, HRPAP20
• Description: NADH dehydrogenase [Source:RefSeq peptide;Acc:NP_001126910]

Sequence

>retro_pabe_2241
ATGGGGGCTGCGGTGACTCGCAGGATCAGGCATTTCAACCTAGAGAACCGAGCGGAATGGGAAATCGGCAAGATGAAGCC
CCCTCCCACTCCCAGGCACCCCTCTACCAACAGCCTCCTGTGAGAGCAGATTAGTCTCTATGCAGAAATTAAGGGAGAGA
CTGCTCATAAAGATGACAAGCTGCTGCCATTTCTAAAAGATGTGTACGTTGATTCCAAAGATCTTGTGTCTTCCACGCAG
GTAAAAGCTGCTGAAACACATCAAGAGCCAAAGGAATTCAGACTGCTGAAAGGCCATCACTTTGATATGATAAATATTAA
GAGCATTCCCAAAGGCAAAATTTCCATTGTAGAAGCACTGATACTTCTTAACAATCATAAACTTTATCCAGAAACATGGA
CTGCTGGGAAAATGGTGCAAGAATACCATTTAGAACAGAAGATGTGAATACCCTTCTTAAATATTTTGTTACTTTTGAAG
TCAAAATCTTCCCTCCTGAAGACAAGAAAGCAATACAATCAAAA

Alignment

ORF - retro_pabe_2241 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.41 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGALVIRGIRNFNLENRAEREISKMKPSVAPRHPSTNSLLREQISLYPEVKGEIARKDNKLLSLLKDVYV
          MGA.V.R.IR.FNLENRAE.EI.KMKP...PRHPSTNSLL.EQISLY.E.KGE.A.KD.KLL..LKDVYV
Retrocopy MGAAVTRRIRHFNLENRAEWEIGKMKPPPTPRHPSTNSLL*EQISLYAEIKGETAHKDDKLLPFLKDVYV

Parental  DSKDPVPSLQVQAAETCQEPKEFRLPKDHHLDMINTKSIPKGKISITEALSLLNNHKLFPETWTAEKIAQ
          DSKD.V.S.QV.AAET.QEPKEFRL.K.HH.DMIN.KSIPKGKISI.EAL.LLNNHKL.PETWTA.K..Q
Retrocopy DSKDLVSSTQVKAAETHQEPKEFRLLKGHHFDMINIKSIPKGKISIVEALILLNNHKLYPETWTAGKMVQ

Parental  EYQLEQK-DVNSLLKYFATFEVEIFPPEDTKAIQSK
          EY.LEQK.DVN.LLKYF.TFEV.IFPPED.KAIQSK
Retrocopy EYHLEQK<DVNTLLKYFVTFEVKIFPPEDKKAIQSK

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	0.06 RPM	27.37 RPM
SRP007412_cerebellum	0.12 RPM	20.19 RPM
SRP007412_heart	0.00 RPM	17.16 RPM
SRP007412_kidney	0.03 RPM	11.87 RPM
SRP007412_liver	0.09 RPM	14.11 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2241 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2241 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2241 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2774
Pan troglodytes	retro_ptro_1877
Gorilla gorilla	retro_ggor_1931

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003174	1 retrocopy	retro_btau_1763,
Choloepus hoffmanni	ENSCHOG00000005145	2 retrocopies	retro_chof_2271, retro_chof_891,
Callithrix jacchus	ENSCJAG00000001235	2 retrocopies	retro_cjac_1613, retro_cjac_1700,
Cavia porcellus	ENSCPOG00000007618	1 retrocopy	retro_cpor_425,
Homo sapiens	ENSG00000123545	4 retrocopies	retro_hsap_1494, retro_hsap_2774, retro_hsap_3761, retro_hsap_477,
Gorilla gorilla	ENSGGOG00000012070	4 retrocopies	retro_ggor_1147, retro_ggor_1931, retro_ggor_2529, retro_ggor_451,
Microcebus murinus	ENSMICG00000015734	1 retrocopy	retro_mmur_1624,
Macaca mulatta	ENSMMUG00000018843	4 retrocopies	retro_mmul_1717, retro_mmul_2138, retro_mmul_578, retro_mmul_734,
Mus musculus	ENSMUSG00000028261	3 retrocopies	retro_mmus_1153, retro_mmus_1290, retro_mmus_3668,
Nomascus leucogenys	ENSNLEG00000013568	4 retrocopies	retro_nleu_171, retro_nleu_1716, retro_nleu_678, retro_nleu_890,
Oryctolagus cuniculus	ENSOCUG00000002152	1 retrocopy	retro_ocun_1162,
Pongo abelii	ENSPPYG00000016857	4 retrocopies	retro_pabe_1244, retro_pabe_2241 , retro_pabe_257, retro_pabe_3160,
Pan troglodytes	ENSPTRG00000018435	4 retrocopies	retro_ptro_1013, retro_ptro_1877, retro_ptro_2552, retro_ptro_358,
Rattus norvegicus	ENSRNOG00000007506	3 retrocopies	retro_rnor_1617, retro_rnor_2973, retro_rnor_675,
Tursiops truncatus	ENSTTRG00000010911	1 retrocopy	retro_ttru_628,