RetrogeneDB ID: retro_pabe_478

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:190603096..190603972(-)
• Located in intron of: ENSPPYG00000001507

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKFZP459B1627
• Ensembl ID: ENSPPYG00000015428
• Aliases: None
• Description: succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial [Source:RefSeq peptide;Acc:NP_001126667]

Sequence

>retro_pabe_478
ATGGCGGCGCTGCGGCTCCTGGCGTCGGTGCTCGGGCGCGGGGTCCCCGCCGGCGGCTCAGGGCTCGCGCTGTCCCAGGG
CTGCGCCCGCTGCTTTGCCACCAGTCCCCGGCCTCGCGCCAAGTTCTACACGGACCCGGTGGAGATGGTGAAGGACATCT
CTGATGGGGCGACCATCATGGTCGGGGTTTCGGGCTCTGCGGGATCCCCGAGAACCTGATCGCCGCGCTGCTCAGGACCC
GCGTGAAAGACCTGCAGGTGGTCAGCAGCAACGTGAGCATGGAGGACTTCGGCTGGGCCTCCTGCTGGCCGCCAGGCAGG
TCCGCCGCATCGTCTGTTCCTACGTGGGCGAGAACACGCTGTGCGAGAGCCAGTACCTGGCAGGAGAGCTGGAGCTGGAG
CTCACGCCCCAGGGCACCCTGGCCGAGCGCATCCGCGCGGGGGGCGCTGGGGTGCCCGCCTTCTACACCCCCACGGGCTA
CGGGACCCTGGTCCAGGAAGGGGGCGCCCCCATCCGCTACACCCCGGACGGCCACCTGGCGCTCATGAGCCAGCCCCGAG
AGGTGAGGGAGTTCAACGGCGACCACTTCCTTTTGGAGCGCGCCATCCGGGCAGACTTTGCCCTAATGAAAGGCTGGAAG
GCCGACCGGGCAGGAAACGTGGTCTTCAGGAGAAGCGCCCGCAATTTCAACGTGCCCATGTGCAAAGCTGCAGACGTCAC
GGCGGTGGAGGTGGAAGAGATCGTGGACGTGGGGGCTTTCCCCCCAGAAGACATCCACGTTCCTAACATTTATGTAGGTC
GCATAATAAAGAGGCAGAATACGAAAAACGAATTGAGCGCTTAACGATCACGAAAGAGGAAGATGGAGACGCCGAA

Alignment

ORF - retro_pabe_478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.26 %
• Parental protein coverage: 56.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAALKLLSSGLRLCASARGSGGTWYKGCVCSFSTSAHRHTKFYTDPVEAVKDIPDGATVLVG-GFGLCGI
          MAAL.LL.S.L.....A.GSG.....GC...F.TS.....KFYTDPVE.VKDI.DGAT..VG.GFGLCGI
Retrocopy MAALRLLASVLGRGVPAGGSGLALSQGCARCFATSPRPRAKFYTDPVEMVKDISDGATIMVG<GFGLCGI

Parental  PENLIDALLKTGVKGLTAVSNNAGVDNFG-LGLLLRSKQIKRMVSSYVGENAEFERQYLSGELEVELTPQ
          PENLI.ALL.T.VK.L..VS.N.....FG.LGLLL...Q..R.V.SYVGEN...E.QYL.GELE.ELTPQ
Retrocopy PENLIAALLRTRVKDLQVVSSNVSMEDFG<LGLLLAARQVRRIVCSYVGENTLCESQYLAGELELELTPQ

Parental  GTLAERIRAGGAGVPAFYTPTGYGTLVQEGGSPIKYNKDGSVAIASKPREVREFNGQHFILEEAITGDFA
          GTLAERIRAGGAGVPAFYTPTGYGTLVQEGG.PI.Y..DG..A..S.PREVREFNG.HF.LE.AI..DFA
Retrocopy GTLAERIRAGGAGVPAFYTPTGYGTLVQEGGAPIRYTPDGHLALMSQPREVREFNGDHFLLERAIRADFA

Parental  LVKAWKADRAGNVIFRKSARNFNLPMCKAAETTVVEVEEIVDIGAFAPEDIHIPQIYVHRLIKGE-KYEK
          L.K.WKADRAGNV.FR.SARNFN.PMCKAA..T.VEVEEIVD.GAF.PEDIH.P.IYV.R.IK....YEK
Retrocopy LMKGWKADRAGNVVFRRSARNFNVPMCKAADVTAVEVEEIVDVGAFPPEDIHVPNIYVGRIIKRQ<EYEK

Parental  RIERLSIRKEGDGEAK
          RIERL.I.KE.DG.A.
Retrocopy RIERLTITKEEDGDAE

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	151.16 RPM
SRP007412_cerebellum	0.12 RPM	117.59 RPM
SRP007412_heart	0.09 RPM	229.15 RPM
SRP007412_kidney	0.07 RPM	186.05 RPM
SRP007412_liver	0.03 RPM	4.71 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_478 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_478 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_478 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Oryctolagus cuniculus	retro_ocun_672

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033186	2 retrocopies	retro_btau_1243, retro_btau_1302,
Dipodomys ordii	ENSDORG00000016318	1 retrocopy	retro_dord_282,
Equus caballus	ENSECAG00000018312	1 retrocopy	retro_ecab_511,
Homo sapiens	ENSG00000083720	1 retrocopy	retro_hsap_14,
Gorilla gorilla	ENSGGOG00000025087	1 retrocopy	retro_ggor_378,
Myotis lucifugus	ENSMLUG00000009431	1 retrocopy	retro_mluc_194,
Nomascus leucogenys	ENSNLEG00000016656	1 retrocopy	retro_nleu_2438,
Oryctolagus cuniculus	ENSOCUG00000009231	1 retrocopy	retro_ocun_672,
Otolemur garnettii	ENSOGAG00000009909	2 retrocopies	retro_ogar_2773, retro_ogar_2781,
Pongo abelii	ENSPPYG00000015428	2 retrocopies	retro_pabe_336, retro_pabe_478 ,
Pan troglodytes	ENSPTRG00000016829	1 retrocopy	retro_ptro_140,
Rattus norvegicus	ENSRNOG00000043094	2 retrocopies	retro_rnor_2177, retro_rnor_2256,
Ictidomys tridecemlineatus	ENSSTOG00000008271	1 retrocopy	retro_itri_747,
Tarsius syrichta	ENSTSYG00000013641	1 retrocopy	retro_tsyr_1455,
Tursiops truncatus	ENSTTRG00000004331	1 retrocopy	retro_ttru_875,
Vicugna pacos	ENSVPAG00000002550	1 retrocopy	retro_vpac_556,