RetrogeneDB ID: retro_pabe_2576

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:171911252..171913071(-)
• Located in intron of: ENSPPYG00000015179

Retrocopy information

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

Parental gene information

• Parental gene symbol: HADHA
• Ensembl ID: ENSPPYG00000012583
• Aliases: None
• Description: trifunctional enzyme subunit alpha, mitochondrial [Source:RefSeq peptide;Acc:NP_001126017]

Sequence

>retro_pabe_2576
TGCCAATACAGAATAGCAACAAAAGACAGAAAAACAGTATTCGGTGCTCCTGAAGTCTTGCTGGGGATCTTACCAGGAGC
AGGAGGCACACAAAGGCTGCCCAAAATGGTGGGTGTGCCTGCTGCTTTTGACATGATGCTGACTGGTAGAAACATTCGTG
CAGACAGGGCAAAGAAAATGGGACTGGTTGACCAATTGGTGGAATCTCTGGGACCAGGACTAAAACTTCCAGAGGAATGG
ACAATCAAATACATAGAAGAAGTCGCAATTACTTTCCCAAAGGACTAGCTGATAAGAAGATCTCTCCAAAGAGAGACAAG
GGATTGGTGGAAAAATTAACATCATATGCCATGACTATTCCATTTGTCAGGCAACAGATTTACAAAAAAGTGGAAGAAAA
AGTGTGAAAGCAGACTAAAGGGCTTTATCCCACACCTCTGAAAATAACTGATGTGGTAAAGACTGGAATTGAGCAAGGGA
GTGATGCTAGTTATCTCTCTGAATCTCAGAAATTTGGAGAGCTTGCAATGACCAAAGAATCAAAGGCCTTGATGAGACTC
TACCAGGGTCAGGTCCTGTGCAAGAATACATCTGGAGCTCCACAGAAGGATGTTAAGCATTTGGCTATTCCTGGTGCAGG
GATGATGGGAGCAGGCATCGCCCAAGTCTCCGTGGATAAGGGGCGAAAGACTATACTTAAAGATGCCACACTCACTGGGC
TAGGCCGAGGACAGCAACAAGTGTTCAAAGGATTGAATGATAAAGTAAAGAAGAAAGCTCTAACATCATTTGAAAGGGAT
TCCATCTTCAGCAACTTGACTGGGAAGCTTGATTACCAAGGTTTTGAAAGGCAGACATGGTGATGGATGCTGTGTTCTAG
GACCTTAGTTCTAAGCACAGAGTGCTAAAGGAAGTAGAAGCAGTGATTCCAGATCACTGCGTCTTTGCCAGTAACACATC
TCCTCTCCCAATCAGTGAAATCGCTGCTGTCAGCAAAAGACCTGAGAAGGTGATTGGCAGGCACTACTTCTCTCCCGCAG
ACAAGATGCAGCTGCTGGAGATGATCGCAACCCAGAAGACTTCCAAAGACACCAGTGCTTCAGCTGTAGCAGTCGGTCTC
AAGCAGGGGAAGGTCATCATTGTGGTTAAGGATGGACCTGGCTTCTATATCACCAGGTATCTTGCACCCATGATGTCTGA
AGTCATCCGAATCCTCCAGGAAGGAGTTGACCCGAAGAAGCTGGATTCCCTGACCACAGGCCTTGGCTTTCCTGTGAGTG
CTGCCACACTGGTGGATGAAGTTGGCATGGATATAGCGAAACATGTGGCCAAAGATCTGGGCAAAGCCTTTGGGGAGCAG
TTTGGAGGTGGAAACCCAGAACTACTGACATAGATGGTGTCCAAGGGCTTCCTAGGTCGCGAGTCTGGGAAGGGCTTTTC
CATCTATCAGGAGAGTGTGAAGAGTAAGAATTTGAATTCTGACATGGATAGTATTTTAGCAAGTCTGAAGATGCCTCCTA
AGTCTGAAGTCTTCTCAGATGAAGACATCCAGTTCCGCCTGGTGACAAGATTTGTGAATGAGGCAGTCACGTGCCTGCAA
GAGCGGATCTTGGCCACACCTGCAGAGGGAGACATTGGAGCCATCTTCCGGCTCAGCTTCCCACCTTGTCTTGGAGGGCC
TCTCTACTTTGTGGATCTGTATGAAGCCCAGAAGATAGTGGACCGGCTCAAGAAGTATGAGGCTGCCTATGGAAAACAGT
TCACCGCAAGCCAGCTACTAGCTGACCACACTAACAGCCCTAACAAGAAGTTTCATCAG

Alignment

ORF - retro_pabe_2576 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.87 %
• Parental protein coverage: 79.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CQYRIATKDRKTVLGTPEVLLGALPGAGGTQRLPKMVGVPAALDMMLTGRSIRADRAKKMGLVDQLVEPL
          CQYRIATKDRKTV.G.PEVLLG.LPGAGGTQRLPKMVGVPAA.DMMLTGR.IRADRAKKMGLVDQLVE.L
Retrocopy CQYRIATKDRKTVFGAPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLVESL

Parental  GPGLKPPEERTMEYLEEVAITFAK-GLADKKISPKRDKGLVEKLTAYAMTIPFVRQQVYKKVEEKVRKQT
          GPGLK.PEE.T..Y.EEVAITF.K.GLADKKISPKRDKGLVEKLT.YAMTIPFVRQQ.YKKVEEKV.KQT
Retrocopy GPGLKLPEEWTIKYIEEVAITFPK<GLADKKISPKRDKGLVEKLTSYAMTIPFVRQQIYKKVEEKV*KQT

Parental  KGLYPAPLKIIDVVKTGIEQGSDAGYLSESQKFGELVMTKESKALMGLYHGQVLCKKNKFGAPQKDVKHL
          KGLYP.PLKI.DVVKTGIEQGSDA.YLSESQKFGEL.MTKESKALM.LY.GQVLCK.N..GAPQKDVKHL
Retrocopy KGLYPTPLKITDVVKTGIEQGSDASYLSESQKFGELAMTKESKALMRLYQGQVLCK-NTSGAPQKDVKHL

Parental  AILGAGLMGAGIAQVSVDKGLKTILKDATLTALDRGQQQVFKGLNDKVKKKALTSFERDSIFSNLTGQLD
          AI.GAG.MGAGIAQVSVDKG.KTILKDATLT.L.RGQQQVFKGLNDKVKKKALTSFERDSIFSNLTG.LD
Retrocopy AIPGAGMMGAGIAQVSVDKGRKTILKDATLTGLGRGQQQVFKGLNDKVKKKALTSFERDSIFSNLTGKLD

Parental  YQGFE-KADMVIEAVFEDLSLKHRVLKEVEAVIPDHCIFASNTSALPISEIAAVSKRPEKVIGMHYFSPV
          YQGFE.KADMV..AVF.DLS.KHRVLKEVEAVIPDHC.FASNTS.LPISEIAAVSKRPEKVIG.HYFSP.
Retrocopy YQGFE<KADMVMDAVF*DLSSKHRVLKEVEAVIPDHCVFASNTSPLPISEIAAVSKRPEKVIGRHYFSPA

Parental  DKMQLLEIITTEKTSKDTSASAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLDS
          DKMQLLE.I.T.KTSKDTSASAVAVGLKQGKVIIVVKDGPGFY.TR.LAPMMSEVIRILQEGVDPKKLDS
Retrocopy DKMQLLEMIATQKTSKDTSASAVAVGLKQGKVIIVVKDGPGFYITRYLAPMMSEVIRILQEGVDPKKLDS

Parental  LTTSFGFPVGAATLVDEVGVDVAKHVAEDLGKVFGERFGGGNPELLTQMVSKGFLGRKSGKGFYIYQEGV
          LTT..GFPV.AATLVDEVG.D.AKHVA.DLGK.FGE.FGGGNPELLT.MVSKGFLGR.SGKGF.IYQE.V
Retrocopy LTTGLGFPVSAATLVDEVGMDIAKHVAKDLGKAFGEQFGGGNPELLT*MVSKGFLGRESGKGFSIYQESV

Parental  KRKDLNSDMDSILASLKLPPKSEVSSDEDIQFRLVTRFVNEAVMCLQEGILATPAEGDIGAVFGLGFPPC
          K.K.LNSDMDSILASLK.PPKSEV.SDEDIQFRLVTRFVNEAV.CLQE.ILATPAEGDIGA.F.L.FPPC
Retrocopy KSKNLNSDMDSILASLKMPPKSEVFSDEDIQFRLVTRFVNEAVTCLQERILATPAEGDIGAIFRLSFPPC

Parental  LGGPFRFVDLYGAQKTVDRLKKYEAAYGKQFTPCQLLADHANSPNKKFYQ
          LGGP..FVDLY.AQK.VDRLKKYEAAYGKQFT..QLLADH.NSPNKKF.Q
Retrocopy LGGPLYFVDLYEAQKIVDRLKKYEAAYGKQFTASQLLADHTNSPNKKFHQ

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	0.17 RPM	49.76 RPM
SRP007412_cerebellum	0.97 RPM	45.60 RPM
SRP007412_heart	0.12 RPM	218.31 RPM
SRP007412_kidney	0.07 RPM	139.08 RPM
SRP007412_liver	0.31 RPM	94.41 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2576 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2576 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2576 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2109
Macaca mulatta	retro_mmul_1987

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006972	1 retrocopy	retro_dnov_1863,
Homo sapiens	ENSG00000084754	1 retrocopy	retro_hsap_958,
Gorilla gorilla	ENSGGOG00000004918	1 retrocopy	retro_ggor_772,
Macaca mulatta	ENSMMUG00000004380	2 retrocopies	retro_mmul_1987, retro_mmul_787,
Mustela putorius furo	ENSMPUG00000008546	1 retrocopy	retro_mputfur_705,
Nomascus leucogenys	ENSNLEG00000001616	2 retrocopies	retro_nleu_1588, retro_nleu_772,
Pongo abelii	ENSPPYG00000012583	2 retrocopies	retro_pabe_2576 , retro_pabe_817,
Pongo abelii	ENSPPYG00000014986	1 retrocopy	retro_pabe_1296,
Pan troglodytes	ENSPTRG00000011732	2 retrocopies	retro_ptro_2109, retro_ptro_664,
Ictidomys tridecemlineatus	ENSSTOG00000001593	1 retrocopy	retro_itri_681,