RetrogeneDB ID: retro_pabe_817

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:8661104..8662395(+)
• Located in intron of: None

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_817
ATAGTGGCCTACCGGACGATTGGCATCCTCAGCCGCTTCTGTGACTTCAGGATCCTCTGATCCCAAGGTTATATACGCCG
CAATTTTACAGTCTTCTGCTTCGCTGACCAGAACCCACATTAACTATGGAGTCAAAGGGGATGTGGCAGTTATTTGAATT
AAATCTCCCAATTCAAAGGTAAATACACTGAATAAAGAGCTGCATTCAGAGTTCACAGAAGTTATGAATGAAGTCTGGGC
TACTAATCAAATCACAAGTGCCGTCCTTATCTCATCAAAGCCAGGCTGCTTTATTGCAGGTGCTGATATCAATATGTTAG
CCACTTGCAAGACCCCTCAAGAAGTAACACAGATATCACAAGAAGCACGGAGAACATTTGAGAAACTTGAAAAGGCCACA
AAGCCTGTTATAGCTTCCGTCAGTGGATCCTGCCTGGGGGGAAGGCTTCAGCTTGCCATTTCATGCCAATACAGAATAGC
AACAAAAGATGGAAAAACAATATTAGGTGCCCCTGAAGTCTTGCTGGGGATCTTACCAGGAGCAGGAGGCACACAAAGGC
TGCCCAAAATGGTGGGTGTGCCTGCTGCTTTTGTCATGATGCTGACTAGTAGAAACATTCGTGCAGATAGGGCAAAGAAA
ATGGGACTGGTTGACCAATTGGTAGAACCCCTGGGACCAGGACTAAAACCTGCAGAGGAATGGACAATCGAATACCTAGA
AGAAGTTGCAATAACTTTTGCCAAAGGACTAGCTGATAAGAAGATCTCTCCAAAGAGAGACAAGGGATTGGTGGAAAAAT
TGACAGTGTACACCATGACTATTCCATTTGTCAGGCAACAGGTATACAAAAAAGTGGAAGAAAAAGTGCAAAAGGAGACT
AACGGCCTTTATCCTGCACCTCTGAAAATAATTGACGTGGTAAAGACTGAAATTGAGTGAGGGAGTGATGCTGGTTATCT
CTCTGAATCTCAGAAATTTGGAGACCTTGCCATGACCAGTGAATCAAAGGCCTTGATGGGACTCTACCGTGGTCAGGTCT
TGTGCAAGAAGAATCAATTTGGAGCACCACAGAAGGATGCTAAGCGTCTGGCTATTCTTGGTGAAGGGCTGAAGGGAGCA
GGCATCACCTAAGTCTCTGTGGATAAGAGGCTAAAGACTATACTTAAAGATGCCACACTCGCTAGGCTAGGCCAAAGACA
GCAACGAGTGTTCAAAGGATTGAATGATAAAGTGAAGAAGAAAGCTCTAACATCATTTGAAAGGGATTCCATCTTCAGCA
ACTTGACTGGG

Alignment

ORF - retro_pabe_817 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 56.49 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVACRAIGILSRFSAFRILRSRGYICRNFT-GSSALLTRTHINYGVKGDVAVVRINSPNSKVNTLSKELH
          .VA.R.IGILSRF..FRIL.S.GYI.RNFT..S..L.TRTHINYGVKGDVAV..I.SPNSKVNTL.KELH
Retrocopy IVAYRTIGILSRFCDFRIL*SQGYIRRNFT>SSASL-TRTHINYGVKGDVAVI*IKSPNSKVNTLNKELH

Parental  SEFSEVMNEIWASDQIRSAVLISSKPGCFIAGADINMLAACKTLQEVTQLSQEAQRIVEKLEKSTKPIVA
          SEF.EVMNE.WA..QI.SAVLISSKPGCFIAGADINMLA.CKT.QEVTQ.SQEA.R..EKLEK.TKP..A
Retrocopy SEFTEVMNEVWATNQITSAVLISSKPGCFIAGADINMLATCKTPQEVTQISQEARRTFEKLEKATKPVIA

Parental  AINGSCLGGGLELAISCQYRIATKDRKTVLGTPEVLLGALPGAGGTQRLPKMVGVPAALDMMLTGRSIRA
          ...GSCLGG.L.LAISCQYRIATKD.KT.LG.PEVLLG.LPGAGGTQRLPKMVGVPAA..MMLT.R.IRA
Retrocopy SVSGSCLGGRLQLAISCQYRIATKDGKTILGAPEVLLGILPGAGGTQRLPKMVGVPAAFVMMLTSRNIRA

Parental  DRAKKMGLVDQLVEPLGPGLKPPEERTMEYLEEVAITFAKGLADKKISPKRDKGLVEKLTAYAMTIPFVR
          DRAKKMGLVDQLVEPLGPGLKP.EE.T.EYLEEVAITFAKGLADKKISPKRDKGLVEKLT.Y.MTIPFVR
Retrocopy DRAKKMGLVDQLVEPLGPGLKPAEEWTIEYLEEVAITFAKGLADKKISPKRDKGLVEKLTVYTMTIPFVR

Parental  QQVYKKVEEKVRKQTKGLYPAPLKIIDVVKTGIEQGSDAGYLSESQKFGELVMTKESKALMGLYHGQVLC
          QQVYKKVEEKV.K.T.GLYPAPLKIIDVVKT.IE.GSDAGYLSESQKFG.L.MT.ESKALMGLY.GQVLC
Retrocopy QQVYKKVEEKVQKETNGLYPAPLKIIDVVKTEIE*GSDAGYLSESQKFGDLAMTSESKALMGLYRGQVLC

Parental  KKNKFGAPQKDVKHLAILGAGLMGAGIAQVSVDKGLKTILKDATLTALDRGQQQVFKGLNDKVKKKALTS
          KKN.FGAPQKD.K.LAILG.GL.GAGI..VSVDK.LKTILKDATL..L...QQ.VFKGLNDKVKKKALTS
Retrocopy KKNQFGAPQKDAKRLAILGEGLKGAGIT*VSVDKRLKTILKDATLARLGQRQQRVFKGLNDKVKKKALTS

Parental  FERDSIFSNLTG
          FERDSIFSNLTG
Retrocopy FERDSIFSNLTG

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	49.76 RPM
SRP007412_cerebellum	0.00 RPM	45.60 RPM
SRP007412_heart	0.00 RPM	218.31 RPM
SRP007412_kidney	0.00 RPM	139.08 RPM
SRP007412_liver	0.06 RPM	94.41 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_817 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_817 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_817 has 0 orthologous retrocopies within eutheria group .

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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,