RetrogeneDB ID: retro_ptro_664

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:8858020..8859313(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HADHA
• Ensembl ID: ENSPTRG00000011732
• Aliases: None
• Description: None

Sequence

>retro_ptro_664
ATGGTGGCCTACCGGGCGATTGGCATCCTCAGCCGCTTCTCTGACTTCAGGATCCTCTGATCCTAAGGTTATAGACGCCG
CAATTTTACAGAGTCTTCTGCTTTGCTGACCAGAACCCATATTAACTATGGAGTCAAAGGGGATGTGGCAGTTATTCGAA
TTAAATCTTCCACTTCAAAGGTAAATACACTGAGTAAAGAGCTGCATTCAGAGTTCATGGAAGTTATGAATGAAGTCTGG
GCTACTAATCAAATCAGAAATGCTGTCCTTATTTCATCAAAGCCAGGCCGCTTTATTGCAGGTGCTGATATAAATATGTT
AGCCACTTGCAAGACCCCTCAAGAAGTAACACAGGTATCACAAGAAGCACAGAGAACATTTGAGAAACTTGAAAAGGCCA
CAAAGCCTGTTATAGCTGCCATCAGTGGATCCTGCCTGGGAGGAGGGCTTGAGCTTGCCATTTCATGCCAATACAGAATA
GCAACAAAAGATGGAAAAACAATATTAGGTGCCCCTGAAGTCTTGCTGGGGATCTTACCAGGAGCAGGAGGCACACAAAG
GCTGCCCGAAATGGTGGGTGTGCCTGCTCTTTTTGACATGATGCTGACTAGTAGAAACATTCATGCAGATAGCGCAAAGA
AAATGGGACTGGTTGACCAATTGGTAGAACCCCTGGGACCGGGAATAAAACCTCCAGAGGAATGGACAATCGAATACCTG
GAAGCAGTTGCAATTACTTTTGCCAAAGGACTAGCTGATAAGAAGATCTCTCCAAAGAGAGACAAGGGATTGGTGGAAAA
ATTGACAGCGTACACCATGACTATTCCATTTGTCAGGCAACAGGTTTACAAAAAAGTGGAAGAAAAAGTGCAAAAGGAGA
CTAAAGGCCTTTATCCTGCACCTCTGAAAATAATTGACGTGGTAAAGACTGGAATTGAGCGAGGGAGTGATGCTGGTTAT
CTCTCTGAATCTCAGAAATTTGGATCACTTGCAATGATCAGTGAATCAAAGGCCTTGATGGGTCTCTACCATGGTCAGGT
CTTGTGCAAGAAGAATAAATTTGGAGCACCACAGAAGGATGTTAAGCGTCTGGCTATTCTTGGTGAAGGGCTGAAGGGAG
CAGGCATCACCCAAGTCTCTGTGGATAAGAGGCTAAAGACTATACTTAAAGATGCCACACTCACTAGGCTAGGCCAAGGA
CAGCAACAAGTGTTCAAAGGATTGAATGATAAAGTGAATAAGAAAGCTCTAACATCATTTGAAAGGGATTCCATCTTCAG
CAACTTGACTGGG

Alignment

ORF - retro_ptro_664 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.54 %
• Parental protein coverage: 56.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVACRAIGILSRFSAFRILRSRGYICRNFTGSSALLTRTHINYGVKGDVAVVRINSPNSKVNTLSKELHS
          MVA.RAIGILSRFS.FRIL.S.GY..RNFT.SSALLTRTHINYGVKGDVAV.RI.S..SKVNTLSKELHS
Retrocopy MVAYRAIGILSRFSDFRIL*S*GYRRRNFTESSALLTRTHINYGVKGDVAVIRIKSSTSKVNTLSKELHS

Parental  EFSEVMNEIWASDQIRSAVLISSKPGCFIAGADINMLAACKTLQEVTQLSQEAQRIVEKLEKSTKPIVAA
          EF.EVMNE.WA..QIR.AVLISSKPG.FIAGADINMLA.CKT.QEVTQ.SQEAQR..EKLEK.TKP..AA
Retrocopy EFMEVMNEVWATNQIRNAVLISSKPGRFIAGADINMLATCKTPQEVTQVSQEAQRTFEKLEKATKPVIAA

Parental  INGSCLGGGLEVAISCQYRIATKDRKTVLGTPEVLLGALPGAGGTQRLPKMVGVPAALDMMLTGRSIRAD
          I.GSCLGGGLE.AISCQYRIATKD.KT.LG.PEVLLG.LPGAGGTQRLP.MVGVPA..DMMLT.R.I.AD
Retrocopy ISGSCLGGGLELAISCQYRIATKDGKTILGAPEVLLGILPGAGGTQRLPEMVGVPALFDMMLTSRNIHAD

Parental  RAKKMGLVDQLVEPLGPGLKPPEERTIEYLEEVAITFAKGLADKKISPKRDKGLVEKLTAYAMTIPFVRQ
          .AKKMGLVDQLVEPLGPG.KPPEE.TIEYLE.VAITFAKGLADKKISPKRDKGLVEKLTAY.MTIPFVRQ
Retrocopy SAKKMGLVDQLVEPLGPGIKPPEEWTIEYLEAVAITFAKGLADKKISPKRDKGLVEKLTAYTMTIPFVRQ

Parental  QVYKKVEEKVRKQTKGLYPAPLKIIDVVKTGIEQGSDAGYLSESQKFGELVMTKESKALMGLYHGQVLCK
          QVYKKVEEKV.K.TKGLYPAPLKIIDVVKTGIE.GSDAGYLSESQKFG.L.M..ESKALMGLYHGQVLCK
Retrocopy QVYKKVEEKVQKETKGLYPAPLKIIDVVKTGIERGSDAGYLSESQKFGSLAMISESKALMGLYHGQVLCK

Parental  KNKFGAPQKDVKHLAILGAGLMGAGIAQVSVDKGLKTILKDATLTALDRGQQQVFKGLNDKVKKKALTSF
          KNKFGAPQKDVK.LAILG.GL.GAGI.QVSVDK.LKTILKDATLT.L..GQQQVFKGLNDKV.KKALTSF
Retrocopy KNKFGAPQKDVKRLAILGEGLKGAGITQVSVDKRLKTILKDATLTRLGQGQQQVFKGLNDKVNKKALTSF

Parental  ERDSIFSNLTG
          ERDSIFSNLTG
Retrocopy ERDSIFSNLTG

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	74.68 RPM
SRP007412_cerebellum	0.00 RPM	91.70 RPM
SRP007412_heart	0.15 RPM	327.92 RPM
SRP007412_kidney	0.05 RPM	220.98 RPM
SRP007412_liver	0.07 RPM	126.62 RPM
SRP007412_testis	0.11 RPM	184.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_664 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_664 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_664 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_958
Gorilla gorilla	retro_ggor_772
Macaca mulatta	retro_mmul_787

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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,
Pan troglodytes	ENSPTRG00000011732	2 retrocopies	retro_ptro_2109, retro_ptro_664 ,
Pan troglodytes	ENSPTRG00000016351	1 retrocopy	retro_ptro_1058,
Ictidomys tridecemlineatus	ENSSTOG00000001593	1 retrocopy	retro_itri_681,