RetrogeneDB ID: retro_ggor_772

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 12:8874494..8875787(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000022717
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HADHA
• Ensembl ID: ENSGGOG00000004918
• Aliases: None
• Description: None

Sequence

>retro_ggor_772
ATGGTGGCCTACCGGGCGATTGGCATCCTCAGCCGCTTCTCTGACTTCAGGATCCTCTGATCCCAAGGTTATATACGCCG
CAATTTTACAGAGTCTTCTGCTTTGCTGACCAGAACCCATATTAACTATGGAGTCAAAGGGGATGTGGCAGTTATTCGAA
TTAAATCTTCCACTTCAAAGGTAAATACACTGAGTAAAGAGCTGCATTCAGAGTTCACGGAAGTTATGAATGAAGTCTGG
GCGACTAATCAAATCAGAAATGCTGTCCTTATTTCAGCAAAGCCAGGCCGCTTTATTGCAGGTGCTGATATCAATATGTT
AGCCACTTGCAAGACCCCTCAAGAAGTAACACAGGTATCACAAGAAGCACAGAGAACATTTGAGAAACTTGAAAAGGCCG
CAAAGCCTGTTATAGCTGCCATCAGTGGATCCTGCCTGGGAGGAGGGCTTGAGCTTGCCATTTCATGCCAATACAGAATA
GCAACAAAAGATGGAAAAACAATATTAGGTGCCCCTGAAGTCTTGCTGGGGATCTTACCAGGAGCAGGAGGCACACAAAG
GCTGCCCAAAATGGTGGGTGTGCCTGCTGTTTTTGGCATGATGCTGACTAGTAGAAACATTCATGCAGATAGCGCAAAGA
AAATGGGACTGGTTGACCAATTGGTAGAACCCCTGGGACCGGGAATAAAACCTCCAGAGGAATGGACAATCGAATACCTG
GAAGCAGTTGCAATTACTTTTGCCAAAGGACTAGCTGATAAGAAGATCTCTCCAAAGAGAGACAAGGGATTGGTGGAAAA
ATTGACAGCGTACACCATGACTATTCCATTTGTCAGGCAACAGGTTTACAAAAAAGTGGAAGAAAAAGTGCAAAAGGAGA
CTAAAGGCCTTTATCCTGCACCTCTGAAAATAATTGACGTGGTAAAGACTGGAATTGAGCGAGGGATTGATGCTGGTTAT
CTCTCTGAATCTCAGACATTTGGATAGCTTGCAATGACCAGTGAATCAAAGGCCTTGATGGGTCCCTACCATGGTCAGGT
CTTGTGCAAGAAGAATAAATTTGGAGCACCACAGAAGGATGTTAAGCGTCTGGCTATTCTTGGTGAAGGGCTGAAGGGAG
CAGGCATCTACCAAGTCTCTGTGGATAAGAGGCTAAAGACTATACTTAAAGATGCCACACTCACTAGGCTAGGCCAAGGA
CAGCAACAAGTGTTCAAAGGATTGAATGATAAAGTGAATAAGAAAGCTCTAACATCATTTGAAAGGGATTCCATCTTCAG
CAACTTGACTGGG

Alignment

ORF - retro_ggor_772 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.74 %
• 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.GYI.RNFT.SSALLTRTHINYGVKGDVAV.RI.S..SKVNTLSKELHS
Retrocopy MVAYRAIGILSRFSDFRIL*SQGYIRRNFTESSALLTRTHINYGVKGDVAVIRIKSSTSKVNTLSKELHS

Parental  EFSEVMNEIWASDQIRSAVLISSKPGCFIAGADINMLAACKTLQEVTQLSQEAQRIVEKLEKSTKPIVAA
          EF.EVMNE.WA..QIR.AVLIS.KPG.FIAGADINMLA.CKT.QEVTQ.SQEAQR..EKLEK..KP..AA
Retrocopy EFTEVMNEVWATNQIRNAVLISAKPGRFIAGADINMLATCKTPQEVTQVSQEAQRTFEKLEKAAKPVIAA

Parental  INGSCLGGGLEVAISCQYRIATKDRKTVLGTPEVLLGALPGAGGTQRLPKMVLIFSIPQILFAGKLISIE
          I.GSCLGGGLE.AISCQYRIATKD.KT.LG.PEVLLG.LPGAGGTQRLPKMV..............I...
Retrocopy ISGSCLGGGLELAISCQYRIATKDGKTILGAPEVLLGILPGAGGTQRLPKMVGVPAVFGMMLTSRNIHAD

Parental  HKRKQGLCIAILTPARPGLKPPEERTIEYLEEVAITFAKGLADKKISPKRDKGLVEKLTAYAMTIPFVRQ
          ...K.GL......P..PG.KPPEE.TIEYLE.VAITFAKGLADKKISPKRDKGLVEKLTAY.MTIPFVRQ
Retrocopy SAKKMGLVDQLVEPLGPGIKPPEEWTIEYLEAVAITFAKGLADKKISPKRDKGLVEKLTAYTMTIPFVRQ

Parental  QVYKKVEEKVRKQTKGLYPAPLKIIDVVKTGIEQGSDAGYLSESQKFGELIMTKESKALMGLYHGQVLCK
          QVYKKVEEKV.K.TKGLYPAPLKIIDVVKTGIE.G.DAGYLSESQ.FG.L.MT.ESKALMG.YHGQVLCK
Retrocopy QVYKKVEEKVQKETKGLYPAPLKIIDVVKTGIERGIDAGYLSESQTFG*LAMTSESKALMGPYHGQVLCK

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

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	0.48 RPM	61.24 RPM
SRP007412_cerebellum	0.24 RPM	55.83 RPM
SRP007412_heart	1.34 RPM	181.52 RPM
SRP007412_kidney	0.45 RPM	174.84 RPM
SRP007412_liver	0.21 RPM	116.80 RPM
SRP007412_testis	0.83 RPM	257.65 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_772 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_772 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_958
Pan troglodytes	retro_ptro_664
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	ENSGGOG00000004423	1 retrocopy	retro_ggor_1196,
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,
Ictidomys tridecemlineatus	ENSSTOG00000001593	1 retrocopy	retro_itri_681,