RetrogeneDB ID: retro_ggor_378

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:41022793..41023672(-)
• Located in intron of: ENSGGOG00000015791

Retrocopy information

• Ensembl ID: ENSGGOG00000015797
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OXCT1
• Ensembl ID: ENSGGOG00000025087
• Aliases: None
• Description: Succinyl-CoA:3-ketoacid-coenzyme A transferase [Source:UniProtKB/TrEMBL;Acc:G3S0S5]

Sequence

>retro_ggor_378
ATGGCGGCGCTGCGGCTCCTGGCGTCGGTGCTCGGGCGCGGGGTCCCTGCCGGCGGCTCAGGGCTCGCGCTGTCCCAGGG
CTGCGCCCGCTGCTTTGCCACCAGCCCCCGGCCCCGCGCCAAGTTCTACGCGGACTCGGTGGAGATGGTGAAGGACATCT
CTGACGGGGCGACCGTCATGATCGGGGGCTTCGGGCTCTGCGGGATCCCCGAGAACCTGATCGCCGCGCTGCCCGGGACC
CGCGTGAAGCACCTGCAGGTGGTCAGCAGCAACGTGGGCGTGGAGGACTTCGGCCTGGGCCTCCTGCTGGCCGCTCGGCA
GGTCCGCGGCATCGTCTGTTTCTACGTGGGCGAGAACACGCTGTGCAAGAGCCAGTACCTGGCAGGAGAGCTGGAGCTGG
AGCTCACGCCCCAGGGCACCCTGGCCGAGCGCATCCGCGCGGGGGGCGCTGGGGTGCCCGCCTTCTACACTCCCACGGGC
TACGGGACCCTGGTCCAGGAAGGGGGCGCCCCCATCCGCTACACCCCGGACGGCCACCTGGCGCTCATGAGCCAGCCCCG
AGAGGTGAGGGAGTTCCACGGCGACCACTTCGTTTTGGAGCGCGCCATCCGGGCGGACTTCGCCCCAATGAACGGGTGGA
AGGCCGACCCCGCAGGAAACGTGGTCTTCAGGAGAAGCGCCCGCAATTTCAACGTGCCCATGTGCAAAGCTGCAGACGTC
ACGGCGGTGGAGGTGGAAGAGATCGTGGACGTGGGGGCTTTCCCCCCAGAAGACATCCACGTTCCTAACATTTATGTAGA
TCGCATAATAAAGAGGCAGAAATGCGAGAAACTAATCGAGCGCTTAACGATCAGGAAAGAGGAAGATGGAGACGCCGAA

Alignment

ORF - retro_ggor_378 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.89 %
• Parental protein coverage: 56.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAALKLLSSGLRLCASARGSGGTWYKGWVCSFSTSAHRHTKFYTDPVEAVKDIPDGATVLVGGFGLCGIP
          MAAL.LL.S.L.....A.GSG.....G....F.TS.....KFY.D.VE.VKDI.DGATV..GGFGLCGIP
Retrocopy MAALRLLASVLGRGVPAGGSGLALSQGCARCFATSPRPRAKFYADSVEMVKDISDGATVMIGGFGLCGIP

Parental  ENLIDALLKTGVKGLTAVSNNAGVDNFGLGLLLRSKQIKRMVSSYVGENAEFERQYLSGELEVELTPQGT
          ENLI.AL..T.VK.L..VS.N.GV..FGLGLLL...Q....V..YVGEN.....QYL.GELE.ELTPQGT
Retrocopy ENLIAALPGTRVKHLQVVSSNVGVEDFGLGLLLAARQVRGIVCFYVGENTLCKSQYLAGELELELTPQGT

Parental  LAERIRAGGAGVPAFYTPTGYGTLVQEGGSPIKYNKDGSVAIASKPREVREFNGQHFILEEAITGDFALV
          LAERIRAGGAGVPAFYTPTGYGTLVQEGG.PI.Y..DG..A..S.PREVREF.G.HF.LE.AI..DFA..
Retrocopy LAERIRAGGAGVPAFYTPTGYGTLVQEGGAPIRYTPDGHLALMSQPREVREFHGDHFVLERAIRADFAPM

Parental  KAWKADRAGNVIFRKSARNFNLPMCKAAETTVVEVEEIVDIGAFAPEDIHIPQIYVHRLIKGEKYEKRIE
          ..WKAD.AGNV.FR.SARNFN.PMCKAA..T.VEVEEIVD.GAF.PEDIH.P.IYV.R.IK..K.EK.IE
Retrocopy NGWKADPAGNVVFRRSARNFNVPMCKAADVTAVEVEEIVDVGAFPPEDIHVPNIYVDRIIKRQKCEKLIE

Parental  RLSIRKEGDGEAK
          RL.IRKE.DG.A.
Retrocopy RLTIRKEEDGDAE

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	0.29 RPM	154.03 RPM
SRP007412_cerebellum	0.32 RPM	84.51 RPM
SRP007412_heart	0.28 RPM	121.30 RPM
SRP007412_kidney	0.04 RPM	161.31 RPM
SRP007412_liver	0.00 RPM	5.06 RPM
SRP007412_testis	11.40 RPM	53.56 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_378 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_378 has 0 orthologous retrocopies within eutheria group .

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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,