RetrogeneDB ID: retro_ptro_140

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:39783826..39785375(+)
• Located in intron of: ENSPTRG00000000572

Retrocopy information

• Ensembl ID: ENSPTRG00000040091
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OXCT1
• Ensembl ID: ENSPTRG00000016829
• Aliases: None
• Description: Succinyl-CoA:3-ketoacid-coenzyme A transferase [Source:UniProtKB/TrEMBL;Acc:H2QQT8]

Sequence

>retro_ptro_140
ATGGCAGCGCTGCGGCTCCTGGCGTCGGTGCTCGGGCGCGGGGTCCCCGCCGGCGGCTCAGGGCTCGCGCTGTCCCAGGG
CTGCGCCCGCTGCTTTGCCACCAGTCCCCGGCCCCGTGCCAAGTTCTACGCGGACCCGGTGGAGATGGTGAAGGACATCT
CTGACGGGGCGACCGTCATGATCGGGGGCTTCGGGCTCTGCGGGATCCCCGAGAACCTGATCGCCGCGCTGCTCAGGACC
CGCGTGAAAGACCTGCAGGTGGTCAGCAGCAACGTGGGCGTGGAGGACTTCGGCCTGGGCCTCCTGCTGGCCACCAGGCA
GGTCCGTCGCATCGTCTGTTCCTACGTGGGCGAGAACACCCTGTGCGAGAGCCAGTACCTGGCAGGAGAGCTGGAGCTGG
AGCTCACGCCCCAGGGCACCCTGGCCGAGCGCATCCGCGCGGGGGGCGCCGGGGTGCCCGCCTTCTACACCCCCACGGGC
TACGGGACCCTGGTCCAGGAAGGGGGCGCCCCCATCCGCTACACCCCGGACGGCCACCTGGCGCTCATGAGCCAGCCCCG
AGAGGTGAGGGAGTTCAACGGCGACCACTTCCTTTTGGAGCGCGCCATCCGGGCAGACTTCGCCCTGGTGAAAGGGTGGA
AGGCCGACCGGGCAGGAAACGTGGTCTTCAGGAGAAGCGCCCGCAATTTCAACGTGCCCATGTGCAAAGCTGCAGACGTC
ACGGCGGTGGAGGTGGAAGAGATCGTGGACGTGGGGGCTTTCCCCCCAGAAGACATCCACGTTCCTAACATTTATGTAGA
TCGCGTGATAAAGGGGCAGAAATACGAGAAACGAATTGAGCGCTTAACGATCCGGAAAGAGGAAGATGGAGACGCTGGAA
AGGAAGAGGACGCCAGGACGCGCATCATCAGACGCGCAGCTCTGGAATTTGAGGACGGCAATGTACGCCAATCTGGGCAT
AGGCATCCCCCTGCTGGCCAGCAACTTCATCAGTCCCAGCATGACTGTCCATCTTCACAGTGAGAACGGGATCCTGGGCC
TGGGCCCGTTTCCCACGGAAGATGAGGTGGATGCCGACCTCATCAATGCAGGCAAGCAGACGGTCACGGTGCTTCCCGGG
GGCTGCTTCTTCGCCAGCGACGACTCCTTCGCCATGATCCGAGGGGGACACATCCAACTAACCATGCTTGGAGCCATGCA
GGTTTCCAAATACGGCGACCTGGCGAACTGGATGATCCCTGGCAAGAAGGTGAAAGGCATGGGCGGTGCCATGGACTTGG
TGTCCAGTCAGAAGACCAGAGTGGTGGTCACCATGCAGCACTGCACAAAGGACAACACCCCCAAGATCATGGAGAAATGC
ACCATGCCGCTGACCGGGAAGCGGTGCGTGGACCGCATCATCACCGAGAAGGCCGTGTTTGACGTGCACAGGAAGAAAGG
GCTGACGCTGAGGGAGCTCTGGGAGGGCCTGACGGTGGACGACATCAAAAAGAGCACGGGGTGTGCCTTTGCTGTGTCCC
CGAACCTCAGGCCCATGCAGCAGGTGGCA

Alignment

ORF - retro_ptro_140 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.42 %
• Parental protein coverage: 99.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAALKLLSSGLRLCASARGSRGTWYKGCVCSFSTSAHRHTKFYTDPVEAVKDIPDGATVLVGGFGLCGIP
          MAAL.LL.S.L.....A.GS......GC...F.TS.....KFY.DPVE.VKDI.DGATV..GGFGLCGIP
Retrocopy MAALRLLASVLGRGVPAGGSGLALSQGCARCFATSPRPRAKFYADPVEMVKDISDGATVMIGGFGLCGIP

Parental  ENLIDALLKTGVKGLTAVSNNAGVDNFGLGLLLRSKQIKRMISSYVGENAEFERQYLSGELEVELTPQGT
          ENLI.ALL.T.VK.L..VS.N.GV..FGLGLLL...Q..R...SYVGEN...E.QYL.GELE.ELTPQGT
Retrocopy ENLIAALLRTRVKDLQVVSSNVGVEDFGLGLLLATRQVRRIVCSYVGENTLCESQYLAGELELELTPQGT

Parental  LAERIRAGGAGVPAFYTPTGYGTLVQEGGSPIKYNKDGSVAIASKPREVREFNGQHFILEEAITGDFALV
          LAERIRAGGAGVPAFYTPTGYGTLVQEGG.PI.Y..DG..A..S.PREVREFNG.HF.LE.AI..DFALV
Retrocopy LAERIRAGGAGVPAFYTPTGYGTLVQEGGAPIRYTPDGHLALMSQPREVREFNGDHFLLERAIRADFALV

Parental  KAWKADRAGNVIFRKSARNFNLPMCKAAETTVVEVEEIVDIGAFAPEDIHIPQIYVHRLIKGEKYEKRIE
          K.WKADRAGNV.FR.SARNFN.PMCKAA..T.VEVEEIVD.GAF.PEDIH.P.IYV.R.IKG.KYEKRIE
Retrocopy KGWKADRAGNVVFRRSARNFNVPMCKAADVTAVEVEEIVDVGAFPPEDIHVPNIYVDRVIKGQKYEKRIE

Parental  RLSIRKEGDGEAKSAKPGDDVRERIIKRAALEFEDG-MYANLGIGIPLLASNFISPNITVHLQSENGVLG
          RL.IRKE.DG.A.......D.R.RII.RAALEFEDG.MYANLGIGIPLLASNFISP..TVHL.SENG.LG
Retrocopy RLTIRKEEDGDAGKE---EDARTRIIRRAALEFEDG>MYANLGIGIPLLASNFISPSMTVHLHSENGILG

Parental  LGPYPRQHEADADLINAGKETVTILPGASFFSSDESFAMIRGGHVNLTMLGAMQVSKYGDLANWMIPGKM
          LGP.P...E.DADLINAGK.TVT.LPG..FF.SD.SFAMIRGGH..LTMLGAMQVSKYGDLANWMIPGK.
Retrocopy LGPFPTEDEVDADLINAGKQTVTVLPGGCFFASDDSFAMIRGGHIQLTMLGAMQVSKYGDLANWMIPGKK

Parental  VKGMGGAMDLVSSAKTKVVVTMEHSAKGNAHKIMEKCTLPLTGKQCVNRIITEKAVFDVDKKKGLTLIEL
          VKGMGGAMDLVSS.KT.VVVTM.H..K.N..KIMEKCT.PLTGK.CV.RIITEKAVFDV..KKGLTL.EL
Retrocopy VKGMGGAMDLVSSQKTRVVVTMQHCTKDNTPKIMEKCTMPLTGKRCVDRIITEKAVFDVHRKKGLTLREL

Parental  WEGLTVDDVQKSTGCDFAVSPKLMPMQQIA
          WEGLTVDD..KSTGC.FAVSP.L.PMQQ.A
Retrocopy WEGLTVDDIKKSTGCAFAVSPNLRPMQQVA

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	1.43 RPM	61.35 RPM
SRP007412_cerebellum	2.15 RPM	92.74 RPM
SRP007412_heart	0.17 RPM	207.52 RPM
SRP007412_kidney	0.24 RPM	260.89 RPM
SRP007412_liver	0.16 RPM	1.60 RPM
SRP007412_testis	246.39 RPM	16.97 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

2 EST(s) were mapped to retro_ptro_140 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DC529450	39783800	39784206	96.7	387	4	376
DC529588	39783822	39784221	99	383	1	380

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_140 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_140 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2256
Bos taurus	retro_btau_1302
Equus caballus	retro_ecab_511

---

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,