RetrogeneDB ID: retro_ecab_511

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:18488142..18489687(-)
• Located in intron of: ENSECAG00000010065

Retrocopy information

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

Parental gene information

• Parental gene symbol: OXCT1
• Ensembl ID: ENSECAG00000018312
• Aliases: None
• Description: Succinyl-CoA:3-ketoacid-coenzyme A transferase [Source:UniProtKB/TrEMBL;Acc:F7A396]

Sequence

>retro_ecab_511
ATGGCGGGCCTAGTGGTACTCTCGGCGGCGCTCGGGCGCCGCGTCTCTACCGGTCGCTCGGGGCGCGCGCTGGCCGAGGG
CGGGGTGTGCGGCTTCGCCAGCAGCGCTCGCGCCCGCGCCCGGTTCTACACGGATCCCGTGGAGGCGGTGAGAGACATCG
CCGACGGGGCGAAGATCATGGTCGGGGGCTTCGGGCTCTGTGGGATTCCGGAGAACCTGATCCGGGCGCTGCTCAAGACC
CGCGTGAGAGACTTGACCGTGGTCAGCAGCAACGTGGGGGTGGACGACTTCGGGCTGGGCCTGCTGCTGGGGACCAAGCA
GATCACCCGCATCATCTGCTCTTACGCGGGAGAGAACGCGCTGTGCGAGCAGCAGTACCTGGCGGGCGAGCTGGAGCTGG
AGCTGACGCCCCAGGGCACCCTGGCCGAGCGCATCCGCGCCGGCGGGGCCGGAGTGCCCGCCTTCTACACGCCCACGGCC
TACGGGACCCTGGTGCAGGAAGGCGGCGCCCCCATCAGGTACTTCCAGGACGGCCACATCGCCATCCTGAGTCAGCCGAG
AGAGGTGCGGGAGTTCCACGGGCACCACTACCTCCTGGAGCACGCCATCACGGCGGATTTCGCTTTGGTCAAAGGGTGGA
AGGCCGACCGCGCAGGAAACGTCATCTTCAGGCGAAGCGCCAGGAATTTCAACGTGCCCATGTGCAAAGCTGCGAACACC
TCGGTGGTCGAAGTTGAAGAAATTGTGGATGTGGGGTCGTTTGCCCCAGAAGACATCCATGTTCCTAACATTTATGTAGA
TCGCGTCATCCAGGGGGAGAAATATGAGAAAAGAATTGAGCGTTTAACAATCCGGAAGGAGGAAAGTGGAAAAGCCAAGG
CTGCCGAGGATATAAGAACATGGATCATCAAGCGGGCGGCTCTCGAATTTGAGGATGGCATGTATGCCAATCTGGGCATA
GGCATCCCTCTTCTGGCCAGCAACTACATCAGCCCGAATATAACCGTCCACCTTCACAGCGAGAACGGCATCCTGGGCTT
GGGTCCGTTCCCACGGAAAGACCAGGTGGATGCAGACCTCATCAATGCCGGCAAGCAAACCGTCACCATTTTCCCCGGGG
GCTGTTTCTTCTCCAGCGATGACTCGTTTGCCATGATCCGAGGGGGACACATCCACCTCACCATGCTGGGAGCCATGCAG
GTGTCCAAATACGGCGACCTGGCCAACTGGATGATCCCCGGAAAGAGGGTGAAGGGCATGGGGGGTGCGATGGATTTGGT
GTCCAGTGCCAAGACCAGGGTGGTGGTCACCATGGAGCACTCCACCAAGGCCAACGAACCCAAAATCTTGGAGAAATGCA
CGATGCCCCTGACCGGGAAGCGGTGCGTGGACCGAGTCATCACGGAGAGGGCCGTGTTTGACGTGGACAAGAAGAGAGGG
CTGACGCTGACCGAGCTCTGGGAAGGCCTGACGGTGGAGGACATCAGGAAGAGCACGGGGAGCACCTTCGCCGTCTCCCC
CGATCTCAGACCCATGCAGCAGGTG

Alignment

ORF - retro_ecab_511 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.13 %
• Parental protein coverage: 99.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAALKLLSSWQRPWASARGSGGAWLKGCVCYFSTSTRHHTKFYTDPVEAVKDIPDGATVLVGGFGLCGIP
          MA.L..LS.......S...SG.A...G.VC.F..S.R....FYTDPVEAV.DI.DGA...VGGFGLCGIP
Retrocopy MAGLVVLSAALGRRVSTGRSGRALAEGGVCGFASSARARARFYTDPVEAVRDIADGAKIMVGGFGLCGIP

Parental  ENLIGALLKTGVKGLTAVSNNAGVDNFGLGLLLRSKQIKRMVSSYVGENAEFERQYLAGELEVELTPQGT
          ENLI.ALLKT.V..LT.VS.N.GVD.FGLGLLL..KQI.R...SY.GENA..E.QYLAGELE.ELTPQGT
Retrocopy ENLIRALLKTRVRDLTVVSSNVGVDDFGLGLLLGTKQITRIICSYAGENALCEQQYLAGELELELTPQGT

Parental  LAERIRAGGAGVPAFYTSTGYGTLVQEGGSPIKYNTDGSIAIASKPREVREFNGQNFILEEAITGDFALV
          LAERIRAGGAGVPAFYT.T.YGTLVQEGG.PI.Y..DG.IAI.S.PREVREF.G....LE.AIT.DFALV
Retrocopy LAERIRAGGAGVPAFYTPTAYGTLVQEGGAPIRYFQDGHIAILSQPREVREFHGHHYLLEHAITADFALV

Parental  KAWKADRAGNVIFRKSARNFNLPMCKAAETTVVEVEEIVDIGSFAPEDIHIPKIYVHRLIKGEKYEKRIE
          K.WKADRAGNVIFR.SARNFN.PMCKAA.T.VVEVEEIVD.GSFAPEDIH.P.IYV.R.I.GEKYEKRIE
Retrocopy KGWKADRAGNVIFRRSARNFNVPMCKAANTSVVEVEEIVDVGSFAPEDIHVPNIYVDRVIQGEKYEKRIE

Parental  RLSVRKEGDVKAKSGKPGDNVRERIIKRAALEFEDGMYANLGIGIPLLASNFISPDMTVHLQSENGILGL
          RL..RKE...KAK........R..IIKRAALEFEDGMYANLGIGIPLLASN.ISP..TVHL.SENGILGL
Retrocopy RLTIRKEESGKAKA---AEDIRTWIIKRAALEFEDGMYANLGIGIPLLASNYISPNITVHLHSENGILGL

Parental  GPYPLQNEVDPDLINAGKETVTVLPGAAYFSSDESFAMIRGGHVNLTMLGAMQVSKYGDLANWMIPGKMV
          GP.P....VD.DLINAGK.TVT..PG...FSSD.SFAMIRGGH..LTMLGAMQVSKYGDLANWMIPGK.V
Retrocopy GPFPRKDQVDADLINAGKQTVTIFPGGCFFSSDDSFAMIRGGHIHLTMLGAMQVSKYGDLANWMIPGKRV

Parental  KGMGGAMDLVSSARTKVVVTMEHSAKGNTHKILEKCTLPLTGKQCVNRIITEKAVFDVDNKKGLTLIELW
          KGMGGAMDLVSSA.T.VVVTMEHS.K.N..KILEKCT.PLTGK.CV.R.ITE.AVFDVD.K.GLTL.ELW
Retrocopy KGMGGAMDLVSSAKTRVVVTMEHSTKANEPKILEKCTMPLTGKRCVDRVITERAVFDVDKKRGLTLTELW

Parental  EGLTVDDIKKSTGCDFAVSPKLMPMRQI
          EGLTV.DI.KSTG..FAVSP.L.PM.Q.
Retrocopy EGLTVEDIRKSTGSTFAVSPDLRPMQQV

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
SRP021940_articular_cartilage	3.31 RPM	42.74 RPM
SRP021940_cerebellum	14.13 RPM	17.24 RPM
SRP021940_embryo	0.56 RPM	24.75 RPM
SRP021940_placental_villous	1.92 RPM	7.46 RPM
SRP021940_synovial_membrane	0.85 RPM	21.96 RPM
SRP021940_testis	410.52 RPM	5.63 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_511 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_511 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_511 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_140
Rattus norvegicus	retro_rnor_2256
Bos taurus	retro_btau_1302

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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,