RetrogeneDB ID: retro_btau_1243

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:106902855..106904400(+)
• Located in intron of: ENSBTAG00000017892

Retrocopy information

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

Parental gene information

• Parental gene symbol: OXCT1
• Ensembl ID: ENSBTAG00000033186
• Aliases: None
• Description: succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial [Source:RefSeq peptide;Acc:NP_001069538]

Sequence

>retro_btau_1243
ATGGCGGCCCTGCGGCTCCTGGCGTCGGTGCTCGGGCGCCGGGTCCCCGCCGGCCGCTCGGGGCGCGCGCTGGCGAAGGG
TGGCGCGTGCGGCTTCGCCTGCAGCGCCCCCGCGCGCGTCAGGTTCTACACGGACCCGGTGAAGGCCGTGGGAGACATCA
CTGATGGCTCGAGGATCATGATCGGGGGCTTCGGGCTCTGCGGCATCCCGGAGAACCTGATAGGGGCGCTGCTGAAGACC
CGCGTGAAGGACTTGACTGTGATCAGCAGCAACGTGGGGGTGGAGAGCTTCGGTCTCGGCCTTTTACTGGGGACCAAGCA
GATCACCCGCATCATCTGCTCCTACCTGGGGGAGAACTCGCTCTGTGAGCACCAGTACCTGGCGGGTGAGCTGGAGCTAG
AGATCACGCCCCAGGGCACCCTGGCCGAGCGCATCCGCGCAGGGGGCGCCGGTGTGCCCGCCTTCTACACCCCCACGGCC
TACGGGACCTTGGTCCAGGAGGGAGGCGCACCCATCAGGTACTTACCAGACGGCCACATCGCCATCCTCAGCCAGCCCAG
GGAGGTGAGGGAGTTCCATGGGCAGCACTACCTGCTGGAACACGCCATCTCCGCTGATTTTGCTTTGGTGAAAGGGTGGA
AGGCCGACTGGGCAGGAAATGTCATCTTCAGGGCCAGCGCCAGGAACTTCAACGTGCCCATGTGCAAAGCCGCCAGAACC
TCCGTGGTGGAGGTCGAAGAAATTGTGGACGTGGGGTCCTTTGCCCCAGAAGACATCCATGTTCCTAACATTTATGTAGA
TCGCATAATACAGGGGGAAAAATATGAGAAAAGAATTGAGCGTTTAACCGTCCGGAAAGAGGATGATGAAATTTGCACGT
CTTCAGATAACATAAGGACACGGATCATCAAGCGGGCAGCTCTTGAATTTGAGGATGGCATGTATGCCAATCTGGGCATC
GGCATCCCTCTCCTGGCCCCCAACTACATCAGCCCCAACATCACCGTGCACCTTCACAGTGAGAACGGGATCTTGGGCTT
GGGTCCCTTTCCATTAAAAGAGGAGGTGGACGCGGACCTCATCAACGCGGGCAAGCAGACAGTCACCCTTCTTCCCGGGG
GCTCTTTTTTCTCTAGCGATGAATCATTTGCCATGATTCGAGGGGGGCACATCAACCTGACCTTGCTGGGAGCCATGCAG
GTTTCCAAATACGGTGACCTGGCTAACTGGATGATACCCGGCAAGAAGGTGACAGGCATGGGGGGTGCGATGGATCTGGT
GTCCAGTTCCAAGACTCGAGTGGTAGTCACCATGGAGCACTGCAACAAGGCCAACGAACCCAAGATCGTGGAGAAGTGCA
CCATGCCACTGACTGGGAAGCGGTGCGTGGACCGAATCATCACCGAGAAGGCCGTGTTTGACGTGCACAAGAAGACAGGG
CTGACCCTGATGGAGCTCTGGGACGGCCTAACAGTGGAGGACATCAAAAAGAGCACGGGGAGCCCCTTTGCCGTCTCCCC
GAGCCTCAGACCCATGCAGCAGGTC

Alignment

ORF - retro_btau_1243 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.94 %
• Parental protein coverage: 99.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAALARLSSRLRFCASALSSAGVWSKGCICYFSTSTRHHTKFYTDPVEAVKDIPDGATILVGGFGLCGIP
          MAAL..L.S.L.....A..S.....KG..C.F..S......FYTDPV.AV.DI.DG..I..GGFGLCGIP
Retrocopy MAALRLLASVLGRRVPAGRSGRALAKGGACGFACSAPARVRFYTDPVKAVGDITDGSRIMIGGFGLCGIP

Parental  ENLIGALLKTGVKGLTAVSNNAGVDNFGLGLLLRSKQIKRMVSSYVGENAEFERQYLSGELEVELTPQGT
          ENLIGALLKT.VK.LT..S.N.GV..FGLGLLL..KQI.R...SY.GEN...E.QYL.GELE.E.TPQGT
Retrocopy ENLIGALLKTRVKDLTVISSNVGVESFGLGLLLGTKQITRIICSYLGENSLCEHQYLAGELELEITPQGT

Parental  LAERIRAGGAGVPAFYTSTGYGTLVQEGGSPIKYNKDGSIAIASKPREVREFKGQHFILEEAITGDFALV
          LAERIRAGGAGVPAFYT.T.YGTLVQEGG.PI.Y..DG.IAI.S.PREVREF.GQH..LE.AI..DFALV
Retrocopy LAERIRAGGAGVPAFYTPTAYGTLVQEGGAPIRYLPDGHIAILSQPREVREFHGQHYLLEHAISADFALV

Parental  KAWKADRAGNVIFRKSARNFNLPMCKAAETTVVEVEEIVDIGSFAPEDIHIPKIYVHRLIKGEKYEKRIE
          K.WKAD.AGNVIFR.SARNFN.PMCKAA.T.VVEVEEIVD.GSFAPEDIH.P.IYV.R.I.GEKYEKRIE
Retrocopy KGWKADWAGNVIFRASARNFNVPMCKAARTSVVEVEEIVDVGSFAPEDIHVPNIYVDRIIQGEKYEKRIE

Parental  RLSIRKEEDIKTTSGKPGDNVRERIIKRAALEFEDGMYANLGIGIPLLASNYISPDMTVHLQSENGVLGL
          RL..RKE.D...TS....DN.R.RIIKRAALEFEDGMYANLGIGIPLLA.NYISP..TVHL.SENG.LGL
Retrocopy RLTVRKEDDEICTS---SDNIRTRIIKRAALEFEDGMYANLGIGIPLLAPNYISPNITVHLHSENGILGL

Parental  GPYPLKNEVDADLINAGKETVTVLPGASYFSSDESFAMIRGGHVNLTMLGAMQVSKYGDLANWMIPGKMV
          GP.PLK.EVDADLINAGK.TVT.LPG.S.FSSDESFAMIRGGH.NLT.LGAMQVSKYGDLANWMIPGK.V
Retrocopy GPFPLKEEVDADLINAGKQTVTLLPGGSFFSSDESFAMIRGGHINLTLLGAMQVSKYGDLANWMIPGKKV

Parental  KGMGGAMDLVSSARTKVVVTMEHSAKGNAHKIMEKCTLPLTGKQCVNRIITEKAVFDVDSKKGLTLIELW
          .GMGGAMDLVSS..T.VVVTMEH..K.N..KI.EKCT.PLTGK.CV.RIITEKAVFDV..K.GLTL.ELW
Retrocopy TGMGGAMDLVSSSKTRVVVTMEHCNKANEPKIVEKCTMPLTGKRCVDRIITEKAVFDVHKKTGLTLMELW

Parental  EGLTVDDIKKSTGCDFTVSPKLIPMRQI
          .GLTV.DIKKSTG..F.VSP.L.PM.Q.
Retrocopy DGLTVEDIKKSTGSPFAVSPSLRPMQQV

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
ERP005899_liver	0.00 RPM	1.59 RPM
ERP005899_muscle	0.05 RPM	48.09 RPM
SRP017611_brain	0.05 RPM	20.05 RPM
SRP017611_kidney	0.00 RPM	732.95 RPM
SRP017611_liver	0.00 RPM	1.96 RPM
SRP030211_testis	50.83 RPM	11.38 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

3 EST(s) were mapped to retro_btau_1243 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DT832437	106902828	106903621	100	793	0	793
DY128944	106903064	106903447	98.7	378	5	373
DY139579	106902992	106903307	100	315	0	315

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1243 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1243 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,