RetrogeneDB ID: retro_ocun_672

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:126983006..126984428(-)
• Located in intron of: ENSOCUG00000023797

Retrocopy information

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

Parental gene information

• Parental gene symbol: OXCT1
• Ensembl ID: ENSOCUG00000009231
• Aliases: None
• Description: 3-oxoacid CoA transferase 1 [Source:HGNC Symbol;Acc:8527]

Sequence

>retro_ocun_672
TTCTACACGGACCCCGTGGAGATGGTGAAGGACATCTCCGATGGGGCGACCGTCATGGTCGGGGGCTTCGGGCTCTGCGG
GATCCCCGAGAACCTGATCGCGGCGCTGCTGCGGACGCGCGTGAGGGACTTGCGGGTGATCAGCAGCAACGTGGGCGTGG
ACGACTTCGGCCTGGGCCTCCTCCTGGCCACCAAGCAGATCCGCCGCATCGTGTGCTCGTACCTGGGCGAGAACGCGCTG
TGCGAGCGCCAGTACCTGGCCGGCGAGCTGGAGCTGGAGCTGACGCCGCAGGGCACCCTGGCCGAGCGCATCCGCGCGGG
CGGCGCCGGGGTGCCGGCCTTTTACACGCCCACGGCCTACGGGACGCTGGTGCAGGAAGGGGGCGCCCCCATCCGCTACT
ACCCGGACGGCCACTTGGCCATCCGCAGCCAGCCCCGGGAGGTGAGGGAGTTCGAGGGCCGCCACTACCTGCTGGAGCGC
GCGCTCAGGGCCGACTTCGCGCTCGTCAAGGGCTGGAAGGCCGACCGCGCGGGCAACGTGGTCTTCAGGGGCAGCGCCAG
GAACTTCAACGCGCCCATGTGCAAAGCCGCCGACGTGGCGGCCGTGGAGGTGGAAGAGATCGTGGACGTGGGCGCTTTCC
GCCCGGAAGACATCCACGTGCCCAACATCTACGTGGACCGCGTGATCAAGGGCCGCGCGTTCGAGAAGCGGATCGAGCGC
CTGACCGTGCGGCCCGAGGTCGCCGCGGGCGCCTGCGCGGGAGCCAACGCGAGGACGCGCATCGTCAAGCGCGCAGCCCT
GGAGTTCGAGGACGGCATGTACGCCAGCCTGGGCATAGGCATCCCTCTGCTGGCCAGCAACTTCATCCGCCCGGGCGTCA
CGGTCCACCTGCACAGCGAGAACGGCATCCTGGGCCTGGGCCCCTTCCCGACCAGAGGGGAGGCGGATGCCGACGTCATC
AACGCGGGCAAGCAGACGGTCACCGTGCTGCCCGGCGGCTCTTTCTTCTCCAGCGACGACTCCTTCGCCATGATCCGCGG
GGGACACATCCAGCTGACCATGCTGGGGGCCATGCAGGTCTCCAAATACGGGGACCTGGCCAACTGGATGATCCCCGGCA
AGAAGGTGAAAGGGAAGGGCGGGGCCATGGATTTGGTGTCCAGTGACAAGACCAAAGTGGTGGTCACCATGGAGCACTGC
ACCAAGGACAAGAGCCCCAAGATCCTGGACAAGTGCAGCATGCCGCTGACCGGGAAGCAGTGCGTGGACCGCATCATCAC
TGAGAAGGCCGTGTTCGACGTGCACAAGAAGAGGGGGCTGACGCTCATCGAGCTCTGGGAGGGCCTGACCGTGACCGACG
TCCAGAACAGCACGGGCTGCGCCTTTGCCGTATCTCCCAACCTCAGGCCCATGCAGCAGGTG

Alignment

ORF - retro_ocun_672 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.17 %
• Parental protein coverage: 91.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FYADPVEAVKDIPDGATILVGGFGLCGIPENLIGALLKTGVKGLTAVSNNAGVDNFGLGLLLRSKQIKRM
          FY.DPVE.VKDI.DGAT..VGGFGLCGIPENLI.ALL.T.V..L...S.N.GVD.FGLGLLL..KQI.R.
Retrocopy FYTDPVEMVKDISDGATVMVGGFGLCGIPENLIAALLRTRVRDLRVISSNVGVDDFGLGLLLATKQIRRI

Parental  VSSYVGENAEFERQFLSGELEVELTPQGTLAERIRAGGAGVPAFYTSTGYGTLVQEGGSPIKYNKDGSIA
          V.SY.GENA..ERQ.L.GELE.ELTPQGTLAER..........FYT.T.YGTLVQEGG.PI.Y..DG..A
Retrocopy VCSYLGENALCERQYLAGELELELTPQGTLAERXXXXXXXXXXFYTPTAYGTLVQEGGAPIRYYPDGHLA

Parental  IASKPREVREFNGQHFILEEAITGDFALVKAWKADRAGNVIFRKSARNFNLPMCKAAETTVVEVEEIVDI
          I.S.PREVREF.G.H..LE.A...DFALVK.WKADRAGNV.FR.SARNFN.PMCKAA....VEVEEIVD.
Retrocopy IRSQPREVREFEGRHYLLERALRADFALVKGWKADRAGNVVFRGSARNFNAPMCKAADVAAVEVEEIVDV

Parental  GSFAPEDIHIPKIYVHRLIKGEKYEKRIERLSIRKEGDGKAKSTQAGDNVRERIIRRAALEFEDGMYANL
          G.F.PEDIH.P.IYV.R.IKG...EKRIERL..R.E....A....AG.N.R.RI..RAALEFEDGMYA.L
Retrocopy GAFRPEDIHVPNIYVDRVIKGRAFEKRIERLTVRPE---VAAGACAGANARTRIVKRAALEFEDGMYASL

Parental  GIGIPLLASNFISPNMTVHLQSENGVLGLGPYPLQHEADADLINAGKETVTVLPGASFFSSDESFAMIRG
          GIGIPLLASNFI.P..TVHL.SENG.LGLGP.P...EADAD.INAGK.TVTVLPG.SFFSSD.SFAMIRG
Retrocopy GIGIPLLASNFIRPGVTVHLHSENGILGLGPFPTRGEADADVINAGKQTVTVLPGGSFFSSDDSFAMIRG

Parental  GHVNLTMLGAMQVSKYGDLANWMIPGKMVKGMGGAMDLVSSAKTKVVVTMEHSAKGNAHKIMEKCTLPLT
          GH..LTMLGAMQVSKYGDLANWMIPGK.VKG.GGAMDLVSS.KTKVVVTMEH..K....KI..KC..PLT
Retrocopy GHIQLTMLGAMQVSKYGDLANWMIPGKKVKGKGGAMDLVSSDKTKVVVTMEHCTKDKSPKILDKCSMPLT

Parental  GKQCVNRIITEKAVFDVDKKKGLTLIELWEGLTVEDIQKSTGCDFAVSPKLMPMQQI
          GKQCV.RIITEKAVFDV.KK.GLTLIELWEGLTV.D.Q.STGC.FAVSP.L.PMQQ.
Retrocopy GKQCVDRIITEKAVFDVHKKRGLTLIELWEGLTVTDVQNSTGCAFAVSPNLRPMQQV

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
SRP017611_brain	0.33 RPM	59.49 RPM
SRP017611_kidney	0.00 RPM	487.83 RPM
SRP017611_liver	0.00 RPM	4.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_672 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_672 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_672 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_478

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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,