RetrogeneDB ID: retro_rnor_2177

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:144604474..144606028(+)
• Located in intron of: ENSRNOG00000033209

Retrocopy information

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

Parental gene information

• Parental gene symbol: Oxct1
• Ensembl ID: ENSRNOG00000043094
• Aliases: Oxct1, SCOT
• Description: Succinyl-CoA:3-ketoacid coenzyme A transferase 1, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:B2GV06]

Sequence

>retro_rnor_2177
ATGGCGGCGCTGAGGCTTCTGGCCTGGGCGTTCTCACGCCGGGTCTCTGCTCACCGCCCACAGCCCACGTTGCCCCACCA
CCTAATCCGCCACTATCCTACGACCCGCTGCGGGAAAGTTAAATTCTACACGGACCCGGTGAAGGCGGTGGAGGGCATCA
AGGACGGGGCGAGCGTCATGCTCGGGGGCTTCGGGCTCTGCGGCATCCCGGAGAACCTGATTGGTGCGCTGAAGACCAAG
GGCGTGAAGGACCTGAAGATCATCAGCAGCAACGTGGGCGTGGACGACTTCGGCCTGGGCATTTTGCTGGCCTCTAAGCA
GGTCAGGCGCGTGGTGTGCTCCTACCTGGGGGAGAACAAGCTCTGTGAGCAGCTCTACCTAGCGGGGAAGCTGGAGCTGG
AGATGACGCCGCAGGGAACCCTGGCAGAGCGCATCCGCGCGGGTGGCACGGGCGTGCCCGCCTTCTACACGCCCACTGGC
TACGGCACGCAGGTGCAGGAAGGGGGCGTCCCGATTCGGTACTCTCCCGAAGGCCACCTGATTACTCTAAGTCAGCCGCG
GGAAGTGCGCGAGTTCGAGGGCCAACACCACCTACTGGAGCGCGCTATCCGCGCTGACTTCGCCCTGATCAAGGGCTGGA
AGGCTGACCGCTCGGGCAATGTGATCTTCAGGGGCAGCGCGCGCAACTTCAACGTGCCCATGTGCAAGGCCGCGGACATC
TCGGTGGTGGAGGTGGAGGAGATCGTGGACGTGGGTACTTTCGCCCCGGAGGACATCCACATCCCCAACATTTACGTGAA
ACGCGTGATCAAGGGGCCGAGGTTCGAGAAGCGCATAGAGCGCCTGACCACACGTGACAGCCCGCCCGCACCCGGGAGCA
AAGACCAGGACCCTAAAAGGACGCGCATCATCAAGCGCGCGGCTCTCGAGTTCAAGGACGGCATGTATGCCAATCTGGGC
ATCGGGATCCCTGTCTTGGCCAGCAACTACATCAGCCCCAAGATGACCGTCTACCTGCACAGTGAAAACGGGATCCTGGG
CTTGGGCCCGTTCCCTTTGAAAAAGGAAGTAGATCCCGACATCATCAACGCGGGCAAGCAGACAGTGACGGTGATTCCCG
GGGGCTGTTTCTTCGCCAGCGATGACTCTTTTGCCATGATCCGCGGCGGACACATCCAACTGACCATGCTAGGTGCCATG
CAAGTTTCTAAATACGGCGACCTGGCCAACTGGATGGTGCCAGGCAAGAAGGTGAAGGGCATGGGCGGGGCCATGGACTT
GGTGTCTAGTAAGAAAACCAAAGTGGTGGTCACCATGGAGCACTGCACCAAGACAAAGCAGCCCAAAATCTTAGAGAAAT
GCACCATGCCGCTGACTGGCAAGTCCTGCGTCGACCTCATCATCACAGAGAAAGCGGTGTTTGAAGTGGATCGGAGTAAG
GGACTGAAGCTCGTGGAGCTGTGGGAGGGCTCGTCGTTGGACGAGGTCAAGGCCACCACTGGCTGTTCGTTTAAGGTGTG
CCCCAACCTCAAGCCCATGCAGCAGATTAAATCT

Alignment

ORF - retro_rnor_2177 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.35 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAALKLLSSGLRLCASARNSRGALHKGCACYFSVSTRHHTKFYTDPVEAVKDIPNGATLLVGGFGLCGIP
          MAAL.LL........SA......L................KFYTDPV.AV..I..GA....GGFGLCGIP
Retrocopy MAALRLLAWAFSRRVSAHRPQPTLPHHLIRHYPTTRCGKVKFYTDPVKAVEGIKDGASVMLGGFGLCGIP

Parental  ENLIGALLKTGVKDLTAVSNNAGVDNFGLGLLLRSKQIKRMISSYVGENAEFERQFLSGELEVELTPQGT
          ENLIGAL...GVKDL...S.N.GVD.FGLG.LL.SKQ..R...SY.GEN...E...L.G.LE.E.TPQGT
Retrocopy ENLIGALKTKGVKDLKIISSNVGVDDFGLGILLASKQVRRVVCSYLGENKLCEQLYLAGKLELEMTPQGT

Parental  LAERIRAGGAGVPAFYTSTGYGTLVQEGGSPIKYNKDGSVAIASKPREVREFRGQHFILEEAITGDFALV
          LAERIRAGG.GVPAFYT.TGYGT.VQEGG.PI.Y...G.....S.PREVREF.GQH..LE.AI..DFAL.
Retrocopy LAERIRAGGTGVPAFYTPTGYGTQVQEGGVPIRYSPEGHLITLSQPREVREFEGQHHLLERAIRADFALI

Parental  KAWKADRAGNVIFRKSARNFNLPMCKAAGTTVVEVEEIVDIGSFAPEDIHIPKIYVHRLIKGEKYEKRIE
          K.WKADR.GNVIFR.SARNFN.PMCKAA...VVEVEEIVD.G.FAPEDIHIP.IYV.R.IKG...EKRIE
Retrocopy KGWKADRSGNVIFRGSARNFNVPMCKAADISVVEVEEIVDVGTFAPEDIHIPNIYVKRVIKGPRFEKRIE

Parental  RLSLRKEGEGKAKSGKPGEDVRERIIKRAALEFEDGMYANLGIGIPLLASNFISPNMTVHLQSENGVLGL
          RL..R......A...K.....R.RIIKRAALEF.DGMYANLGIGIP.LASN.ISP.MTV.L.SENG.LGL
Retrocopy RLTTR--DSPPAPGSKDQDPKRTRIIKRAALEFKDGMYANLGIGIPVLASNYISPKMTVYLHSENGILGL

Parental  GPYPLKDEADADLINAGKETVTVLPGASFFSSDESFAMIRGGHVNLTMLGAMQVSKYGDLANWMIPGKMV
          GP.PLK.E.D.D.INAGK.TVTV.PG..FF.SD.SFAMIRGGH..LTMLGAMQVSKYGDLANWM.PGK.V
Retrocopy GPFPLKKEVDPDIINAGKQTVTVIPGGCFFASDDSFAMIRGGHIQLTMLGAMQVSKYGDLANWMVPGKKV

Parental  KGMGGAMDLVSSSKTKVVVTMEHSAKGNAHKIMEKCTLPLTGKQCVNRIITEKGVFDVDKKNGLTLIELW
          KGMGGAMDLVSS.KTKVVVTMEH..K....KI.EKCT.PLTGK.CV..IITEK.VF.VD...GL.L.ELW
Retrocopy KGMGGAMDLVSSKKTKVVVTMEHCTKTKQPKILEKCTMPLTGKSCVDLIITEKAVFEVDRSKGLKLVELW

Parental  EGLTVDDIRKSTGCDFAVSPNLMPMQQIST
          EG...D.....TGC.F.V.PNL.PMQQI..
Retrocopy EGSSLDEVKATTGCSFKVCPNLKPMQQIKS

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	0.00 RPM	182.83 RPM
SRP017611_kidney	0.00 RPM	1095.65 RPM
SRP017611_liver	0.00 RPM	2.15 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

10 EST(s) were mapped to retro_rnor_2177 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CK469297	144604463	144605218	99	748	4	741
CK595353	144604522	144605245	97.1	694	19	664
CK596687	144604467	144605180	100	704	0	695
CK652878	144604457	144605191	99.5	720	4	707
CK653192	144604445	144605266	98.9	787	5	770
CV108978	144604452	144605197	99.6	742	3	739
CV110170	144604482	144605245	99.3	754	6	748
CV111202	144604452	144605190	99.4	731	4	724
CV112546	144604459	144605180	99.8	704	0	691
CV126150	144604482	144605165	99.5	670	2	660

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2177 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2177 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,