RetrogeneDB ID: retro_rnor_209

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:107446735..107447923(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000045720
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Idh3g
• Ensembl ID: ENSRNOG00000037284
• Aliases: Idh3g, IDH
• Description: isocitrate dehydrogenase [Source:RefSeq peptide;Acc:NP_113739]

Sequence

>retro_rnor_209
ATGCTGGCAGCAGGCAGCTGTTCTGTGAGAACAATCCTCCAACCTGCTCTTCTCCTTGGCCATTCTAGGGAGGTAGTATG
TGAGCTTGTGACCTCCTTCAGAAATTTCTGCTCAAAGTACTCAGTGCCTCCTTCACCAAAGTATGGTGGAAAGCATACAG
TGACTATGATTCCTGGAGATGGCATTGGTCCTGAGCTCATGGTTCACGTCAAGAGAATATTCCGATCAAATTGTGTGCCA
GTGGAGTTTGAGGAGGTGTGGGCCACCTCCACGTCTAGCGAAGAGGAGATCAACAATGCTCTCATGGCCATCCGTCGGAA
CCGTATCACTCTGAAGGGCAATATTGCGACCAACCACCATCTGCCTGCCAAGTACAAATCTCACAACACCAAGTTTCGCA
CTGCTCTTGACCTCTATGCCAGTGTCGTCCATTTCAAGACTTTTCCTGGTGTGGAGACCCGACACAAGGACATAGACATC
CTGGTTGTTCGGGAGAATACTGAGGGCGAGTACACTAACCTGGAGCATGAGAGCGTGAGGGGAGTGGTAGAGAGCCTAAA
GATTGTGACAAAAACCAAGTCCGTGCGCATTGCTGATTATGCCTTCAGGTTGGCTCAAAAGATGGGGCGGAAAAAGGTGA
CCGTTGTTCACAAAGCCAACATCATGAAACTGGGAGATGGACTCTTCCTTCAGTGCTGTAAGGATGTGGCAGCTCATTAT
CCTCAGATCACCTTGGAGAGCATGATTATAGATAACACTGCAATGCAGTTGGTTTCCAAACCCCAGCAGTTTGATGTTAT
GTTGATGCCCAATCTTTATGGCAACATCATCAACAGTGTCTGCACAGGGCTGGTTGGAGGGTCAGGAATTGTACCTGGAG
CCAATTATGGTGATTCATATGCAATATTTGAGACAGGTTCAAAAGAAATAGGTCAAGATTTAGCTCACAGAAATATTGCC
AACCCTGTCGCCATGCTGCTGACCAGCTGTATCATGCTGGACTACCTTGATCTCCAACTCTATGCCGCTCACATCCGCTC
TGCAGTCATGGCATCCTTACAAAACAAATCCATCTGCACTCCAGATATAGGAGGTCAGGGGACCACGGCAGGTGTTGTAG
AGTATATCTTAGACCATATGAAAGACCAAAATAGCGGTTGTCAGCCAAGATTCTTCCTGTCCACTTGA

Alignment

ORF - retro_rnor_209 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.53 %
• Parental protein coverage: 96.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IAAGSAA-KAIFKPALLC-RPWEVLAAHEAPRRSISSQQTIPPSAKYGGRHTVTMIPGDGIGPELMLHVK
          .AAGS.....I..PALL.....EV........R...S....PPS.KYGG.HTVTMIPGDGIGPELM.HVK
Retrocopy LAAGSCSVRTILQPALLLGHSREVVCELVTSFRNFCSKYSVPPSPKYGGKHTVTMIPGDGIGPELMVHVK

Parental  SVFRHACVPVDFEEVHVSSNADEEDIRNAIMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTSLDLYAN
          ..FR..CVPV.FEEV...S...EE.I.NA.MAIRRNR..LKGNI.TNH.LP...KS.N...RT.LDLYA.
Retrocopy RIFRSNCVPVEFEEVWATSTSSEEEINNALMAIRRNRITLKGNIATNHHLPAKYKSHNTKFRTALDLYAS

Parental  VIHCKSLPGVVTRHKDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLRIAEYAFKLAQESGRK
          V.H.K..PGV.TRHKDIDIL.VRENTEGEY..LEHESV.GVVESLKI.TK.KS.RIA.YAF.LAQ..GRK
Retrocopy VVHFKTFPGVETRHKDIDILVVRENTEGEYTNLEHESVRGVVESLKIVTKTKSVRIADYAFRLAQKMGRK

Parental  KVTAVHKANIMKLGDGLFLQCCREVAARYPQITFDSMIVDNTTMQLVSRPQQFDVMVMPNLYGNIVNNVC
          KVT.VHKANIMKLGDGLFLQCC..VAA.YPQIT..SMI.DNT.MQLVS.PQQFDVM.MPNLYGNI.N.VC
Retrocopy KVTVVHKANIMKLGDGLFLQCCKDVAAHYPQITLESMIIDNTAMQLVSKPQQFDVMLMPNLYGNIINSVC

Parental  AGLVGGPGLVAGANYGHVYAVFETATRNTGKSIANKNIANPTATLLASCMMLDHLKLHSYATSIRKAVLA
          .GLVGG.G.V.GANYG..YA.FET.....G...A..NIANP.A.LL.SC.MLD.L.L..YA..IR.AV.A
Retrocopy TGLVGGSGIVPGANYGDSYAIFETGSKEIGQDLAHRNIANPVAMLLTSCIMLDYLDLQLYAAHIRSAVMA

Parental  SMDNENMHTPDIGGQGTTSQAIQDIIRHIR
          S..N....TPDIGGQGTT......I..H..
Retrocopy SLQNKSICTPDIGGQGTTAGVVEYILDHMK

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	92.46 RPM
SRP017611_kidney	0.00 RPM	231.40 RPM
SRP017611_liver	0.00 RPM	27.57 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_209 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_209 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_209 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018466	1 retrocopy	retro_amel_1892,
Bos taurus	ENSBTAG00000001059	1 retrocopy	retro_btau_1194,
Canis familiaris	ENSCAFG00000019286	1 retrocopy	retro_cfam_1023,
Callithrix jacchus	ENSCJAG00000011185	1 retrocopy	retro_cjac_1597,
Equus caballus	ENSECAG00000018509	1 retrocopy	retro_ecab_941,
Homo sapiens	ENSG00000067829	1 retrocopy	retro_hsap_759,
Latimeria chalumnae	ENSLACG00000007365	1 retrocopy	retro_lcha_17,
Loxodonta africana	ENSLAFG00000006904	1 retrocopy	retro_lafr_560,
Macropus eugenii	ENSMEUG00000013934	1 retrocopy	retro_meug_203,
Myotis lucifugus	ENSMLUG00000004457	1 retrocopy	retro_mluc_396,
Mustela putorius furo	ENSMPUG00000008781	1 retrocopy	retro_mputfur_644,
Mus musculus	ENSMUSG00000002010	1 retrocopy	retro_mmus_134,
Nomascus leucogenys	ENSNLEG00000013540	1 retrocopy	retro_nleu_394,
Otolemur garnettii	ENSOGAG00000006735	1 retrocopy	retro_ogar_25,
Pteropus vampyrus	ENSPVAG00000013163	1 retrocopy	retro_pvam_373,
Rattus norvegicus	ENSRNOG00000037284	1 retrocopy	retro_rnor_209 ,
Sus scrofa	ENSSSCG00000012783	1 retrocopy	retro_sscr_662,
Tursiops truncatus	ENSTTRG00000011728	1 retrocopy	retro_ttru_848,