RetrogeneDB ID: retro_btau_1194

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 29:23839077..23839803(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH3G
• Ensembl ID: ENSBTAG00000001059
• Aliases: None
• Description: Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q58CP0]

Sequence

>retro_btau_1194
TCGCAGGATCTCTGTGCCAATGTCGTCCAGTTTGAGAGTCAGCCACGGGTGGAAACCAGACACAAGAACATAGACATCTT
AGTTGTTCGGGACAACACAGAGGGTGAATACAGCAACCTGGAGGATGAGAGCATGAACAGAGTGGTAGAAAGCCTAAGGA
CCGTTACTAAGGCCAAGTGTTTGCGCCTTGCTGAATATGCTTTCCAGCTGGCTCATCGGATGGGGTGCAAGAAAGTGACA
GCCACGTACAAGGCCAACATCATGAGACTGGGAGATTGTCTCTTCATCCAGTGCTGTAGGGAGGTGGCATCCCACTATCC
CCAGCTCTCCTTTGAGGGCATGATTGTGGGTAACACCCCCATGCAGCTGGTATCCGGACCCCAGCAGTTTGATGTCATGG
TGATGCCCAGTCTCTACGGCAACATTGTCAATAATGTCTGCACAGGGTTGGTTGGGGGAGCAGGCCTTGTGCCTGCTGCC
AGCTATGGGCAAATATATGCAGTGTCTGAAACAGCTGCGAGGCAGTCGGGCAAGACTATAGCCAGTAATGTGGCTAACTC
TACTGCCACGCTGCTGGCACATTGCATTAGGCTGGATTACCTCAAGCTCCATTTCTATGCCACCTCCATTCGTACTGCAG
TCTTGGCATCCATGGAGAACAAGGACATCCAAACTCCAGACATTGGAGGCCAGGGTACCACATTGGATGCCATTCAAAAT
ATCATA

Alignment

ORF - retro_btau_1194 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.78 %
• Parental protein coverage: 62.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLDLYANVIHCKSLPGVVTRHRDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLRIAEYAFQL
          S.DL.ANV....S.P.V.TRH..IDIL.VR.NTEGEYS.LE.ES...VVESL...TKAK.LR.AEYAFQL
Retrocopy SQDLCANVVQFESQPRVETRHKNIDILVVRDNTEGEYSNLEDESMNRVVESLRTVTKAKCLRLAEYAFQL

Parental  AQESGRKKVTAVHKANIMKLGDGLFLQCCREVAARYPQITFENMIVDNTTMQLVSRPQQFDVMVMPNLYG
          A...G.KKVTA..KANIM.LGD.LF.QCCREVA..YPQ..FE.MIV.NT.MQLVS.PQQFDVMVMP.LYG
Retrocopy AHRMGCKKVTATYKANIMRLGDCLFIQCCREVASHYPQLSFEGMIVGNTPMQLVSGPQQFDVMVMPSLYG

Parental  NIVNNVCAGLVGGPGLVAGANYGHVYAVFETATRNTGKSIANKNIANPTATLLASCMMLDHLKLHSYATS
          NIVNNVC.GLVGG.GLV..A.YG..YAV.ETA.R..GK.IA..N.AN.TATLLA.C..LD.LKLH.YATS
Retrocopy NIVNNVCTGLVGGAGLVPAASYGQIYAVSETAARQSGKTIAS-NVANSTATLLAHCIRLDYLKLHFYATS

Parental  IRKAVLASMDNENMHTPDIGGQGTTSEAIQDII
          IR.AVLASM.N....TPDIGGQGTT..AIQ.II
Retrocopy IRTAVLASMENKDIQTPDIGGQGTTLDAIQNII

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	16.37 RPM
ERP005899_muscle	0.00 RPM	71.74 RPM
SRP017611_brain	0.00 RPM	30.83 RPM
SRP017611_kidney	0.00 RPM	63.72 RPM
SRP017611_liver	0.00 RPM	37.98 RPM
SRP030211_testis	0.05 RPM	21.62 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1194 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1194 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1194 has 7 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_759
Pan troglodytes	retro_ptro_534
Mus musculus	retro_mmus_134
Oryctolagus cuniculus	retro_ocun_80
Sus scrofa	retro_sscr_662
Canis familiaris	retro_cfam_1023
Equus caballus	retro_ecab_941

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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,