RetrogeneDB ID: retro_ocun_80

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:160305458..160306610(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023768
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: IDH3G
• Ensembl ID: ENSOCUG00000016554
• Aliases: None
• Description: isocitrate dehydrogenase 3 (NAD+) gamma (IDH3G), nuclear gene encoding mitochondrial protein, mRNA [Source:RefSeq mRNA;Acc:NM_001171363]

Sequence

>retro_ocun_80
GTGGCATTGAAGATGCTGACAACAATCAGTTGCTCTGTGAAGGCGATATTCCAACTTACCATTCCAGGTCACTCCTGGGA
AATTTTACTTGGCCGTAAGATATCCTTGAGGAGCTTTTCTTTTTATCATACAACCCCTCCACCAGCCAATTATGGTGGCC
AGCACATGGTGACTATGATTCCTGGGGATGGCATTGGGCCAGAACTCATGCTGCATATCAAATCTATATTCAAACATGCC
TGTGTGCCTGTGGACTTTGAGGAAGTGTTAGTAACTTCTGCTTCTAGTGAAGAGGATGTTCACAATGCCATCATGGCTGT
CCGTCGAAACCGTGTGGCTTTGAAGGGCAACATTGAAACAGATCACACTCTACCACCTTCTCATAAGTCCTACAACAACA
TGTTTCGCACTACCCTAGATCTCTATGCCAATGTCATCCATTTCAAGAATCTGCCAAGTGTGGAGACCCAGCACAAGGAC
ATAGATATCTTAGTTGTTCGAGAAAACACAGAGGGTGAGTACAGCAACCTGGAGCATGAGAGTGTGAGAGGAGTAATAGA
GAGCTTAAAGATCATTACTAAAGCCAAATCAATGCGCATTGCTGAATATGCCTTCCAGCTGACCCAGAAGATGGGTCGCA
AAAAAGTGACAGCTGTGCACAAGGCTAACATCATGAAACTGGGAGATGGTCTCTTCCTCCAATGCTGTACAGAGGTGGCA
TCCCACTATCCTCAGCTTACCTTAGAAGGCATGATTGTGGACAATACTACAATGCAATTGGTATCCCGTCCTCAACAGTT
TGATGTCATGGTGATGCCTAATCTTTATGGCAACATTGTCAACAATGTATGCACAGGATTGGTCGGGGGAGCAGGCCTGG
TACCTGGAGCCAACTATGGCCACTTATATGCAGTGTTTGAGACAGCTGCAAGGCAATCAGGCAAGCATTTAGTCAATAAG
AATAGTGTCAACCCTACTGCCATGTTGCTGACAAGTTGCACTATGCTGGACTACCTCAAACTCCACTCCTATGCCACTCA
CATTCGTACTGCAGTATTGGCATCACTAGACAACAAAAATGTTCACACCCCAGACATTGGAGGCCAGGGTACCACGCTGG
ACATCATTCACAGCATAATGGATCACATCTAA

Alignment

ORF - retro_ocun_80 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.58 %
• Parental protein coverage: 97.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALKLTTTAGAVARAVFKPAVLSRPWEVLSTHEAPWRSISSQQTIPPSAKYGGRHTVTMIPGDGIGPELM
          .ALK..TT......A.F........WE.L.......RS.S...T.PP.A.YGG.H.VTMIPGDGIGPELM
Retrocopy VALKMLTTISCSVKAIFQLTIPGHSWEILLGRKISLRSFSFYHTTPPPANYGGQHMVTMIPGDGIGPELM

Parental  LHVKSVFRHACVPVDFEEVHVSSNADEEDIRNAIMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTSLD
          LH.KS.F.HACVPVDFEEV.V.S...EED..NAIMA.RRNRVALKGNIET.H.LPPSHKS.NN..RT.LD
Retrocopy LHIKSIFKHACVPVDFEEVLVTSASSEEDVHNAIMAVRRNRVALKGNIETDHTLPPSHKSYNNMFRTTLD

Parental  LYANVIHCKSLPGVVTRHKDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLRIAEYAFKLAQE
          LYANVIH.K.LP.V.T.HKDIDIL.VRENTEGEYS.LEHESV.GV.ESLKIITKAKS.RIAEYAF.L.Q.
Retrocopy LYANVIHFKNLPSVETQHKDIDILVVRENTEGEYSNLEHESVRGVIESLKIITKAKSMRIAEYAFQLTQK

Parental  SGRKKVTAVHKANIMKLGDGLFLQCCREVAAGYPQIAFESMIVDNTTMQLVSRPQQFDVMVMPNLYGNIV
          .GRKKVTAVHKANIMKLGDGLFLQCC.EVA..YPQ...E.MIVDNTTMQLVSRPQQFDVMVMPNLYGNIV
Retrocopy MGRKKVTAVHKANIMKLGDGLFLQCCTEVASHYPQLTLEGMIVDNTTMQLVSRPQQFDVMVMPNLYGNIV

Parental  NNVCAGLVGGPGLVAGANYGHVYAVFETATRNTGKSIANKNIANPTATLLASCMMLDHLKLHTYAASIRK
          NNVC.GLVGG.GLV.GANYGH.YAVFETA.R..GK...NKN..NPTA.LL.SC.MLD.LKLH.YA..IR.
Retrocopy NNVCTGLVGGAGLVPGANYGHLYAVFETAARQSGKHLVNKNSVNPTAMLLTSCTMLDYLKLHSYATHIRT

Parental  AVLASMHNDNMHTPDIGGQGTTSEAIQDIIRNI
          AVLAS..N.N.HTPDIGGQGTT...I..I...I
Retrocopy AVLASLDNKNVHTPDIGGQGTTLDIIHSIMDHI

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	141.17 RPM
SRP017611_kidney	0.00 RPM	160.85 RPM
SRP017611_liver	0.00 RPM	55.03 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_80 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_80 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_80 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
Bos taurus	retro_btau_1194
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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000006029	1 retrocopy	retro_dord_38,
Erinaceus europaeus	ENSEEUG00000015625	1 retrocopy	retro_eeur_248,
Latimeria chalumnae	ENSLACG00000007365	1 retrocopy	retro_lcha_17,
Macropus eugenii	ENSMEUG00000013934	1 retrocopy	retro_meug_203,
Myotis lucifugus	ENSMLUG00000004457	1 retrocopy	retro_mluc_396,
Oryctolagus cuniculus	ENSOCUG00000016554	1 retrocopy	retro_ocun_80 ,
Procavia capensis	ENSPCAG00000008973	1 retrocopy	retro_pcap_361,
Pan troglodytes	ENSPTRG00000024398	1 retrocopy	retro_ptro_534,