RetrogeneDB ID: retro_dord_38

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_1044:506339..507251(+)
• Located in intron of: ENSDORG00000001739

Retrocopy information

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

Parental gene information

• Parental gene symbol: Idh3g
• Ensembl ID: ENSDORG00000006029
• Aliases: None
• Description: isocitrate dehydrogenase 3 (NAD+), gamma [Source:MGI Symbol;Acc:MGI:1099463]

Sequence

>retro_dord_38
GCCTGTGTGCCTGTGGACTTTGAGGTGGTACAAGTGACCTCCTTGTCTCCGGAGAAGGAAGTTTACAATGCCATTCAGGC
AGTTCGTCGAAACCGCATCTGTTTGAAGGGTAACATCGAAATGGATCACAACTTGCCACTGGATCACCAATCCCGTAACA
ACATGCTTCGTACCTCTCTGGATCTCTATGCCAATGTCATCCATTTCAAGAATCTGCCAAGTATAGAGACCCGGCACAAG
AACGTAGACATCATAGTTGTTCGAGAAAACACAGAGGGTGAGTACAGCAACCTGGAGCATGAGGGTGTGAAAGGCGTAGT
AGAGAGCCTGAAGATTATCACAAAGGTCAAGTCATTGCGCATTGCCGAGCACGCCTTCCAGCTAGCCCAGAAGATGAGGC
GCCAAAAAGTGACAGTAGTGCACAAGGCCAACATCATGAAGCTAGGAGATGGACTCTTTCTTAAGTGCTGTGAGGAAGTA
GCAAGTCGCTATCCTCAGCTCTTCTTTGAAAACATGGTTGTGGACAATGCTACCATGCAATTGGTATCCCACCCCCAACA
GTTTGATGTCATGTTGATGCCCAATCTCTATGGCAACGTTATCAACAACGTCTGTACAGGATTGGTGGGAGGGGCTGGCG
TGGTACCTGGAGCCAACTATGGCAGCATGTGTGCAGTGTTTGAGACAGCCTCCAGGCAATCAGGCAAAAACGTAGCCAAT
AGGAATTTAGCCAACCCGACTGCCATGCTACTATCAAGTTGCAATATGCTAGATTACCTCAAACTCCACTCTCATGCCAC
CTGCATTCGGAATGCAGTTTTGAGATCCATTGAGAACAAAGCTATCCATACACCAGACATGGGAGGCAAAGGCAGCACAT
TGGATATCATTCACAGCATCACAAAGAAAATT

Alignment

ORF - retro_dord_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.42 %
• Parental protein coverage: 77.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASVPVDFEEVHVSS-NDEEDIRNAIMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTSLDLYANVIHCK
          A.VPVDFE.V.V.S...E....NAI.A.RRNR..LKGNIE..HNLP..H.SRNN.LRTSLDLYANVIH.K
Retrocopy ACVPVDFEVVQVTSLSPEKEVYNAIQAVRRNRICLKGNIEMDHNLPLDHQSRNNMLRTSLDLYANVIHFK

Parental  SLPGVVTRHKDIDILIVRENTEGEYSSLEHESVTGVVESLKIITKAKSLRIAEYAFKLAHESGRKKVTAV
          .LP...TRHK..DI..VRENTEGEYS.LEHE.V.GVVESLKIITK.KSLRIAE.AF.LA....R.KVT.V
Retrocopy NLPSIETRHKNVDIIVVRENTEGEYSNLEHEGVKGVVESLKIITKVKSLRIAEHAFQLAQKMRRQKVTVV

Parental  HKANIMKVGDGLFLQCCREVAARYPQISLENMKMDNTPMQEVSRPQQFDVMVMPNLYGNIVNNVCAGLVG
          HKANIMK.GDGLFL.CC.EVA.RYPQ...ENM..DN..MQ.VS.PQQFDVM.MPNLYGN..NNVC.GLVG
Retrocopy HKANIMKLGDGLFLKCCEEVASRYPQLFFENMVVDNATMQLVSHPQQFDVMLMPNLYGNVINNVCTGLVG

Parental  GPGLVAGANYGHVYAVFETATRNTGKSIANKNIANPTATLLASCMMLDHLKLHSYATSIRKAVLASMDNE
          G.G.V.GANYG...AVFETA.R..GK..AN.N.ANPTA.LL.SC.MLD.LKLHS.AT.IR.AVL.S..N.
Retrocopy GAGVVPGANYGSMCAVFETASRQSGKNVANRNLANPTAMLLSSCNMLDYLKLHSHATCIRNAVLRSIENK

Parental  NMHTPDIGGQGTTSEAIQDIIRHI
          ..HTPD.GG.G.T...I..I...I
Retrocopy AIHTPDMGGKGSTLDIIHSITKKI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_38 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,