RetrogeneDB ID: retro_ttru_848

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_3636:547000..547666(+)
• Located in intron of: ENSTTRG00000001700

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH3G
• Ensembl ID: ENSTTRG00000011728
• Aliases: None
• Description: isocitrate dehydrogenase 3 (NAD+) gamma [Source:HGNC Symbol;Acc:5386]

Sequence

>retro_ttru_848
GTTCGGGAAAGCACAGAGGGTGAATACAGCAACCTGGAGCATGAGAGTGTGAAAGGAGTGATAGAGGGCCTTAAAGATCA
TTCCTAAGGCCAAGCTTTTGCATGTTGCTGAATATGATTTCCAGCTGGCCCAGCAGATGGGATGCGAAAAAGTGACGGCT
GTGCACAAGGCCAACATCATGAACTGGGAGATGGTCTCTTCCTCCAGTGCTGTAGGGAGGTGGCATCCTGCTATCCTCAG
CTCATTTTTGAGGGCATGATTGTGGATAACACCACCATGCAGCTGGTATCCTGGCCCCAGCAGTCTGATGTCATGGTGAT
GCCCAGTCTTTATGGCAACATTGTTAATAACGTCTGCACAGAGTTGGTTGGGGGAGCAGGCCTTGTGCCTAGTGCCAACT
ATGGCCACATATATGCGGTGTTTGAAATGGCCTCAAGGCAATCAGGCAAGACTATAACCAATAAAAATGTGGCCAACCCT
ACTGCCATGCTGCTGGCAAGTTGTATCATTCTGGATTACCTCAAGTTCCATTCCTCTGCCACCTCCATTCGTATTGCAGT
CTTGGCATCCATGGAGAACAAAGACATCCAAACTCCAGACATTGGAGGCCAGGGTACCACATCGGATGTCATTCAGAATA
TCATAGATGACATCAGTGTTGCCAAT

Alignment

ORF - retro_ttru_848 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 56.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VRENTEGEYSSLEHESVAGVVE-SLKIITEARSLRIAEYAFTLARESGRKKVTAVHKANIM-KLGDGLFL
          VRE.TEGEYS.LEHESV.GV.E..LKII..A..L..AEY.F.LA...G..KVTAVHKANIM..LGDGLFL
Retrocopy VRESTEGEYSNLEHESVKGVIE>ALKIIPKAKLLHVAEYDFQLAQQMGCEKVTAVHKANIM<ELGDGLFL

Parental  QCCKAVAARYPQITFENMIVDNTTMQLVSRPQQFDVMVMPNLYGNIVNNVCAGLVGGPGLVAGANYGHVY
          QCC..VA..YPQ..FE.MIVDNTTMQLVS.PQQ.DVMVMP.LYGNIVNNVC..LVGG.GLV..ANYGH.Y
Retrocopy QCCREVASCYPQLIFEGMIVDNTTMQLVSWPQQSDVMVMPSLYGNIVNNVCTELVGGAGLVPSANYGHIY

Parental  AVFETATRNTGKSIANRNIANPTATLLASCMMLDHLKLHSYATSIRKAVLASMDNENMHTPDIGGQGTTS
          AVFE.A.R..GK.I.N.N.ANPTA.LLASC..LD.LK.HS.ATSIR.AVLASM.N....TPDIGGQGTTS
Retrocopy AVFEMASRQSGKTITNKNVANPTAMLLASCIILDYLKFHSSATSIRIAVLASMENKDIQTPDIGGQGTTS

Parental  EAIQDIIRRIRVIN
          ..IQ.II..I.V.N
Retrocopy DVIQNIIDDISVAN

Legend:

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

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_848 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_848 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 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 ,