RetrogeneDB ID: retro_pvam_373

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2793:530085..531000(+)
• Located in intron of: ENSPVAG00000001758

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH3G
• Ensembl ID: ENSPVAG00000013163
• Aliases: None
• Description: isocitrate dehydrogenase 3 (NAD+) gamma [Source:HGNC Symbol;Acc:5386]

Sequence

>retro_pvam_373
TACGCGCATGTGCCTGTGGACTTTGAGGAGGTGAGAGTTAATGCCACTTCTTGTGAAGAGGACCTTCACAATGCCATCAT
GGCAGTCCGTCGAAACCGTGTGGCCCTGAAGGGCAACATTGAAACTGACCACAACCTGCCACCATCTCAGAAATCCCTCA
ACAACATGTTTCGCACTGCTCTAGATCTCTATGCCAATGTCATCCATTTTAAGAGTCTGCCAGGTGTGAAGACCCGGCAC
AATAACGTTGACATCTTAGTTGTTCGAGAAAACACAGAGGGTGAATACAGCAACTTGGAGTATGAGAGTGTGAAAGGAGT
GATACAGAGCCTAAAGATCATTACTGAGGCCAAGTCTCTGCGCATTGCTAAATATGCCTTCTGGCTGGCCCAGAAGATGG
GGCGCAAAAAAGTGACAGCTGTGCACAAGGCCAACATCATGAAACAGGGAGATGGTCTCTTCCTCCAGTGCTGTAAGGAG
GTGGCATCCCACTATCCCCAGATCACCTTTGAAGGCATGATTGTGGATAACACCACCATGCAGCTGGTATCCCGACCCCA
GCAGTTTGATGTCATGGTAATGCCCAATCTTTATGGCAACATTGTCAACAATATCTGCACAGGGTTAGTTGGTGGAGCGG
GCCTTGTGCCTGGTGCCAACTACGGCTCCAAACACGCAGTATTTGAAACAGCCGCAAGACAGTCAGGCAAGAATATAGCC
AATAAGAATATAGCTAACCCTACTGCCATGCTACTGGCAAGTTGTATTATGCTGGATTACCTGAAGCTATACTCCTATGC
CACCTCCATTCGAAATGCAGTCTTGGCATCCATAAAGAACAAAGATGTCCATACTCCAGATATCGGAGGCCAGGCTACCA
CAGTAGATGTCACTAATAATATCATAAACCACATC

Alignment

ORF - retro_pvam_373 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.36 %
• Parental protein coverage: 77.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HACVPVDFEEVHVTSNADEEDIRNAIMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTSLDLYANVIHC
          .A.VPVDFEEV.V.....EED..NAIMA.RRNRVALKGNIET.HNLPPS.KS.NN..RT.LDLYANVIH.
Retrocopy YAHVPVDFEEVRVNATSCEEDLHNAIMAVRRNRVALKGNIETDHNLPPSQKSLNNMFRTALDLYANVIHF

Parental  KSLPGVVTRHRDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLRIAEYAFKLAQESGRKKVTA
          KSLPGV.TRH...DIL.VRENTEGEYS.LE.ESV.GV..SLKIIT.AKSLRIA.YAF.LAQ..GRKKVTA
Retrocopy KSLPGVKTRHNNVDILVVRENTEGEYSNLEYESVKGVIQSLKIITEAKSLRIAKYAFWLAQKMGRKKVTA

Parental  VHKANIMKLGDGLFLQCCKEVAARYPQITFENMIVDNTTMQLVSRPQQFDVMVMPNLYGNIVNNVCAGLV
          VHKANIMK.GDGLFLQCCKEVA..YPQITFE.MIVDNTTMQLVSRPQQFDVMVMPNLYGNIVNN.C.GLV
Retrocopy VHKANIMKQGDGLFLQCCKEVASHYPQITFEGMIVDNTTMQLVSRPQQFDVMVMPNLYGNIVNNICTGLV

Parental  GGPGLVAGANYGHVYAVFETATRNTGKSIANKNIANPTATLLASCMMLDHLKLHSYATSIRRAVLASMDN
          GG.GLV.GANYG...AVFETA.R..GK.IANKNIANPTA.LLASC.MLD.LKL.SYATSIR.AVLAS..N
Retrocopy GGAGLVPGANYGSKHAVFETAARQSGKNIANKNIANPTAMLLASCIMLDYLKLYSYATSIRNAVLASIKN

Parental  ENMHTPDIGGQGTTSEAIQDIIRHI
          ...HTPDIGGQ.TT......II.HI
Retrocopy KDVHTPDIGGQATTVDVTNNIINHI

Legend:

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

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_373 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus 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,