RetrogeneDB ID: retro_lafr_560

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_21:28406450..28407485(-)
• Located in intron of: ENSLAFG00000015587

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH3G
• Ensembl ID: ENSLAFG00000006904
• Aliases: None
• Description: None

Sequence

>retro_lafr_560
GTTCCTCCATCAGCCAAGTATGGTGGGCGGCACACAGTGACTATGATTCCTGGGGATGGCATTGGGCCTGAACTTATGTC
GCATGTGAAGTCTGTGTTCACACACTCATGTGTTCCTGTGGATTTTGAGGAGGTCCAGGTGCACTCCACTTGTAGTTTAG
AGGACATTCACAATGCCATCTTCTCCATCCGTCGAAACGGTGTGGCACTAAAGGGCAACATTGCAACTGACCATAACCTG
CCATTGACTCACGCATCCCTCAACAACATGCTTCGCACCTCCCTAGATCTCTTTGCCAGTGTCATCCATTGTAAGAGCCT
GCCAAGTGTGGTCACCCGGCACAATGATGTAGACATCATTGTCATTCGGGAAAGTACAGAGGGTGAGTACACCAACCTGG
AGCATGAGAGTGTGAATGGAGTGGTAGAGACCCTGAAGATCACTACTGAGACCAAGTCTTTGCGCATTGCTGAATATGCC
TTCCAGCTAGCACAGGAGATGGGGCGCAAGAAAGTGACAGCTGTGCACAAGGCCAACATCATGAAACTGACAGATGGTCT
CTTCCTCCAGTGCTGTGCTGAGGTGGCATCACACTATCCTCAGATCACCTTTGAGACCATGACTGTGGACTATACCACCA
TGCAGTTGGTAACCCAGCCCCAGCAGTTTGATGTCATGTTGATGCCTAATCTTTACGGCAATGTTATCCACAATATTTGC
ACAGGGTTGGTTGGGGGCGCAGGCCTTGTGCCTGGAGCCAACTATGGCCAACTGTATGCAGTGTTTGAGACAGGTACAAG
GCAAACAGGCAAGTATATAGCCAAGAAGAATGTTGCTAACCCTACTGCTATACTTCTGGCAAGTTGTATTATGCTGGATT
ACCTTGAGCTCAGCTCCTATGCCACCTCCATTCGCAATGCGGTCTTGACATCCATGGACAACAAAGGTATCCATACACCA
GACATTGGAGGATGTGGTACCACGTCGGAAATCATTCAAGACATCATGAATCGCATCCAGACCTAAAATGCTAAA

Alignment

ORF - retro_lafr_560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.36 %
• Parental protein coverage: 87.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IPPSAKYGGRHTVTMIPGDGIGPELMLHVKSVFRHACVPVDFEEVHVSSTADEEDIRNAIMAIRRNRVAL
          .PPSAKYGGRHTVTMIPGDGIGPELM.HVKSVF.H.CVPVDFEEV.V.ST...EDI.NAI..IRRN.VAL
Retrocopy VPPSAKYGGRHTVTMIPGDGIGPELMSHVKSVFTHSCVPVDFEEVQVHSTCSLEDIHNAIFSIRRNGVAL

Parental  KGNIETNHNLPPSHKSRNNILRTSLDLYANVIHCKSLPGVVTRHKDIDILIVRENTEGEYSSLEHESVAG
          KGNI.T.HNLP..H.S.NN.LRTSLDL.A.VIHCKSLP.VVTRH.D.DI...RE.TEGEY..LEHESV.G
Retrocopy KGNIATDHNLPLTHASLNNMLRTSLDLFASVIHCKSLPSVVTRHNDVDIIVIRESTEGEYTNLEHESVNG

Parental  VVESLKIITKAKSMRIAEYAFKLAHESGRKKVTAVHKANIMKLGDGLFLQCCREVAARYPQITFENMIVD
          VVE.LKI.T..KS.RIAEYAF.LA.E.GRKKVTAVHKANIMKL.DGLFLQCC.EVA..YPQITFE.M.VD
Retrocopy VVETLKITTETKSLRIAEYAFQLAQEMGRKKVTAVHKANIMKLTDGLFLQCCAEVASHYPQITFETMTVD

Parental  NTTMQLVSRPQQFDVMVMPNLYGNIVNNVCAGLVGGPGLVAGANYGHVYAVFETATRNTGKSIANKNIAN
          .TTMQLV..PQQFDVM.MPNLYGN...N.C.GLVGG.GLV.GANYG..YAVFET.TR.TGK.IA.KN.AN
Retrocopy YTTMQLVTQPQQFDVMLMPNLYGNVIHNICTGLVGGAGLVPGANYGQLYAVFETGTRQTGKYIAKKNVAN

Parental  PTATLLASCMMLDHLKLHSYAASIRKAVLASMDNENMHTPDIGGQGTTSEAIQDIIRHIRIINGR
          PTA.LLASC.MLD.L.L.SYA.SIR.AVL.SMDN...HTPDIGG.GTTSE.IQDI...I...N..
Retrocopy PTAILLASCIMLDYLELSSYATSIRNAVLTSMDNKGIHTPDIGGCGTTSEIIQDIMNRIQT*NAK

Legend:

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

Expression

RNA-Seq

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq

Loxodonta africana was not studied using ChIP-Seq data.

EST

Loxodonta africana was not studied using EST data.

TSS

Loxodonta africana was not studied using FANTOM5 data.

Lab

retro_lafr_560 was not experimentally validated.

Homology

Retrocopy orthology:

Loxodonta africana 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,