RetrogeneDB ID: retro_lafr_266

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_108:3203464..3204571(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC5
• Ensembl ID: ENSLAFG00000014912
• Aliases: None
• Description: None

Sequence

>retro_lafr_266
GATTATCCATGACCCTGAGCAAACAACTGTATTAGTCATGATAACTACCCTATTTCTTCCTCTTACTTCTTTCTCTGGTA
GCCCAAATTATGGGTGTGTTTAACTTTGGTCTCATGTATGTCCTCAACCACATAGAGGAACTCTCAGGGCCTGCACAGAT
GTCACAATGGCAGTGATGTTGTGGTTAGCTTATTCTTCATCCATGTAGCTGGGCTCACAGGGTTTTACATGGTGCTGGAG
GATAGGGGGTGCCCAACTCATGAATAGGTTACAGGACATTTCCAAGGAGATGTGATCCCCTTCACTAATGGCTGCTGTAA
CAATGTCAGGCAGGTACTGTGCAGTTCCCTAGCACCCAGGTATTCAGGAGACCAAAGGAAGAAAAGACAATTGTAATCTG
ACCTCACTTCCTTTGATCAGAAGTAACAGATGGACAGATAACTCTGAAGATTATGGACAGCAGTATCCAAGGAAATCTGA
GGAAAACTAAGTCTAAGGGGAAAGAGGAGAAATCAGAGAACCGGTCCACAGATGTTGAATCTCCAATTCCTTCTAAGCCA
GACCTGAGCCACTACACAGGGCTATGAACACACCTCAGCCTGTCTACTACTGAAGATAGCAGCCTCTTGGGTAAGGGAAG
CTACCTTATACCTACCATGTACAAGTATCAGCCAGGCTACACTAACAGCAGTGTATCAGCTGCCATACCTCATTTCTCCA
GCACCAAGTTGAGTTGTGGGGACAGCTTGAAGGAGCTAACCTCAACTGCAGAGAGCAGCTGCCATCCCATCTACTACTGA
AGAGCCCAGCTTTGAGCCAGCTTCAGTTCTCCTAACTTTGGCAAAAATTCACTTTGTTACACTACCCAGTGGCTCAAGCT
CCTCCAGCCCCAAGTCAGCCCAGGACACAGTGTTTGAGCTGGGTTAGGTGCAGTCCATTCATTCAGATAATACAACCTCC
ACCTCCTATAACTCCTATAACAGCCTGGCCAACCAGACAGAAAGTGAAGATCTATCTTGTGAGAGCCTACTTACTTCTTC
AGATAGCCCTGATTTCCAGTCAGAGCAGGCAGGGTCTGAGCCAGACCTGCCTTTATGCTACACCTCT

Alignment

ORF - retro_lafr_266 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.76 %
• Parental protein coverage: 51.68 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DHHCPWVNNCIGRRNYR-YFFLFLLSLTAHIMGVFGFGLLYVLYHMEELSGVR-TAVTMAVMC-VAGLFF
          D...P..NNCI...NY..YFFL.LLSL.A.IMGVF.FGL.YVL.H.EELSG...T.VTMAVM..V..LFF
Retrocopy DYP*P*ANNCISHDNYP<YFFLLLLSLVAQIMGVFNFGLMYVLNHIEELSGPA<TDVTMAVML<VVSLFF

Parental  IPVAGLTGFHVVLVARGRTTNEQVTGKFRGGVNPFTNGCCNNVSRVLCSSPAPRYLG-RPKKEKTVVIRP
          I.VAGLTGF..VL..RG..T.E.VTG.F.G.V.PFTNGCCNNV..VLCSS.APRY.G.RPK.EKT.VI.P
Retrocopy IHVAGLTGFYMVLEDRGCPTHE*VTGHFQGDVIPFTNGCCNNVRQVLCSSLAPRYSG<RPKEEKTIVI*P

Parental  PFLRPDVSDGQITVKIMDNGIQGELRRTKSKGSLEITESQSVDAEPPPPPKPDLSRYTGLRTHLSLAATE
          .FL...V.DGQIT.KIMD..IQG.LR.TKSKG..E..E..S.D.E.P.P.KPDLS.YTGL.THLSL..TE
Retrocopy HFL*SEVTDGQITLKIMDSSIQGNLRKTKSKGKEEKSENRSTDVESPIPSKPDLSHYTGL*THLSLSTTE

Parental  ADNSLLAKDSPPTPTMYKYRPGYSSSSTSAAMPHSSSAKLSRGDSLKEPTSIAESSRHPSY-RSEPSLEP
          .D.SLL.K.S...PTMYKY.PGY..SS.SAA.PH.SS.KLS.GDSLKE.TS.AESS.HP.Y...EPS.EP
Retrocopy -DSSLLGKGSYLIPTMYKYQPGYTNSSVSAAIPHFSSTKLSCGDSLKELTSTAESSCHPIY>TEEPSFEP

Parental  ESFRSPTFGKSFHFDPLSSGSRSSSLKSAQGTGFELGQLQSIRSEGTTSTSYKS---LANQTRNGSLSYD
          .S.........F...P..S.S..SS.KSAQ.T.FELG..QSI.S..TTSTSY.S...LANQT....LS..
Retrocopy ASVLLTLAKIHFVTLPSGSSS--SSPKSAQDTVFELG*VQSIHSDNTTSTSYNSYNSLANQTESEDLSCE

Parental  SLLTPSDSPDFESVQAGPEPEPPLGYTS
          SLLT.SDSPDF.S.QAG.EP..PL.YTS
Retrocopy SLLTSSDSPDFQSEQAGSEPDLPLCYTS

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_266 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000014912	1 retrocopy	retro_lafr_266 ,
Oryctolagus cuniculus	ENSOCUG00000007047	1 retrocopy	retro_ocun_1688,