RetrogeneDB ID: retro_lafr_175

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_1:8108465..8109905(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MBOAT2
• Ensembl ID: ENSLAFG00000008586
• Aliases: None
• Description: None

Sequence

>retro_lafr_175
CAGGTCAACTTTGTAGTGTGCTAACTCTTTGCCTTACTGGCAGCCATTTGGTTTTGAGCTCATCTATGTTCAAGCAAAAC
TAGCTCTTTTATAAGACATATACGTAGTTGCTACACCTTGGGGATTTTATCTTGCACTTTTTTGCTTTGGATGGTATGCC
TTACATTTTCTTATACAAACAGGAATTTCTTACTATATCATAATCATAATAGGAGTAGAAAACATGCATAAATATTGTTT
TGTGTTTGCTCTGAGATACCTCACAGTGTATCAAATTACTAGAGTCTGTATCTTTGATTACGGACACTATTCTGCTGATT
CTTGGGGCCCAGTGATGATAATTACACAGATGATCACTACTTTCACTTACAAAATTCATAACGGGGTGTTTGATGGGATT
GACGATGGCATGAAAAGCTAACTCCATCGTAGTCTTGCTGTAAGGTGAGTGCCAACTCTACTGGAGTATTTAAGTTGCAA
CTATAACTTCATAGATATCCTGGCAGGCCCACACTGTTCTTACAAAGACTACATTACTTTCATTAAAGGCAGATCATACC
ATATTACACAACCAGGTGAAGATAAAGAAGAAGAAATACAGTATGAAAGAACAGAGCCATCTCCAAAGTCATAGTTATTC
AGAAGCTCTGAGTCTGTAGACTTTCCTTATTATTTCATTTGTCTATCTCTAAAATATTACCTGTAGGGTGTAACAGTGAT
GAGTATTTTCAAGCTACAACTTCATGCCCAACAAAGGTTATCTATCTGTATGTCTCTCATTTTGCTTACAGACCCAAATA
CTATTTTTCATGGACATTAACTGATGCCATTAATAATGCTGCAGGTTTTAATTTCAGAGGATATGACAAAAATGGAGCAG
CTCATTGGGACTGAGTTCCCAATTTGAGAATTCAGCAAACAGAGATGTCAACAAGTTTCAAGATGTTTCTTAATAATTGG
AATATTCAGACAGCTGTTTGGCTCAAAAGGGTGTGTTATGAACCAGCCTCCATCAGTCCAGCTCTCCAGAAGTTCATTCT
TTCTGCCATTTGGCATGGGGTATACCCAGGATATTATCTAACTTTTCCAAAAGGGGTATTAGTGACATTAGCAGCATGAG
CTTTGGGAAATAACATTAGACATTATTTCATTGAACTTCCATAACTTAAATTATTTTATGATGTTATAACATGGGTAGTA
ACACAAACATCAATAAGCTACACAGTTGTGCCATTTGTACTTTTTTCTATAAAACCATCATTCATGTTTTACAGCTCCTG
GTATTATAGCCTTCACATTGCTGGTATCTTAGTGTTATTGTTGTTGCCGGTGAAAAAAACTCAAAGAGGAAAGAATACAC
ATGAAAATATTCAGCTCTTATGATCCAAAAAGTTGGATGAACAAGAAAATTCTTTGGGACACAATAGTTTTTCCACTTCA

Alignment

ORF - retro_lafr_175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.99 %
• Parental protein coverage: 96.17 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QVNFVVCQLFALLAAIWFRIYLRSSKTSSFIRHVVAT-LLGL-YLALFCFGWYALHFLVQSGISYCIMII
          QVNFVVC.LFALLAAIWF...L.SSKTSSFIRH......LG..YLALFCFGWYALHFL.Q.GISY.I.II
Retrocopy QVNFVVC*LFALLAAIWF*AHLCSSKTSSFIRHIRSCYTLGI>YLALFCFGWYALHFLIQTGISYYIIII

Parental  IGVENMHKYCFVFALGYLTVCQITRVYIFDYGQYSADFSGPMMIITQKITSLAYEIHDGMFRKDEELTPS
          IGVENMHKYCFVFAL.YLTV.QITRV.IFDYG.YSAD..GP.MIITQ.IT...Y.IH.G.F........S
Retrocopy IGVENMHKYCFVFALRYLTVYQITRVCIFDYGHYSADSWGPVMIITQMITTFTYKIHNGVFDGIDDGMKS

Parental  --QRDLAVRRMPSLLEYLSYNCNFMGILAGPLCSYKDYITFIEGRSYHMAQPGEDGEEEIRYEKTEPSP-
          ...R.LAVR..P.LLEYLS.N.NF..ILAGP.CSYKDYITFI.GRSYH..QPGED.EEEI.YE.TEPSP.
Retrocopy *LHRSLAVR*VPTLLEYLSCNYNFIDILAGPHCSYKDYITFIKGRSYHITQPGEDKEEEIQYERTEPSP<

Parental  NIAVIQKLLVCGLSLLFHLTISKTLPVEYNIDEHFQATASWPTKVIYLYVSLLAARPKYYFAWTLGKPYN
          ...VIQKL.VC.LSLLFHL.ISK.LPV..N.DE.FQAT.S.PTKVIYLYVS..A.RPKYYF.WTL....N
Retrocopy KVIVIQKL*VCRLSLLFHLSISKILPVGCNSDEYFQATTSCPTKVIYLYVSHFAYRPKYYFSWTLTDAIN

Parental  NRERSKFKWYECDYIHRLTLKNRLRLEVLHMSTSFKMFLDNWNIQTALWLKRVCYERASFSPTIQTFILS
          N.....F..Y.............LR.....MSTSFKMFL.NWNIQTA.WLKRVCYE.AS.SP..Q.FILS
Retrocopy NAAGFNFRGYDKNGAAHWD*VPNLRIQQTEMSTSFKMFLNNWNIQTAVWLKRVCYEPASISPALQKFILS

Parental  AIWHGVYPGYYLTFLTGVLMTLAARAMRNNVRHYFIEPPQLKLFYDVITWIVTQIAISYTVVPFVLLSIK
          AIWHGVYPGYYLTF..GVL.TLAA.A..NN.RHYFIE.P.LKLFYDVITW.VTQ..ISYTVVPFVL.SIK
Retrocopy AIWHGVYPGYYLTFPKGVLVTLAA*ALGNNIRHYFIELP*LKLFYDVITWVVTQTSISYTVVPFVLFSIK

Parental  PSFMFYSSWYYCLHIAGISVLLLLPVKKTQSGKNIHENTQFSRSKKFDAQENSLGHNSFSTT
          PSFMFYSSWYY.LHIAGI.VLLLLPVKKTQ.GKN.HEN.Q...SKK.D.QENSLGHNSFST.
Retrocopy PSFMFYSSWYYSLHIAGILVLLLLPVKKTQRGKNTHENIQLL*SKKLDEQENSLGHNSFSTS

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_175 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000008586	1 retrocopy	retro_lafr_175 ,