RetrogeneDB ID: retro_lafr_130

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_0:2389754..2390645(+)
• Located in intron of: ENSLAFG00000014023

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASNS
• Ensembl ID: ENSLAFG00000000909
• Aliases: None
• Description: Asparagine synthetase [Source:UniProtKB/TrEMBL;Acc:G3SMK7]

Sequence

>retro_lafr_130
GCTTCTGTTTCACTACATGCAGTCCACCAGACGCTGCTTCTGGAAGGAAATGCCCACGGAATCAGACCTTTGTTTAAAGC
AACTAGAGAAGAAGGGTTGGGCTGGGTATTCAGAAGTTAAGGGTCTTATTAATTTGATGTACTCTAACACCCCATTTTTT
AAATTTGAGACTTTTCTTCTAGGATATTATGAAATTCTGGATTTAAACCGAATGGTACAGCTGCACCAGTGGCAGGGAGG
AGGTGCCATCAGTGTGGGGATAAACCTCTGCATGGCCTTCAAGCCAGTGTGAGAAACCAGGCCCCGGTTTTGAGCAAGAA
ACATTGACGAGCAACCTCTGGATGCTTTCTGACAATGCTACAAGAACCATTTGACGACAGACAGAAGACATGACTGCCTT
TTCTCAGGTGGTTTGGAACGTAGCTTGGCTGCTGCTACTCTACCGAAGCAACTATAAAAGTTCACAGGACAGAACTTTCC
TCAAACATTTTCCATTGTCATGGAAGAGAGCCCGATCCACTTATTGTCTGGAGAAGTGGCAAATCATATTGGGAGTGAAC
CCCATGAGGTCATCCTTAATTATGAAGACGGCATTCAGGCCCTGGAGAAAGTCACTTTTATCCTGGAAATGTATGACAGG
GTAAAAATTCATGCTTCAGAAGGTTTGTATCTTAATTCCGGGTACATTTGAAAGAATACAGATAGCTTGGTGATCGTCTC
TGGAGAATGTTCAGACGAACTGAAATAGGATTCCATGTATTTTCATACGCAGCCTTCTGCTGTAGAAGCCACAGTGGAGG
AGGGAGACTCCTGACAGAACTGTATTTGTTCACTGTGTTCTGAGCACATTGGATTAATGCTGCTCTCGGCCTTGAGCTGA
TAGTCCCATTC

Alignment

ORF - retro_lafr_130 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.29 %
• Parental protein coverage: 53.3 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AFILLDTASKKVFLGRDTYGVRPLF-KAMTEDGFLAVCSEAKGLVNLKHSGTSFLKVEPFLPGHYEVLDL
          A...L........L.....G.RPLF.K.....G..A..SE.KGL.NL..S.T.F.K.E.FL.G.YE.LDL
Retrocopy ASVSLHAVHQTLLLEGNAHGIRPLF>KQLEKKGW-AGYSEVKGLINLMYSNTPFFKFETFLLGYYEILDL

Parental  -KPNGKVASVEMVKYHHCRDEPLHALYDNV-EKLFPGFEIETVKSNLRILFNNAI-KKRLMTDRRIGCLL
          .KPNG..A.V.....H.C.D.PLH.L...V.EK..PGFE.ET..SNL..L..NA..K..L.TDRR..CL.
Retrocopy <KPNGTAAPVAGRRCHQCGDKPLHGLQASV<EKPGPGFEQETLTSNLWMLSDNAT<KNHLTTDRRHDCLF

Parental  SGGLDSSLVAATLLKQLKEAQVQYPLQTFAIGMEDSPDLQAARKVANHIGSEHHEVLFNSEEGIQALDEV
          SGGL..SL.AATL.KQL.....Q...QTF.I.ME.SP.......VANHIGSE.HEV..N.E.GIQAL..V
Retrocopy SGGLERSLAAATLPKQL*KFTGQNFPQTFSIVMEESPIHLLSGEVANHIGSEPHEVILNYEDGIQALEKV

Parental  IFSLETYDITTVRASVGMYLISKYIRKNTDSVVIFSGEGSDELTQGYIYFHKAPSAEKAEEE-SERLLKE
          .F.LE.YD.....AS.G.YL.S.YI.KNTDS.VI.SGE.SDEL.....YFH..PSA..A..E...RLL.E
Retrocopy TFILEMYDRVKIHASEGLYLNSGYI*KNTDSLVIVSGECSDELK*DSMYFHTQPSAVEATVE<GGRLLTE

Parental  LYLFDVLRADRTTAAHGLELRVPF
          LYLF.V..A....AA.GLEL.VPF
Retrocopy LYLFTVF*AHWINAALGLELIVPF

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_130 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000014303	1 retrocopy	retro_etel_928,
Loxodonta africana	ENSLAFG00000000909	1 retrocopy	retro_lafr_130 ,
Tursiops truncatus	ENSTTRG00000003498	1 retrocopy	retro_ttru_411,