RetrogeneDB ID: retro_lafr_955

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_51:12142940..12144558(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NARS
• Ensembl ID: ENSLAFG00000000559
• Aliases: None
• Description: None

Sequence

>retro_lafr_955
ATGGTACTAGAATAGCTATATGTCTCAGATCAAGAGGGAAATGATGCTACAGGTGATAGAACCAAAGAGAAACCTTTTAA
AACAGGTCTAAAGACTTTGAGGACAGTAGGAAAAGAACCGTTTCCTAACCATTTTATGTAGATTCACAAAAAGAAAATGA
GAGGTGGGATTTTATTCCTAAATCACAGATGAAAAACAGTAGAAAAATGTGGCAAAAGGAACAAATGAAGAGTGAATCCC
AGGAAAAGAAAGGGGCAAAAGAAAATTTCCGAAGAGAAAAAAAAACCTGGAAGAAGCAAAGAAGATTACCATTAAAAATG
ATGCAAGTCTTCCAAAGCCAAAACATGCAAAGATTAATGCATTAGAAACACATAGAGGCCAAAGAGTAAAGGTGTTTGGC
TGGGTCTACAGGCTGCGTAGGCAAGGAAAGAATTTAATGTTTCTGGTGCTGCATGATGGTACAAGATATCTCCAGGAAGT
CTTGTCAGATGAGCGGCGTCAGTGTTACAATGCAGTGATCTTGTCCACCGAGAGTAGTGATGCAGTGTATGGAATGCTAA
ACCTTACCCCAAAGGGCAAGCAGACTCCAGGGGGCCATAAGCTGAGCTGTGACTGCTGGGAACTATTTGGGTTGGCCCCT
GCTAGAGGAGCCGATAACCTGATTAACAAGGAGTTTGATGTCAATGTCCGGCTCAACAACAGACACATGATAACGTGAGG
AGAAAACAAGTCCAAAAATCCTGAAAGTCCAGTCACTGGTCACCAGGCTCTTCAGAAGTTACTTCTCTGACAGGGGGTAC
TATGAAGTTACTCATCCAACATTAGTGCAAACACGAATAGAATGTGGTGTCACACTCTTCAAGCTTGGCTATTTCGGGGA
AGAGGCGTTTCTGACACAGTCCTCTCAGTTGTACCCGGAGACCTGCATCCCAGCGCTTGGAGAAAAGTTTTGCATCACAT
AGTCATACAGGGCAAAGCAATCCAGAACATGAAGGCACCTGGCAGAGTACACTCACGTAGAAGCAGAGTGCCCTTTCCTG
GCCTTTGAGGAGCTCCTGGCCTGACTGGAGGACTTGATTTGTGATGTGGTGGACAGAGTCTTAAATTCCCCACGGCAAGC
ATAGCGTATGACCTCAACCTGAACTTCAAGTGCCCCAAATGGCCTTTTAAACAGATGAACTACTCAGATGCCATTGTGTG
GCAAAAAGAACACAATATAAAGAAAGAAGATGGAACTTTCTGTGAATTTGGAGACGATATCCCAGAAGCTCCTGAGAGAC
TGATGGAAAACACCATTAATGAGCTGTGTCGATTTCCAGTAGAGATCAAATCCTTCTACATGCAGCAATGTCCTGAGGAT
TCCTGCCTTACTGAATCTGTTGAAGTGTTGCTGTCTAATGTTGGTAAAATTGTGCGAGACTCCATGTGTATTTGGGATAG
TGAAGAGATGTTGGCAGGCTACAAAAGAGAAGTGATTGACCCCACTCCCTGTTGTTGGTATATGGATCAGAGAAAATACC
CTCATGGAGGATATGGCTTGGGCTTAGAATGATTCCTAACTTGGATTCTGAATAGGTATCACATCCCAAATGTGTGCTTA
TACCCTTGATTTGTCCAG

Alignment

ORF - retro_lafr_955 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.55 %
• Parental protein coverage: 97.32 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MVLGELYVSDREGNDDTGDGTKEKPFKTGLKALMTVGKEP-FPTI-YVDSQKENERWDVISKSQMKNIRK
          MVL..LYVSD.EGND.TGD.TKEKPFKTGLK.L.TVGKEP.F.TI.YVDSQKENERWD.I.KSQMKN.RK
Retrocopy MVLE*LYVSDQEGNDATGDRTKEKPFKTGLKTLRTVGKEP>FLTI>YVDSQKENERWDFIPKSQMKNSRK

Parental  MWHREQTKSESREKKEAEDNLRREKNL-EEAKKITIK-NDPSLPEPKCVKIHALEAHRGQRVKVFGWVHR
          MW..EQ.KSES.EKK.A..N.RREK...........K.ND.SLP.PK..KI.ALE.HRGQRVKVFGWV.R
Retrocopy MWQKEQMKSESQEKKGAKENFRREKKTWKKQRRLPLK<NDASLPKPKHAKINALETHRGQRVKVFGWVYR

Parental  LRRQGKNLMFLVLRDGTGYLQCVLSDELCQCYNGLVLSTESSVAVYGVLNLTPEGKQAPGGHELSCDFWE
          LRRQGKNLMFLVL.DGT.YLQ.VLSDE..QCYN...LSTESS.AVYG.LNLTP.GKQ.PGGH.LSCD.WE
Retrocopy LRRQGKNLMFLVLHDGTRYLQEVLSDERRQCYNAVILSTESSDAVYGMLNLTPKGKQTPGGHKLSCDCWE

Parental  LIGLAPAGGADNLLNEESDVDVQLNNRHMMIRGENMS-KILRARSLATRCFRDHFFDRGYCEVTPPTLVQ
          L.GLAPA.GADNL.N.E.DV.V.LNNRHM...GEN.S.KIL...SL.TR.FR..F.DRGY.EVT.PTLVQ
Retrocopy LFGLAPARGADNLINKEFDVNVRLNNRHMIT*GENKS>KILKVQSLVTRLFRSYFSDRGYYEVTHPTLVQ

Parental  TQVEGGATLFKLDYFGEEAFLTQSSQLYLETCLPALGDVFSIAQSYRAEQSRTRRHLAEYTHIEAEFPFA
          T..E.G.TLFKL.YFGEEAFLTQSSQLY.ETC.PALG..F.I..SYRA.QSRT.RHLAEYTH.EAE.PF.
Retrocopy TRIECGVTLFKLGYFGEEAFLTQSSQLYPETCIPALGEKFCIT*SYRAKQSRT*RHLAEYTHVEAECPFL

Parental  TFEDLLARVEDLVCDVVDRILKS-PAASIVYDLNPNFKPPKRPFKRMNYSDAIVWLKEHNIKKEDGTFYE
          .FE.LLA..EDL.CDVVDR.L.S.P.ASI.YDLN.NFK.PK.PFK.MNYSDAIVW.KEHNIKKEDGTF.E
Retrocopy AFEELLA*LEDLICDVVDRVLNS<PTASIAYDLNLNFKCPKWPFKQMNYSDAIVWQKEHNIKKEDGTFCE

Parental  FGEDIPEAPERLMTDTINEPILLCRFPVQIKSFYMQRCSEDSRLTESVDVLMPNVGEIVGGSMRIWDSEE
          FG.DIPEAPERLM..TINE...LCRFPV.IKSFYMQ.C.EDS.LTESV.VL..NVG.IV..SM.IWDSEE
Retrocopy FGDDIPEAPERLMENTINE---LCRFPVEIKSFYMQQCPEDSCLTESVEVLLSNVGKIVRDSMCIWDSEE

Parental  MLAGYKREGIDPTPYYWYTDQRKYGTCAHGGYGLGLERFLTWLLNRYHIRDVCLYPRFLQ
          MLAGYKRE.IDPTP..WY.DQRKY....HGGYGLGLE.FLTW.LNRYHI..VCLYP.F.Q
Retrocopy MLAGYKREVIDPTPCCWYMDQRKY---PHGGYGLGLE*FLTWILNRYHIPNVCLYP*FVQ

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_955 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003837	2 retrocopies	retro_cjac_2194, retro_cjac_3091,
Cavia porcellus	ENSCPOG00000013227	3 retrocopies	retro_cpor_1441, retro_cpor_429, retro_cpor_736,
Loxodonta africana	ENSLAFG00000000559	1 retrocopy	retro_lafr_955 ,
Macropus eugenii	ENSMEUG00000000774	1 retrocopy	retro_meug_2019,
Otolemur garnettii	ENSOGAG00000016302	1 retrocopy	retro_ogar_1061,
Ictidomys tridecemlineatus	ENSSTOG00000002118	1 retrocopy	retro_itri_591,