RetrogeneDB ID: retro_lafr_6

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_61:2491572..2493456(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000028012
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TKTL1
• Ensembl ID: ENSLAFG00000005145
• Aliases: None
• Description: None

Sequence

>retro_lafr_6
GCCGCCATGGCTGACGACGCCACGCCGGACGAGGCGACCGTACAAGTGCTACGAGACGTGGCCAACCGCCTCCGGATCCA
TTCCATCCGGGCCACTTGTGCCTCTGGCTCCGGCCACCCCACGTCGTGCTGCAGCGCCGCCGAGATCATGTCGGTATTGT
TCTTCCACACTATGAGGTATAAACAGACAGACCCAGAACACCCGGACAACGACCGGTTCGTCCTCTCCAAGGGCCGTGCT
GCCCCCGTCCTTTATGCCGCTTGGGCAGAGGCTGGCACCATCAGAGAATCCGACCTGCTGAGCTTGAGGAAAATTGACTG
TGACCTAGAGGGACACCCCACCCCTAGACTGTCGTTTGTTGACGTGGCAACCGGATCACTGGGGCACGGGCTGGGCGCTG
CGTGTGGAATGGCTTATACGGGCAAGTACTTGGACAAGGCCAGCTACCGGGTCTTCTGCCTCGTGGGAGATGGCGAATCC
TCGGAAGGCTCAGTCTGGGAAGCCTTGTCCTTCGCTTCTCACTACAACTTGGACAATCTCGTAGCAATCTTTGATGTGAA
CCGCTCGGGACAAAGTGGTGTCACACCACCTGAGAACTGCACGGATGTCCATGAGAAGCGCTGTGAAGCATTTGGATGGA
ACACTTACCTAGCGGATGGCCATGATGTCGAGGCGTTGTGCCAAGCATTTTGGCAAGCCGCTCAAGTGAAGAACAAGCCC
ACTGCTATAATTGCCAAGACTTTCAAGGGCCAGGGTCTTCCAGATGTTGAGAATGCAGAAAATTGGCATGGAAGGCCAGT
GCCAAAAGACAGAGCAGATGAAATTATCAAGTTAAGTGAGAGCCAGATGCAGACCGACAGAAGTCTCCTGCCGAAATCCC
TTGTTGAAGAATCACCTCAAATCAGCATCATGCGTATAAAGATGACCTCTCCACCTGCTTATGGGGTTGGCAACAAGATA
GCTACTCAGAAAGCATTTGGTTTGGCTCTGGCCAAACTTGGCCGTGCCAATGGAAGAGTTATTGTCTTGGATGGTGACAC
AAAGAACTCCACCTTTTATGAGTTACTCAAGAAAGAACACCCTGAGAGGTTCATTGAATGTTTTATTGCTGAGCAAAACA
TGGTAAGTGTGGCACTGGGCTGTGCTGCACGGGGTCGAACCGTTGCCTTTGTTAATACCTTTGCTGCCTTTTTGACCCGA
GCATTTGATCAGATCCGGATGGGAGCCATCTCTCAAACCAACATCAACCTTGCTGGTTCCCACTGCGGGGTGTCCACTGG
TGAAGATGGACCCTCCCAGATGGCCCTGGAGGATCTAGCTATGTTCCGGAGCGTTCCCAGTTGCACTATTTTCTATCCAA
GTGATGCCGTCTCAACAGAGCATGCTGTTTGTCTGGCTGCCAATACCAAGGGAATGTGCTACATTCGGACCAGCCAACCG
GAAACTGCAGTTATTTATGCCCCGCAAGAAAACTTTGAGATTGGACAGGCCAAGGTTGTCCGCCACAGTGACAATGACAA
GGTCACAGTTATCGGAGCTGGAGTTACTCTGCACGAAGCATTAGCAGCTGCTGATGTTCTTTCTGAAGAAGGTATCTCTA
TCCGCATTATCGACCCATTTACCGTTAAACCCCTGGATGCTGCTACTGTCATCTCCAATGCAAAAGCCACAGGCAACCAG
GTTCTCACAGTGGAGGATCACTACCGAGAAGGTGGCCTAGGGGAAGCTGCATGTGCAGCTGTCTCTGGGGAGCCTGGCAT
CCTTGTTCATCAGCTAGCAGTGGCAGGAGTGCCTGGAAGTGGGAAACCTAGGGAGTTGTTGGATATGTTTGGAATTAGTG
CCAAACACATCGTAGCAGCTGTGAAACACATGCTAATGAACTAA

Alignment

ORF - retro_lafr_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.83 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAMAEDAKPDADTVQVLRDMANRLRIRSIRATCASGSGHPTSSSSAAEIMSVLFFHTMRYKQSDPENPHN
          AAMA.DA.PD..TVQVLRD.ANRLRI.SIRATCASGSGHPTS..SAAEIMSVLFFHTMRYKQ.DPE.P.N
Retrocopy AAMADDATPDEATVQVLRDVANRLRIHSIRATCASGSGHPTSCCSAAEIMSVLFFHTMRYKQTDPEHPDN

Parental  DRFIFSKGIAALALRAAW-EAGDISKPNSLSLREIDCDLEGHPTPRLSFVGVASGWLEQGLGAACGMAYT
          DRF..SKG.AA..L.AAW.EAG.I.....LSLR.IDCDLEGHPTPRLSFV.VA.G.L..GLGAACGMAYT
Retrocopy DRFVLSKGRAAPVLYAAWAEAGTIRESDLLSLRKIDCDLEGHPTPRLSFVDVATGSLGHGLGAACGMAYT

Parental  GKYFDKASYRVFCLMGDSESSEGSVWEALAFASHYSLDNLVAIFDVNRLGHSSALPLEHCTTIYQKRCEA
          GKY.DKASYRVFCL.GD.ESSEGSVWEAL.FASHY.LDNLVAIFDVNR.G.S...P.E.CT....KRCEA
Retrocopy GKYLDKASYRVFCLVGDGESSEGSVWEALSFASHYNLDNLVAIFDVNRSGQSGVTPPENCTDVHEKRCEA

Parental  FGWNTYVVDGHDVEALCQAFWLATQVKNKPTAIVAKTFKGRGIPNVESAENWYGKPMSKERADAIIKLIE
          FGWNTY..DGHDVEALCQAFW.A.QVKNKPTAI.AKTFKG.G.P.VE.AENW.G.P..K.RAD.IIKL.E
Retrocopy FGWNTYLADGHDVEALCQAFWQAAQVKNKPTAIIAKTFKGQGLPDVENAENWHGRPVPKDRADEIIKLSE

Parental  SQIETSRDLVPKPPIEDSPQINVMDIKLTTPPAYKVGDKVATRKAYGLALAKLGHANKRVIVLDSDTKNS
          SQ..T.R.L.PK...E.SPQI..M.IK.T.PPAY.VG.K.AT.KA.GLALAKLG.AN.RVIVLD.DTKNS
Retrocopy SQMQTDRSLLPKSLVEESPQISIMRIKMTSPPAYGVGNKIATQKAFGLALAKLGRANGRVIVLDGDTKNS

Parental  TFSEMFQKEHPERFIECFIAEQNMVSVALGCATRGRTIAFASTFAAFLTRAFDQIRMGAISQTNINLAGS
          TF.E...KEHPERFIECFIAEQNMVSVALGCA.RGRT.AF..TFAAFLTRAFDQIRMGAISQTNINLAGS
Retrocopy TFYELLKKEHPERFIECFIAEQNMVSVALGCAARGRTVAFVNTFAAFLTRAFDQIRMGAISQTNINLAGS

Parental  HCGVSIGGDGPSQMALEDLAMFRVIPNCTVFYPSDAVSTEHAVYLAANTKGMCFIRTSRPETAVIYAPEE
          HCGVS.G.DGPSQMALEDLAMFR..P.CT.FYPSDAVSTEHAV.LAANTKGMC.IRTS.PETAVIYAP.E
Retrocopy HCGVSTGEDGPSQMALEDLAMFRSVPSCTIFYPSDAVSTEHAVCLAANTKGMCYIRTSQPETAVIYAPQE

Parental  CFEIGQAKVVRHSDHDKVTVIGAGVTLHEALAAAEELSKQDISVRVIDLFTVKPLDAATIISSAKVTGGH
          .FEIGQAKVVRHSD.DKVTVIGAGVTLHEALAAA..LS...IS.R.ID.FTVKPLDAAT.IS.AK.TG..
Retrocopy NFEIGQAKVVRHSDNDKVTVIGAGVTLHEALAAADVLSEEGISIRIIDPFTVKPLDAATVISNAKATGNQ

Parental  IITVEDHYREGGVGEAVCAAVAMEPDILVHQLAVSGVPQNGQPSDLLDMFGISARHIIETVRGIVMS
          ..TVEDHYREGG.GEA.CAAV..EP.ILVHQLAV.GVP..G.P..LLDMFGISA.HI...V....M.
Retrocopy VLTVEDHYREGGLGEAACAAVSGEPGILVHQLAVAGVPGSGKPRELLDMFGISAKHIVAAVKHMLMN

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_6 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018441	1 retrocopy	retro_amel_119,
Equus caballus	ENSECAG00000021992	1 retrocopy	retro_ecab_6,
Felis catus	ENSFCAG00000011392	1 retrocopy	retro_fcat_84,
Loxodonta africana	ENSLAFG00000005145	1 retrocopy	retro_lafr_6 ,
Pongo abelii	ENSPPYG00000020870	1 retrocopy	retro_pabe_205,
Ictidomys tridecemlineatus	ENSSTOG00000005014	1 retrocopy	retro_itri_30,