RetrogeneDB ID: retro_lafr_539

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_20:25268639..25269920(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DEPDC7
• Ensembl ID: ENSLAFG00000008704
• Aliases: None
• Description: None

Sequence

>retro_lafr_539
TCTGAATATTTTGGTGCTGAAGACATTCCTTGGGCCAAAGTGGTGAAAGTGTGTTAAGCACTTACGGATGACAAAGTATT
CGAAGTTCCAACCAAAGTTTTTGGCAAAGACAGAAAAAACTATATTTGAAGGTACTAGTCAGCCTTTATAGATTCACAAT
GATACCTAACCAAGACAGTCAATGAGGCAAAGAAAACAAACTACATTCACCTTCTAGGTATGCCAATGTACAAGTTAAGT
CACCTGATATCAGATCAACAAGTTTAGAGGATTTATGGGAAAATCTGAGTTTAAAGCCAGCTAACTCCCCTCATGTCAAT
ATCTCTGCAATCTTGTCTCCACAAGTTATTGATGAAGTCTGGCAAAAAGAAACAGCTGGGCGTCTATTACAACTTGTAGA
CCTTCCACTTCTTCACTCCTTACTTAAACAGCAAGAGGTTGTACCTAAAGTTCCTCAACCTAAGAGGAAGCCAGTCTTGA
TCTACAACAGCAGCTATCTAGATCGAGGGATTCTCAAGGGTTATAGTGACTCTCAGGAAAATGAGTGGTTCTCTGCAGCA
ATTGACTACTTGGAATACTTCCCAGACTAGATGGTGGTGGATATAAGCAGAAACTTTCCTAAGCAACCAGATAGTACAGA
TATAGTGAAAGAACTTCTATGTGATGCCATTGGTAATTCTTACAGCAGTAGGAAACCTCTGTTAAATCATTTATCTGATG
TTCGTAATGGAATTGCAGAACTTTTAGTCAATGGGAAGACTGAAATAGCATTAGAAGCTACTCAACACTTTCTAAAACTT
TTGGACTCCCAAAATAGAGAAGAATTTAAAAGACTACTGTATTTCATGGCTGTTGCAGCACGTCCTTCTGAATTTAAATT
ACGCAAAGAAAGTGGCAACCAAATGGCTGTAGAAAGAATATTCTCGAAAGCTATTGTTGACAATAAAATTTATCCAAAGG
CAAAACTGATCTTCTAGTACTCTTTTTAATGGATCATCAAAATGATCTTTTTAAGATTCCTGGAACTTGACATAAAATTG
TTAGCGTTAAGCTCATGGCCATAAAGGTGAGACGAGATCCAAACAGCAAAACAGGATATATTGATAGCCAGAGAATTGAT
GAAAGTGACTATCCCAACAGTACACAGAAGACAATCAAGATGAGCTGTTGAATTTACTAAAAACTATTGATGAGAACTCC
AAATTGTCTGCCAAAGAGAAGAAAAAAATTGCTAGATTAGTTCTGTGTCACTTAAACATCTTCACTGAGTATTGTGGAGC
C

Alignment

ORF - retro_lafr_539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.62 %
• Parental protein coverage: 84.21 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NKYFGDVDIPRTKVVRVCQALMDYKIFEAVPTKVFGKDK-KPTFEDSSSSLYRFTTIPNQDSQLGKENKL
          ..YFG..DIP..KVV.VC.AL.D.K.FE.VPTKVFGKD..K........SLYRFT.IPNQDSQ.GKENKL
Retrocopy SEYFGAEDIPWAKVVKVC*ALTDDKVFE-VPTKVFGKDR<KKLYLKVLVSLYRFTMIPNQDSQ*GKENKL

Parental  HSSSGCADMLFKSSDIKSASLEDLWENLSLKPASSPHVNISAALSPQVINEVWQEETIGRLLQLVDLPLL
          HS.S..A....KS.DI.S.SLEDLWENLSLKPA.SPHVNISA.LSPQVI.EVWQ.ET.GRLLQLVDLPLL
Retrocopy HSPSRYANVQVKSPDIRSTSLEDLWENLSLKPANSPHVNISAILSPQVIDEVWQKETAGRLLQLVDLPLL

Parental  DSLLKQQEVVSKVPQPKRQPDLIYNSSYLDRGILKAYSDSQEDEWLSAAIDCLEYLPDQMVVDISRNFPE
          .SLLKQQEVV.KVPQPKR.P.LIYNSSYLDRGILK.YSDSQE.EW.SAAID.LEY.PD.MVVDISRNFP.
Retrocopy HSLLKQQEVVPKVPQPKRKPVLIYNSSYLDRGILKGYSDSQENEWFSAAIDYLEYFPD*MVVDISRNFPK

Parental  QPDKTDVVKELLFDAIGNYYSSREPLLNHLSDVHNGIAELLAKVNGKTETALEATQLFLKLLDSQNREEF
          QPD.TD.VKELL.DAIGN.YSSR.PLLNHLSDV.NGIAELL..VNGKTE.ALEATQ.FLKLLDSQNREEF
Retrocopy QPDSTDIVKELLCDAIGNSYSSRKPLLNHLSDVRNGIAELL--VNGKTEIALEATQHFLKLLDSQNREEF

Parental  RRLLYFMAVAAHPSEFKLQKESDNRMVVKRIFSKAIVDNK-NLSKGKTDLLVLFLMDHQKDVFKIPGTLH
          .RLLYFMAVAA.PSEFKL.KES.N.M.V.RIFSKAIVDNK.NLSKGKTDLLVLFLMDHQ.D.FKIPGT.H
Retrocopy KRLLYFMAVAARPSEFKLRKESGNQMAVERIFSKAIVDNK<NLSKGKTDLLVLFLMDHQNDLFKIPGT*H

Parental  KIVSDKLMAIQEGRDPNSETGYIYCQRIDQSDYPNSTQKATK-DELLNLLKTIDEDSKLSAKEKKKLLGQ
          KIVS.KLMAI...RDPNS.TGYI..QRID.SDYPNSTQK..K.DELLNLLKTIDE.SKLSAKEKKK....
Retrocopy KIVSVKLMAIKVRRDPNSKTGYIDSQRIDESDYPNSTQKTIK<DELLNLLKTIDENSKLSAKEKKK-IAR

Parental  FYKCHPNIFIEYFGA
          ...CH.NIF.EY.GA
Retrocopy LVLCHLNIFTEYCGA

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_539 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012405	1 retrocopy	retro_dnov_1210,
Echinops telfairi	ENSETEG00000017093	1 retrocopy	retro_etel_1447,
Loxodonta africana	ENSLAFG00000008704	1 retrocopy	retro_lafr_539 ,
Monodelphis domestica	ENSMODG00000009718	1 retrocopy	retro_mdom_1180,