RetrogeneDB ID: retro_lafr_689

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_30:19956526..19957492(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX41
• Ensembl ID: ENSLAFG00000026418
• Aliases: None
• Description: None

Sequence

>retro_lafr_689
ATGGAGGAGTCGGAATCAGAGCACAAGCGGGCACGCATCAACTGGGCGACTGCCTGAGGAAGCCGCTCCGGGGAGGAAGA
GGCGGGTGAGGACTATGTGCCCTATGGGCTACTGCGGCAGCGTTGGCAACTGCTGATCCGGAAGCTTTTACAGCAAAGGC
ACAAGGGGGCTGAGGAGGAGGAGCAGCAGGACAGCAGCAGCGAGCTCCAGAGAGATGAGGGCGACATCTCGCTGGGCCCT
CAGTCCAAAGTCTGCCTCCTGGAGCTACACCAGCCCCTCAAAAAGAAGGCCAAAGCCCACAAAGAGTCCGCCATGGAGAA
GCAGCTAAAGGAAGAAGAGAAGATTCTGGAGAGTGCGGCCGAGGGCTGAGCCTTGATGTCAGTGAAGGAGATGGCCAAGG
GAATCACATACAACCCAATCAAAACCAGTTGGATGCCCCCAGGTTACGCCCTAAGTACATCTGAAGCACAGCACGAGCGC
ATACAGAAGAAGTACCAAATCCTGGTGGAGGGAGATGGTATCCCACCACCTACGAAGAGCTTCAAGGAAATGAAATTCCC
TGCAGCCATCCTGAGATGCCTGAAGAAAGGTATTCAGCACCCGACGCCCATTCAGACCCAGGGCATCCCCACCATTCTAT
CCAGCCGGGACATGATTGGTATTGCCTTCACCGGTTCTGGCATGACATTGGTGCCCATCATCATGCTCTGCCTGGAACAA
GAGAAGAGGTAACCTTTCTCCAAGTATGAGGGCTCCTGTGGACTCATCATCTGCCCTTTGTGGGAGCTGGTCTGACAGAC
TCATGGCATCCTGGAGTACTATTGCCCTCTGCTTCAGGAAGACTGCTCGTCCCTGCTGCACTGTGCACTCTGCGTTGGGG
CATGTTTATGAAAGAGCAGATGGAGACCATCTGACACAGGGCGCACATGATGGTGTCCACCCCCTGGGTGCTTCACAGAT
CTGCTA

Alignment

ORF - retro_lafr_689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.55 %
• Parental protein coverage: 53.43 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEESEPERKRARTDEATAGGGRSEAEDEDDEDYVPYVPLRQRRQLLLQKLLQRRRKGAAEEEQQDSGSEP
          MEESE.E.KRAR...ATA.G.RS..E.E..EDYVPY..LRQR.QLL..KLLQ.R.KGA.EEEQQDS.SE.
Retrocopy MEESESEHKRARINWATA*GSRS-GEEEAGEDYVPYGLLRQRWQLLIRKLLQQRHKGAEEEEQQDSSSEL

Parental  RGDEDDIPLGPQSNVSLLDQHQHLKEKAEARKESAKEKQLKEEEKILESVAEGRALMSVKEM-KGITYDD
          ..DE.DI.LGPQS.V.LL..HQ.LK.KA.A.KESA.EKQLKEEEKILES.AEG.ALMSVKEM.KGITY..
Retrocopy QRDEGDISLGPQSKVCLLELHQPLKKKAKAHKESAMEKQLKEEEKILESAAEG*ALMSVKEMAKGITYN-

Parental  PIKTSWMPPRYVLSMSEERHERVRKKYHILVEGDGIPPPIKSFKEMKFPAAILRGLKKKGIHHPTPIQIQ
          PIKTSWMPP.Y.LS.SE..HER..KKY.ILVEGDGIPPP.KSFKEMKFPAAILR.L.KKGI.HPTPIQ.Q
Retrocopy PIKTSWMPPGYALSTSEAQHERIQKKYQILVEGDGIPPPTKSFKEMKFPAAILRCL-KKGIQHPTPIQTQ

Parental  GIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQEKRLPFSKREGPYGLIICPSRELARQTHGILEYY
          GIPTILS.RDMIGIAFTGSG.TLV...P.IM.CLEQEKR.PFSK.EG..GLIICP..EL..QTHGILEYY
Retrocopy GIPTILSSRDMIGIAFTGSGMTLV---PIIMLCLEQEKR*PFSKYEGSCGLIICPLWELV*QTHGILEYY

Parental  CRLLQEDSSPLLRCALCIG-GMSVKEQMETIRHGVHMMVAT-PGRLMDLL
          C.LLQED.S.LL.CALC.G.GM..KEQMETI.H..HMMV.T.PG...DLL
Retrocopy CPLLQEDCSSLLHCALCVG<GMFMKEQMETI*HRAHMMVST>PGCFTDLL

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_689 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
Cavia porcellus	ENSCPOG00000008770	1 retrocopy	retro_cpor_1521,
Loxodonta africana	ENSLAFG00000026418	1 retrocopy	retro_lafr_689 ,
Macropus eugenii	ENSMEUG00000014375	1 retrocopy	retro_meug_2040,
Otolemur garnettii	ENSOGAG00000011123	1 retrocopy	retro_ogar_1801,
Rattus norvegicus	ENSRNOG00000012771	1 retrocopy	retro_rnor_2396,
Sarcophilus harrisii	ENSSHAG00000014005	1 retrocopy	retro_shar_53,