RetrogeneDB ID: retro_lafr_1140

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_76:1993540..1994334(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NETO2
• Ensembl ID: ENSLAFG00000007257
• Aliases: None
• Description: None

Sequence

>retro_lafr_1140
ATGTATATTTTGGAAGCTGCTCCACGGCAAAGAATAGAGTTGACCTTTGATGAACATTATTATATAGAACCATCATTTGA
ATGTCGGTTTGATCACTTGGAAGTTTGAGACGGGCCATATGGTTTCTCTCTGCTTATAGGTCGTTACTGTGACGTGAAAA
GCAGCCCGTTAATTAGATCAACGGGGAGATTCATGTGGATTAAGTTCAGTTCCGATGAAGAACCAGAAGGACTGGGTTTT
CAAGCAAAATATTCGTTTATTCCAGATCCAGAGTTCACTTACCTAGGAGGTATTTTAAACTCCATCCCAGACTGCCAGTT
TGAGCTCTCAGGAGCTGATGGAACAGTGCATTCTAGTCAGGTAGAACAAGAAGAAAAAACAAAACCTGGCCAAGCCGTTG
ATTGCATATGGACAATTAAAGCTACCCCAAAAGCAAAGATTTATTTGAGGTTCCTAGATTATCAAATGGAGCACTCAAAT
GAATGCAAAAGAAACTTCGTGGCAGTCTATGATAGAAGCAGTTCTATTGAGAACCTGAAAGCCAAGTTTTGCAGCACCGT
GGCCGATGATGTGATGCTTAAAACAGGAGTTGGAGTGATCCGGAGGTGGGCAGAGGAGGGCAGCCGGCTCAGCAGGTTTA
GGATGCTGTTTACATCCTTTGTGGAACCTCTCTGCACAAGCACCACTTTCTTCTGCCACAGTAACATGTGCATCAATAAT
CCTTTAGTCTGCAACATTACCAGAACTGTACATACCCTTGGGATGAAAACCGCTGTAAAGGGCTTGAAGAGGCT

Alignment

ORF - retro_lafr_1140 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.72 %
• Parental protein coverage: 50.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IYILEAAPRQRIELTFDEHYYIEPSFECRFDHLEVRDGPFGFSPLIDRYCGMKSPPLIRSTGRFMWIKFS
          .YILEAAPRQRIELTFDEHYYIEPSFECRFDHLEV.DGP.GFS.LI.RYC..KS.PLIRSTGRFMWIKFS
Retrocopy MYILEAAPRQRIELTFDEHYYIEPSFECRFDHLEV*DGPYGFSLLIGRYCDVKSSPLIRSTGRFMWIKFS

Parental  SDEELEGLGFRAKYSFIPDPDFTYLGGILNPIPDCQFELSGADGIVRSSQVEQEEKTKPGQAVDCIWTIK
          SDEE.EGLGF.AKYSFIPDP.FTYLGGILN.IPDCQFELSGADG.V.SSQVEQEEKTKPGQAVDCIWTIK
Retrocopy SDEEPEGLGFQAKYSFIPDPEFTYLGGILNSIPDCQFELSGADGTVHSSQVEQEEKTKPGQAVDCIWTIK

Parental  ATPKAKIYLRFLDYQMEHSNECKRNFVAVYDGSSSIENLKAKFCSTVANDVMLKTGVGVIRMWADEGSRL
          ATPKAKIYLRFLDYQMEHSNECKRNFVAVYD.SSSIENLKAKFCSTVA.DVMLKTGVGVIR.WA.EGSRL
Retrocopy ATPKAKIYLRFLDYQMEHSNECKRNFVAVYDRSSSIENLKAKFCSTVADDVMLKTGVGVIRRWAEEGSRL

Parental  SRFRMLFTSFVEPPCTGTTFFCHSNMCINNSLVCN-GVQNCAYPWDENHCKEKKKA
          SRFRMLFTSFVEP.CT.TTFFCHSNMCINN.LVCN...QNC.YPWDEN.CK....A
Retrocopy SRFRMLFTSFVEPLCTSTTFFCHSNMCINNPLVCN<HYQNCTYPWDENRCKGLEEA

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_1140 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000007257	1 retrocopy	retro_lafr_1140 ,
Otolemur garnettii	ENSOGAG00000004721	1 retrocopy	retro_ogar_3494,