RetrogeneDB ID: retro_lafr_579

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_23:4160595..4161011(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX3
• Ensembl ID: ENSLAFG00000018131
• Aliases: None
• Description: None

Sequence

>retro_lafr_579
CCACCCAGCAACTTCCCTGAGATCGATTTGAGCAGCCCATAGACAGTGGGGATTGGCTGGGGCCACTTCACTACCGACAA
AATCAGGATCAAAACAAATCTTCCTGTTTTCAAGCTGAGGGAATCTAATGTTGGAAGACACAGTGACTTTGAATGACTGT
GAAGTCGCTAGAAAAAGACAGCAAGGTTGCAGTTATTTTCCCCACTCCCTGGGAAAGCATTTTTGCCTCACTTTCCTTTT
AGAGGCGATGATGGATTCTTTGATGACAGTTTTATTGGAAAAAGAAGAAACGGCTGGAGCAGTTTATGAACAAGGCTGCT
TGTCATCCTCTGGCAGAGAGTGAGTGTTGTCTTCACATATTTTTAGAGGATGAAATAATAGATAAAAGCTATACTCCATC
CAAAATAAGACATGCC

Alignment

ORF - retro_lafr_579 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 85.8 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPSNFLEIDVSNPQTVGVGRGRFTTYEIRVKTNLPIFKLKESTVRRRYSDFEWLRSELERESKV-VVPPL
          PPSNF.EID.S.P.TVG.G.G.FTT..IR.KTNLP.FKL.ES.V.R..SDFE.L.S............PL
Retrocopy PPSNFPEIDLSSP*TVGIGWGHFTTDKIRIKTNLPVFKLRESNVGR-HSDFE*L*SR*KKTARLQLFSPL

Parental  PGKAFLRQLPFRGDDGIFDDSFIEERKQG-LEQFINKVAGHPLAQNERCLHMFLQDEIIDKSYTPSKIRH
          PGKAFL...PFRGDDG.FDDSFI..R..G.LEQF.NK.A.HPLA..E.CLH.FL.DEIIDKSYTPSKIRH
Retrocopy PGKAFLPHFPFRGDDGFFDDSFIGKRRNG<LEQFMNKAACHPLAESECCLHIFLEDEIIDKSYTPSKIRH

Parental  A
          A
Retrocopy A

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_579 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 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000015256	1 retrocopy	retro_eeur_525,
Echinops telfairi	ENSETEG00000003537	3 retrocopies	retro_etel_1331, retro_etel_645, retro_etel_924,
Felis catus	ENSFCAG00000024997	1 retrocopy	retro_fcat_1705,
Loxodonta africana	ENSLAFG00000018131	1 retrocopy	retro_lafr_579 ,
Oryctolagus cuniculus	ENSOCUG00000005858	2 retrocopies	retro_ocun_1022, retro_ocun_750,
Tupaia belangeri	ENSTBEG00000011755	3 retrocopies	retro_tbel_2964, retro_tbel_3503, retro_tbel_3929,
Tursiops truncatus	ENSTTRG00000008868	2 retrocopies	retro_ttru_1028, retro_ttru_1103,