RetrogeneDB ID: retro_lafr_45

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_40:12892183..12892795(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000025695
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RAB13
• Ensembl ID: ENSLAFG00000032079
• Aliases: None
• Description: None

Sequence

>retro_lafr_45
ATGACCAAACGCTACGACCACCTCTTCAAGTTGCTGCTGATCGGAGACTCGGGGGTGGGCAAGACTTGTCTGATCATTGG
CTTTGCAGAGGACAAGTTCAACAACACTTACATCTCCACCATTGGAATTGCCTTCAAGATCCGAACTGTAGACATAGAGG
GGAAGAAGATCAAACTGCAAATCTGGGACACTGCTGGTCAAGAGCGATTCAAGACAATAACAACCGCCTATTACCGTGGA
GCCATGGGTATTATCCTAGTATACGACATCACCGATGAGAAATCCTTCGAGAACATTCAGAACCCGATGAAGAGCATCAA
AGAGAATGCCTCGGCTGGAGTGGAACGCCTCTTGCTGGGGAACAAGTGTGACATGGAAGGCAAGAGGAAAGTGCAGAAGG
AGCAGGCCGATAAGTTGGCACGGGAACATGGAATCAGGTTTTTCGAGACAAGCGCCAAATCCAGCGTGAATGTGGATGAG
GCCTTCAGTTCCCTGGCCCGGGACATCTTGCTCAAGTCCGGAGGCCGGAGATCGGGAAACAGCAACAAGCCCTCCAGCAC
TGACCTGAAAACATGTGACAGGAAGAACACCAACAAGTGCTCCCTGGGCTGA

Alignment

ORF - retro_lafr_45 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.36 %
• Parental protein coverage: 84.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TTPGIDFKIRTVDIEGRRSNCKSDKDTAGQERFKTITTAYYRGAMGIILVYDITDEKSFENIQNWMKSIK
          .T.GI.FKIRTVDIEG.........DTAGQERFKTITTAYYRGAMGIILVYDITDEKSFENIQN.MKSIK
Retrocopy STIGIAFKIRTVDIEGKKIKLQI-WDTAGQERFKTITTAYYRGAMGIILVYDITDEKSFENIQNPMKSIK

Parental  ENASAGVERLLLGNKCDMEAKRKVQKEQANKLAREHGIRFFETSAKSSVNVDEAFSSLARDILFKSGGRR
          ENASAGVERLLLGNKCDME.KRKVQKEQA.KLAREHGIRFFETSAKSSVNVDEAFSSLARDIL.KSGGRR
Retrocopy ENASAGVERLLLGNKCDMEGKRKVQKEQADKLAREHGIRFFETSAKSSVNVDEAFSSLARDILLKSGGRR

Parental  SGNSNKPSSTDLKTCDRKNTNKCSLG
          SGNSNKPSSTDLKTCDRKNTNKCSLG
Retrocopy SGNSNKPSSTDLKTCDRKNTNKCSLG

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_45 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
Canis familiaris	ENSCAFG00000017389	1 retrocopy	retro_cfam_1756,
Homo sapiens	ENSG00000143545	1 retrocopy	retro_hsap_1122,
Loxodonta africana	ENSLAFG00000032079	1 retrocopy	retro_lafr_45 ,
Macaca mulatta	ENSMMUG00000017586	1 retrocopy	retro_mmul_324,
Otolemur garnettii	ENSOGAG00000016969	1 retrocopy	retro_ogar_2441,
Pan troglodytes	ENSPTRG00000001370	1 retrocopy	retro_ptro_681,