RetrogeneDB ID: retro_lafr_692

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_30:23281566..23282095(+)
• Located in intron of: ENSLAFG00000007854

Retrocopy information

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

Parental gene information

• Parental gene symbol: DR1
• Ensembl ID: ENSLAFG00000017540
• Aliases: None
• Description: None

Sequence

>retro_lafr_692
ATGGCTTCCTCATCTGGCAACGACGATGATCTCATTATACCCAGAGCTGCTATCAATAAGATGATCAAAGAGACTCTCCC
CAGTGTCTGGGTGCCCAGTGATGCCCGGGAGCTGCTGGTGAACTGATGCACTGAACTCATTCACCTTATATCTTCTAAAG
CCAATGAAATTTGCAACAAATCGGAAAAGAAGACCATCTCACCTGAGCATGTCATATAAACACCAGAAAGTTTGGGCTTT
GGCTTTTGTATCAGTGAAGTAAAAGAAGCCTTAAAAGAATGGAAGATGGTAGCATTAAAAAGAAGAAAGGCCAATTCTCA
TTTGGAAAACCTTGGCATCCCTGAAAAAGAATTATCTGAGGCAGTAACAGGAATTATTTGCAAAAGCTAGATAGCAACAA
GCAGAATTGGCCCAGCAGGAATGGCTTCAAATGCAGCAGGCTGCCCAACAAGCCCTGCTTCCTGCTGCCTCAGCCAGTGC
ATCCAATGAAGCAGGATCTTCTCAGGATGAAAAAGACAATGGCGATATC

Alignment

ORF - retro_lafr_692 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.49 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASSSGNDDDLTIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEH
          MASSSGNDDDL.IPRAAINKMIKETLP.V.V..DAREL.VN.CTE.IHLISS.ANEICNKSEKKTISPEH
Retrocopy MASSSGNDDDLIIPRAAINKMIKETLPSVWVPSDARELLVN*CTELIHLISSKANEICNKSEKKTISPEH

Parental  VIQALESLGFGSYISEVKEVLQECKTVALKRRKASSRLENLGIPEEEL-LRQQQELFAKARQQQAELAQQ
          VI...ESLGFG..ISEVKE.L.E.K.VALKRRKA.S.LENLGIPE.EL.LRQ.QELFAKAR.QQAELAQQ
Retrocopy VI*TPESLGFGFCISEVKEALKEWKMVALKRRKANSHLENLGIPEKEL>LRQ*QELFAKAR*QQAELAQQ

Parental  EWLQMQQAAQQAQLAAASASASNQAGSSQDEEEDDDI
          EWLQMQQAAQQA.L.AASASASN.AGSSQDE....DI
Retrocopy EWLQMQQAAQQALLPAASASASNEAGSSQDEKDNGDI

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_692 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
Callithrix jacchus	ENSCJAG00000017815	1 retrocopy	retro_cjac_410,
Cavia porcellus	ENSCPOG00000003282	1 retrocopy	retro_cpor_518,
Loxodonta africana	ENSLAFG00000017540	1 retrocopy	retro_lafr_692 ,
Myotis lucifugus	ENSMLUG00000010684	1 retrocopy	retro_mluc_2349,