RetrogeneDB ID: retro_lafr_538

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_2:105069706..105070102(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000032525
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MALSU1
• Ensembl ID: ENSLAFG00000011921
• Aliases: None
• Description: None

Sequence

>retro_lafr_538
AAAAAAAAAAATGCAAGAGATGTTTGTGTAATCAAGGTTCCTCCTGAGATGAAATACACAAATTACTTTGTGATTGGGAG
TGGAACGTCCACCCGACACTTACATTTCATGGCCTACATTGTGAAAATGTACAAATACCTGAAGTATAAAAGTGACCCTC
GTGTTAAGATAGGAGGGAAGGACACTGAAGACTGGCTCTGTGTGGATTTTGGCAACTTGGTGATTCATTTGATGCTTCCA
GAAACCAGAGAAACCTATGAATTAGAGAAATTATGGACCCTGTGTTCTTATGACGACCAGTTAGCGCAGAAAGTGCCTGA
GACATTACCTGAAGACTTCATTCTTGGACCAGAAGACAACACTTCATCCCTGACTCCAGTGGAGTTCAAGTGTGAA

Alignment

ORF - retro_lafr_538 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.96 %
• Parental protein coverage: 58.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RQENARDICVIRVPPDMRYTDYFVIGSGTSTRHLHAMAYYIVKMYKYLKCKSDPHVKIEGKDTDDWLCVD
          ...NARD.CVI.VPP.M.YT.YFVIGSGTSTRHLH.MAY.IVKMYKYLK.KSDP.VKI.GKDT.DWLCVD
Retrocopy KKKNARDVCVIKVPPEMKYTNYFVIGSGTSTRHLHFMAY-IVKMYKYLKYKSDPRVKIGGKDTEDWLCVD

Parental  FGNMVIHLMLPETRETYELEKLWTLRSYDDQLAQMAPETLPEDFILGIEDNISSLTPVEFKCE
          FGN.VIHLMLPETRETYELEKLWTL.SYDDQLAQ..PETLPEDFILG.EDN.SSLTPVEFKCE
Retrocopy FGNLVIHLMLPETRETYELEKLWTLCSYDDQLAQKVPETLPEDFILGPEDNTSSLTPVEFKCE

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_538 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002338	1 retrocopy	retro_chof_1878,
Equus caballus	ENSECAG00000016105	1 retrocopy	retro_ecab_884,
Echinops telfairi	ENSETEG00000015566	1 retrocopy	retro_etel_574,
Loxodonta africana	ENSLAFG00000011921	1 retrocopy	retro_lafr_538 ,
Oryctolagus cuniculus	ENSOCUG00000008972	1 retrocopy	retro_ocun_621,
Otolemur garnettii	ENSOGAG00000017157	1 retrocopy	retro_ogar_2324,
Tursiops truncatus	ENSTTRG00000008920	1 retrocopy	retro_ttru_1715,