RetrogeneDB ID: retro_lafr_230

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_10:45502728..45503196(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYS1-DBNDD2
• Ensembl ID: ENSLAFG00000008154
• Aliases: None
• Description: None

Sequence

>retro_lafr_230
ATGGCAGGCCAGTTCCACCGCTACCTGTGGGACCCATTACTGATCCTGTAGCCCATCATGCTCATGCAGACTGTCTATTA
TGGCTCATTGGGCCTATGGCTAGCTCTAGTAGACGGGCTGGTATACACCTGTCCTTTGCTGGACCAGATGTTCAAGGCAG
AGACCCTGGGCTTCTCCATCCCTCCAGGTTGGTTCTCCATGATGCCTTTCATCCTCAGTGCCCTCACCTGTGCCCTGGGC
TTGGTGTACTTCATTCAGTGAGAGAAGCAGTGCCTGGATTTTACCGTCACTGTCTATTTCTTTCACCTCCCAGGCTGCTG
GCTTTATAGCTCCCCTTTCCCCTTGGCTCTGACCTGGTGGTTTGTCCAAGCCGTGTGCATTGCGTTCATGGCTGTCATCG
GAGACTACCTGAGCATGCAGACAGAGCTCAAGGAAATCTCCCTCAACTCAGTCCCTAAATCCAAAGTC

Alignment

ORF - retro_lafr_230 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGQFRSYVWDPLLILSQIVLMQTVYYGSLGLWLALVDGLVRSSPSLDQMFDAEILGFSTPPGRLSMMSF
          MAGQF..Y.WDPLLIL..I.LMQTVYYGSLGLWLALVDGLV...P.LDQMF.AE.LGFS.PPG..SMM.F
Retrocopy MAGQFHRYLWDPLLIL*PIMLMQTVYYGSLGLWLALVDGLVYTCPLLDQMFKAETLGFSIPPGWFSMMPF

Parental  ILNALTCALGLLYFIRRGKQCLDFTVTVHFFHLLGCWFYSSRFPSALTWWLVQAVCIALMAVIGEYLCMR
          IL.ALTCALGL.YFI...KQCLDFTVTV.FFHL.GCW.YSS.FP.ALTWW.VQAVCIA.MAVIG.YL.M.
Retrocopy ILSALTCALGLVYFIQ*EKQCLDFTVTVYFFHLPGCWLYSSPFPLALTWWFVQAVCIAFMAVIGDYLSMQ

Parental  TELKEIPLNSAPKSNV
          TELKEI.LNS.PKS.V
Retrocopy TELKEISLNSVPKSKV

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_230 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 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011943	2 retrocopies	retro_dnov_1417, retro_dnov_1562,
Echinops telfairi	ENSETEG00000014613	2 retrocopies	retro_etel_1084, retro_etel_710,
Loxodonta africana	ENSLAFG00000008154	2 retrocopies	retro_lafr_230 , retro_lafr_360,