RetrogeneDB ID: retro_lafr_282

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_11:66433823..66434193(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHTOP
• Ensembl ID: ENSLAFG00000002658
• Aliases: None
• Description: None

Sequence

>retro_lafr_282
GTGAATATTCGAGTTTCGATGCAGCAACAACAGCAGCTAGCCAGTGCCAGAAACAGAAGACTGGCCCAGCAGATGGAGAA
TAGACCCTCTGTCCAGGCAGCATTAAAACTTAAGCAGAGCTTAAAACAGAGCTGGGTAAGAGAACATCCAGGCACCGTTA
GGCCCACCCGTAGGTGCCCTGGCCAGGGGAGCAATCGGAGGACGAGGCCCGCCCAGAATCCAGAGAGGCTTGACCAGAGG
AAGACTATGTGGGGGACATGCCAGGAGAATCCTACTTAGAGCCAGGATGTCACTCCGAGGTCTGGGTATGCTAGATCAGG
GAAAAGGGAGCTTTGCAGGCAGACGCAGAGGCCATGGATGAGGGAGTGGT

Alignment

ORF - retro_lafr_282 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.32 %
• Parental protein coverage: 51. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VNIRASMQQQQQLASARNRRLAQQMENRPSVQAALKLKQKSLKQ-RLGK-SNIQARLGRPIGVLARGAIG
          VNIR.SMQQQQQLASARNRRLAQQMENRPSVQAALKLKQ.SLKQ..LGK..NIQA.LG.P.G.LARGAIG
Retrocopy VNIRVSMQQQQQLASARNRRLAQQMENRPSVQAALKLKQ-SLKQ<ELGK<ENIQAPLGPPVGALARGAIG

Parental  GRGLPIIQRGLPRGGLRGGRATRTLLRGGMSLRGQNLLRGGRAVAPRMGLRRGGVRGRG
          GRG.P.IQRGL.RG.L.GG.A.R.LLR..MSLRG...L..G.......G.RRG...G.G
Retrocopy GRGPPRIQRGLTRGRLCGGHARRILLRARMSLRGLGMLDQGK--GSFAGRRRGHG*GSG

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_282 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013518	1 retrocopy	retro_chof_6,
Dasypus novemcinctus	ENSDNOG00000004834	1 retrocopy	retro_dnov_1054,
Equus caballus	ENSECAG00000020889	1 retrocopy	retro_ecab_729,
Loxodonta africana	ENSLAFG00000002658	3 retrocopies	retro_lafr_131, retro_lafr_282 , retro_lafr_656,
Myotis lucifugus	ENSMLUG00000016098	2 retrocopies	retro_mluc_201, retro_mluc_247,
Rattus norvegicus	ENSRNOG00000012760	1 retrocopy	retro_rnor_1095,
Vicugna pacos	ENSVPAG00000010259	1 retrocopy	retro_vpac_353,