RetrogeneDB ID: retro_lafr_414

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_15:55148427..55148663(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CYB5A
• Ensembl ID: ENSLAFG00000010020
• Aliases: None
• Description: None

Sequence

>retro_lafr_414
GCTGGCAGTGATGTTACGAAGAACTTTGAGGATGTTGGGCACTCTACAGATGCTAGAGAAAAGGCCAAAACATTCATCAT
TGGGGAGCTTCATCCAGATGACAGGTCAAAGCTTACCAAACCTTTGGAAACTTTATTACTACTGTTGATTCTTATTCCAG
TTGCTGGACCAGTTGGGTGATCCCAGCTATCTTGGCACTGATTGTAGCCCTCATGTATCACCTCTACATAGCAGAA

Alignment

ORF - retro_lafr_414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.25 %
• Parental protein coverage: 83.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGGDATENFEDVGHSTDAREMSKTFIVGELHPADRSKLTKPSETL-ITTVDSNSSWWTNWVIPAISALIV
          AG.D.T.NFEDVGHSTDARE..KTFI.GELHP.DRSKLTKP.ETL.ITTVDS.SS.WT.WVIPAI.ALIV
Retrocopy AGSDVTKNFEDVGHSTDAREKAKTFIIGELHPDDRSKLTKPLETL<ITTVDSYSSCWTSWVIPAILALIV

Parental  ALMYRLYTAE
          ALMY.LY.AE
Retrocopy ALMYHLYIAE

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_414 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000026	2 retrocopies	retro_cfam_32, retro_cfam_787,
Equus caballus	ENSECAG00000017581	1 retrocopy	retro_ecab_12,
Loxodonta africana	ENSLAFG00000010020	1 retrocopy	retro_lafr_414 ,
Rattus norvegicus	ENSRNOG00000015205	2 retrocopies	retro_rnor_1565, retro_rnor_2455,
Drosophila melanogaster	FBgn0029854	1 retrocopy	retro_dmel_39,