RetrogeneDB ID: retro_lafr_1086

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_67:11870283..11870589(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRTAP12-4
• Ensembl ID: ENSLAFG00000003471
• Aliases: None
• Description: None

Sequence

>retro_lafr_1086
ATGTGCCACACCTTCTGCTCCACGGGCTGCCAGTTGGCCTGCTGTCCACCCCCTTGCTGTGTCCCCACCGCCTGCTGCTC
ACCCTTGGGCTGTGGGAGCTCCTGCTGCTGCCCAGTGTCCTGTGTGACTCTGCTGTGCTGACCTGTGTGTGGCGTGGCCA
GCTCCTGTCAGTCACCCTGTGGGGTTGCCAGCAGCTGCTCTGGTAGTTGCCAGTCCCTGTGCTTCCCTATGGCCTGTGGC
CAGGCCTCCTCCTGCAGCTCGGCCTCCTCCTGCAGCTCAGCCTGCTGTGTGCCCAGCCCCTGCCAA

Alignment

ORF - retro_lafr_1086 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.81 %
• Parental protein coverage: 69.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCHTSCSTGCQSVCCPPPRCVPTACCSPLGCGSSCCHPVSCMTLLCRPVCGVSACCVPSPCQATCCVPIR
          MCHT.CSTGCQ..CCPPP.CVPTACCSPLGCGSSCC.PVSC.TLLC.PVCGV...C..SPC.........
Retrocopy MCHTFCSTGCQLACCPPPCCVPTACCSPLGCGSSCCCPVSCVTLLC*PVCGVASSC-QSPCGVASSCSGS

Parental  CKPALCVPVRCSTVVTCCLPVSCKPAVCVPVSCK
          C...LC.P...................CVP..C.
Retrocopy CQ-SLCFPMXXXXXXXXXXXXXXXXXXCVPSPCQ

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_1086 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000003471	3 retrocopies	retro_lafr_1084, retro_lafr_1085, retro_lafr_1086 ,
Macaca mulatta	ENSMMUG00000022561	1 retrocopy	retro_mmul_270,