RetrogeneDB ID: retro_lafr_1128

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_726:6940..7438(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000025875
• Aliases: None
• Description: None

Sequence

>retro_lafr_1128
TATTTCACCAAGGTGCGCACGGTCAAGGGGGTGGCGGTCGCCTGGCAGACCAAAACCTCCTTTGCCCCCGTGGGCAAGAT
GCCCCAGGTCTTTGAAGCCGAGCTCTCTGAGGAGAGCACCATCGGCTCTGCCCCCAGTCTGGCCAACACTGAGTCCCTGG
TCAGCAACCTGGAGCCCTGGCAGGAGGGGCCCCAGACCTGTACCCAGGAGCCCACCGACCAAGGGGAGGAGCATGGGGAG
AGATCCCGCGCAACCACCCCGGAGTGGCTGGTGACCCGTGAGCGCGGCTTCCGCTGCGTGGCCTGCTGCCGCGTGTTCGA
GTCCCGGGAGGCCCTCGTGGCCCATGCGGAGCATGGTGTGAGCCAGGGCTTCAGCTGGCGGGTCTTCTTTGAAGAGCTGC
TGGAGAGGCGGCTGCCACGCTCAGTGCAGCGCAGGCCCAGACGCTGCCACCAGCTGGCCAGGCGTTGCCTGAGGGCCGCC
AAGAAGAGGGAGGTGAGG

Alignment

ORF - retro_lafr_1128 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.87 %
• Parental protein coverage: 83.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YFTQVRIVKGMAVAWQTKTSLAPVGKMPQVFEAELFLEEGTISSAPSLANTESLVSALEPWQEGPKVHIP
          YFT.VR.VKG.AVAWQTKTS.APVGKMPQVFEAEL..EE.TI.SAPSLANTESLVS.LEPWQEGP.....
Retrocopy YFTKVRTVKGVAVAWQTKTSFAPVGKMPQVFEAELS-EESTIGSAPSLANTESLVSNLEPWQEGPQTCTQ

Parental  EPSVQGEEHGERSNAATLEWLVTCKHGFHCVAYCHVFESREALVVHTEHGMSQGFSCHVFSKELLESSLQ
          EP..QGEEHGERS.A.T.EWLVT...GF.CVA.C.VFESREALV.H.EHG.SQGFS..VF..ELLE..L.
Retrocopy EPTDQGEEHGERSRATTPEWLVTRERGFRCVACCRVFESREALVAHAEHGVSQGFSWRVFFEELLERRLP

Parental  AEKQAGLGRRRERQGEGKRTEEKGQLR
          ...Q....R.........R...K...R
Retrocopy RSVQRRPRRCHQLARRCLRAAKKREVR

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_1128 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000025875	2 retrocopies	retro_lafr_1128 , retro_lafr_640,