RetrogeneDB ID: retro_lafr_884

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_44:12644342..12644629(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPPA5
• Ensembl ID: ENSLAFG00000018513
• Aliases: None
• Description: None

Sequence

>retro_lafr_884
CGCTCTCCTGAAGTGTTCCGGGTCCCCACGTGGCTTCTGGCAGCCGTATTTGACCCAAATGGACCTCAAATCCCATACCT
TGAGCAAGTGAGCAAGACTATGCTTGAGCTGAAAGTTCTGGAATCCTCTAACTTCACTGAGGTTGTGGTCTGTGCTCCTG
CTTGTACAAGTTACAGACCAAGTGGACACTCCAGTCTCTGGCTGCGTGGCACCAGCAGCAACAAGAGCAAGGGATGCTGA
GACTTGAGGAAGCCACGAATGCCCTTAAACTAGACCTCTGATTTAGT

Alignment

ORF - retro_lafr_884 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.26 %
• Parental protein coverage: 82.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KDPEVFQVPTQLLAAIFGPNGSRIPYLEQVSKTMLELKVLESSNFTEVVVYG-SYVYKLRAKWMLQSLAE
          ..PEVF.VPT.LLAA.F.PNG..IPYLEQVSKTMLELKVLESSNFTEVVV...S..YKL..KW.LQSLA.
Retrocopy RSPEVFRVPTWLLAAVFDPNGPQIPYLEQVSKTMLELKVLESSNFTEVVVCA<SCLYKLQTKWTLQSLAA

Parental  WHRQRQERGMQRLEEAMNALGLDLGFS
          WH.Q.QE.GM.RLEEA.NAL.LDL.FS
Retrocopy WHQQQQEQGMLRLEEATNALKLDL*FS

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_884 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 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012338	1 retrocopy	retro_chof_2495,
Dasypus novemcinctus	ENSDNOG00000011544	4 retrocopies	retro_dnov_115, retro_dnov_15, retro_dnov_2318, retro_dnov_53,
Loxodonta africana	ENSLAFG00000018513	1 retrocopy	retro_lafr_884 ,
Myotis lucifugus	ENSMLUG00000004463	1 retrocopy	retro_mluc_1051,