RetrogeneDB ID: retro_lafr_924

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_5:48187872..48188162(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTPN
• Ensembl ID: ENSLAFG00000029544
• Aliases: None
• Description: None

Sequence

>retro_lafr_924
GTGGCCAAGGGAGAAGATGTCAGCCGATCCCTAGAAGGTGGGAGGACACCTTTTCATTATGCAGCAGATTGTGGGCAGCT
TGAAATCCTGGAGTTTCTGGTACTGAAGGGACGGATACTAACGCTGCAGATAAGCATCCTATCACCCCTCTCCTATTTGC
TGGCTATGAGGACCACGTTTCCTTTATGAAGCTGCTTCTGTCAAAGGGTGCTGTTAAGACTGCCAAAGGCCCAGAGCGAC
CAACTGCACTTGAAACCACTGACAACCAGGCCATGAAAGCACTGATCCGG

Alignment

ORF - retro_lafr_924 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.51 %
• Parental protein coverage: 82.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VAKGEDVNRTLEGGRKPLHYAADCGQLEILEFLLLKG-ADINAPDKHHITPLLSAVYEGHVSCVKLLLSK
          VAKGEDV.R.LEGGR.P.HYAADCGQLEILEFL.LKG..D.NA.DKH.ITPLL.A.YE.HVS..KLLLSK
Retrocopy VAKGEDVSRSLEGGRTPFHYAADCGQLEILEFLVLKG<TDTNAADKHPITPLLFAGYEDHVSFMKLLLSK

Parental  GADKTVKGPDGLTALEATDNQAIKALLQ
          GA.KT.KGP...TALE.TDNQA.KAL..
Retrocopy GAVKTAKGPERPTALETTDNQAMKALIR

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_924 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000029544	1 retrocopy	retro_lafr_924 ,
Monodelphis domestica	ENSMODG00000013977	4 retrocopies	retro_mdom_132, retro_mdom_165, retro_mdom_1731, retro_mdom_247,
Oryctolagus cuniculus	ENSOCUG00000005642	4 retrocopies	retro_ocun_1746, retro_ocun_1830, retro_ocun_244, retro_ocun_993,
Drosophila melanogaster	FBgn0051715	1 retrocopy	retro_dmel_34,