RetrogeneDB ID: retro_lafr_1058

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_63:5192775..5193099(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPP19
• Ensembl ID: ENSLAFG00000000755
• Aliases: None
• Description: None

Sequence

>retro_lafr_1058
TCAGGAGAAATCCTGGAGTCGGCCTCCACGGAGGAGCAGAAGAAAATGGAAGATAAAATACAAGCCCAGAGAAAGCTGAA
GAAGTAATATTAAAAGAAAGGTATCCTTGCCTGGGACAAAAGCCTGGAGGTTCAGATTTCTTAAGGAAAGAATCGTGGAA
AGGGCAAAAATATTTTGATTCTGGAGATTACACCATAGCTAAAGCCAAAATGAAGAGCAAGCAGCGTCCTACTGCAGCCC
TTGATAAGGTTGCTGGTGACCACATCCCACTCCACAGGACCTTCTCGATGGAAACCATCCCTTATTGCTAGCAAGCTGAC
TGGG

Alignment

ORF - retro_lafr_1058 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.68 %
• Parental protein coverage: 99.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SAEIPEAASVEEQKEMEDKV-TNPEKAEEAKLKARYPHLGQKPGGSDFLRKRLQKGQKYFDSGDYNMAKA
          S.EI.E.AS.EEQK.MEDK..T.PEKAEE..LK.RYP.LGQKPGGSDFLRK...KGQKYFDSGDY..AKA
Retrocopy SGEILESASTEEQKKMEDKI<TSPEKAEEVILKERYPCLGQKPGGSDFLRKESWKGQKYFDSGDYTIAKA

Parental  KMKNKQLPTAAPDKTEVTGDHI-PTPQDL-PQRKPSLVASKLAG
          KMK.KQ.PTAA.DK..V.GDHI.PTPQDL....KPSL.ASKL.G
Retrocopy KMKSKQRPTAALDK--VAGDHI<PTPQDL<SRWKPSLIASKLTG

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_1058 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000011321	2 retrocopies	retro_dord_194, retro_dord_33,
Gorilla gorilla	ENSGGOG00000025250	1 retrocopy	retro_ggor_198,
Loxodonta africana	ENSLAFG00000000755	2 retrocopies	retro_lafr_1058 , retro_lafr_574,
Loxodonta africana	ENSLAFG00000011261	1 retrocopy	retro_lafr_151,
Otolemur garnettii	ENSOGAG00000013865	1 retrocopy	retro_ogar_591,
Pongo abelii	ENSPPYG00000006487	2 retrocopies	retro_pabe_120, retro_pabe_1923,