RetrogeneDB ID: retro_lafr_1173

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_8:60684642..60685200(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000029927
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPP1R8
• Ensembl ID: ENSLAFG00000017834
• Aliases: None
• Description: None

Sequence

>retro_lafr_1173
CAGTTCAACACTGCCCACGACAAGCGTCTTTCTACTCTTACGATTGAGGAAGGGAATCTGGATATTCAGAGGCCAAAGAG
GAAGAGGAAGAACTCACAGGTGTCTTTCAGTGAGGATGATGAAATCATCAACTCAGAGGATGTGGATCCCTCAGTTAGTG
GCTTCCGGAATACGGTGCAAACTGCTGTGGTCTCAGTTAAGAAGAAGCGAATGGAGGGCTCTGGAAACCCGGGCCTGGAG
GAATCAGGGAGCAGGCACCCACAGAATTTTGCGTTCAGTGGAGGACTCTACCCGGGCTTGCCCCGCCCGCCACCCACAGT
GAAGCAGGCCCTTAGCCGCATGACGTCCATGGGACAGTGCTCATTTGTGTCTTGCCCGTGCCAAATCCTAACTTTGCCCC
TGATGTGGACTTGACTCCCATTGTGGCCTCAGCAGTGAGCATGAACCCTGCACCAAACCCTGCAGTGTGTAATTCTGAAG
CTGTAGATGAACCCAAGAAGAAGAAATTATGCAGAAGAGGCTTGGCTGGGCAAGAAGCCCATACCTTCCTTACTGATT

Alignment

ORF - retro_lafr_1173 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.06 %
• Parental protein coverage: 52.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EFNTAHNKRISTLTIEEGNLDIQRPKRKRKNSRVTFSEDDEIINPEDVDPSVGRFRNMVQTAVVPVKKKR
          .FNTAH.KR.STLTIEEGNLDIQRPKRKRKNS.V.FSEDDEIIN.EDVDPSV..FRN.VQTAVV.VKKKR
Retrocopy QFNTAHDKRLSTLTIEEGNLDIQRPKRKRKNSQVSFSEDDEIINSEDVDPSVSGFRNTVQTAVVSVKKKR

Parental  MEGPGSLGLEESGSRRLQNFAFSGGLYGGLP-PTHSEAGSQP--HGIHGTALIGGLPMPYPNLAPDVDLT
          MEG.G..GLEESGSR..QNFAFSGGLY.GLP.P........P..H..HGT.LI..LP.P.PN.APDVDLT
Retrocopy MEGSGNPGLEESGSRHPQNFAFSGGLYPGLP<PPATHSEAGP*PHDVHGTVLICVLPVPNPNFAPDVDLT

Parental  PVVPSAVNMNPAPNPAVYNPEAVNEPKKKK-YAKEAWPGKKPTPSLLI
          P.V.SAV.MNPAPNPAV.N.EAV.EPKKKK.YA.EAW.GKKP.PSLLI
Retrocopy PIVASAVSMNPAPNPAVCNSEAVDEPKKKK>YAEEAWLGKKPIPSLLI

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_1173 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012023	1 retrocopy	retro_cfam_334,
Homo sapiens	ENSG00000117751	1 retrocopy	retro_hsap_380,
Gorilla gorilla	ENSGGOG00000012062	1 retrocopy	retro_ggor_387,
Loxodonta africana	ENSLAFG00000017834	1 retrocopy	retro_lafr_1173 ,
Macaca mulatta	ENSMMUG00000006933	1 retrocopy	retro_mmul_491,
Pan troglodytes	ENSPTRG00000000417	1 retrocopy	retro_ptro_296,
Ictidomys tridecemlineatus	ENSSTOG00000004381	2 retrocopies	retro_itri_1611, retro_itri_1704,