RetrogeneDB ID: retro_lafr_765

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_36:5793433..5794020(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000030523
• Aliases: None
• Description: None

Sequence

>retro_lafr_765
GGAACGGTGGATTTCCATCCAGGGTCGCCTCCAGAACCGACTGCTGGACCACTGGCTGATGTCAGTCCTGCTCCTGCTGC
AACACTGGAGCTCCATAAAACACTGGCTAGTCCATCACCAGCTCCATTGCCGGCACCAGATGAAGAGATGGCTGGAGGGC
TGGATTGTTATCCTGGGCCACCTCCGGAACCGGCTTCTGTACCACCTGGTGAGGTTGATCCTACTTCTGCTCCAACAATG
GAACTCCATACAGGACCAGCTATTCCATCACTGGCTTTTGTGGTGGCACCTGATGAAAAGCCAGCTGGATGGTCGGATTC
TTATCCTGGGCCACCTCCAGAACCGACTACTGGACCAGTGGCTGTTGTCGATCCTTCTCCTTCTTCAACACCGGAGCTTG
ATGTAGCCCAGGTCCTCCCCCAGCTCCGTCACCAGCGTCAGATGGAGAGCCAGATGGAGAGGTGGATTCCCACCCTGGAC
CACCTCCAGAACCAGATCCTGGGTCACCAGCTGAAGTCAATTCTGCTCCTGCTCCAACGCAGGAGCTCAACAGAGCAGCA
GCTATTCCATCACCAGCTTCAGCTCTG

Alignment

ORF - retro_lafr_765 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.73 %
• Parental protein coverage: 91.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGVDPSPGSPPEMAPGPQADVNPAPAAAPTPELQTAPAIPSPAPSLPPDPELPEGWDSYPGPPPEPAPVP
          G.VD..PGSPPE...GP.ADV.PAPAA..T.EL....A.PSPAP...PD.E...G.D.YPGPPPEPA.VP
Retrocopy GTVDFHPGSPPEPTAGPLADVSPAPAA--TLELHKTLASPSPAPLPAPDEEMAGGLDCYPGPPPEPASVP

Parental  PGEVDPAPAPKPELHRAPLIPSPAPTVEPDEEPAGGSDSYPGPPPEPVPGPPA-DEPPPKPDP-GPPADV
          PGEVDP..AP..ELH..P.IPS.A..V.PDE.PAG.SDSYPGPPPEP..GP.A...P.P...P.G.....
Retrocopy PGEVDPTSAPTMELHTGPAIPSLAFVVAPDEKPAGWSDSYPGPPPEPTTGPVAVVDPSPSSTP<GA*CSP

Parental  NPAPAPTQEEPGEEPAGGPDSHPGPPTEMVPQPPAPAPTPGPPPTGSRQTSDIDPAPTPTL
          .P.PAP.....G.EP.G..DSHPGPP.E..P..PA......P.PT.........P.P...L
Retrocopy GPPPAPSPASDG-EPDGEVDSHPGPPPEPDPGSPAEV-NSAPAPTQELNRAAAIPSPASAL

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_765 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000030523	15 retrocopies	retro_lafr_1087, retro_lafr_1093, retro_lafr_1139, retro_lafr_1250, retro_lafr_259, retro_lafr_568, retro_lafr_577, retro_lafr_614, retro_lafr_723, retro_lafr_762, retro_lafr_765 , retro_lafr_788, retro_lafr_867, retro_lafr_868, retro_lafr_905,