RetrogeneDB ID: retro_lafr_577

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_221:184219..184741(+)
• 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_577
CTGGATTTTTACCCTGGACAACTTCCAAAACACACTCAAGGACTACTTCCTGAATCAGGTCCTGCGCTTGCAGCAACACT
GGAGCTGGGTACAACAACAGGTCCAACATCACCAAGTTCAGCACTGGCACCTGACAGAGAGCCTGCTGAAAGATCGGATT
CTCTCCCTGGGCCAAGACCATAACGAACTCCTGGGCCACCTGCTGAGGTCCACCATGCACCTGGGCTAACACTGGAGCTC
CACAGAGCACCATCACCAGCTCCAACACTGGCAGAAAATGGAGAGCCAGCTGGAAGATCAGATTCTTATCCTGGGCTACA
TCCAGAGCTGGCTCCTGGACCACTGGCTGTTGTCAATCCTACTCCTGTTCCTCTACCAACACCAGAGCTCACTGTAGCCC
AAAGGCCTCCATCTCAATCTCTGGCCCAGGCACCAGGAGAAGAGCCTGCTGGTGGGCTCGATTCCCATCCTGGGCCACCT
ACAGAAATGGTTCCTCAACCACCTGTTCCTGCACCAACACCG

Alignment

ORF - retro_lafr_577 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.89 %
• Parental protein coverage: 81.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VDPSPGSPPEMAPGPQADVNPAPAAAPTPELQTAPAIPSPAPSLPPDPELPEGWDSYPGPPPEPAPVPPG
          .D..PG..P....G......PA.AA..T.EL.T.....SP...L.PD.E..E..DS.PGP.P...P.PP.
Retrocopy LDFYPGQLPKHTQGLLPESGPALAA--TLELGTTTGPTSPSSALAPDREPAERSDSLPGPRP*RTPGPPA

Parental  EVDPAPAPKPELHRAPLIPSPAPTVEPDEEPAGGSDSYPGPPPEPVPGPPAD-EPPPKPDPGPPADVNPA
          EV..AP....ELHRA...PSPAPT.....EPAG.SDSYPG..PE..PGP.A...P.P.P.P.P...V...
Retrocopy EVHHAPGLTLELHRA---PSPAPTLAENGEPAGRSDSYPGLHPELAPGPLAVVNPTPVPLPTPELTVAQR

Parental  PAPTQ---EEPGEEPAGGPDSHPGPPTEMVPQPPAPAPTP
          P.P.Q.....PGEEPAGG.DSHPGPPTEMVPQPP.PAPTP
Retrocopy P-PSQSLAQAPGEEPAGGLDSHPGPPTEMVPQPPVPAPTP

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_577 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,