RetrogeneDB ID: retro_lafr_868

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_414:50966..51488(+)
• 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_868
CTGGATTTTTTCCCTGGGCAACTTCCAGAACACACTCAAGGACCGCTTCCTGAGTCAGATCTCGCTCTTGCAGGAACATT
GGAGCTGGGTACAACAACAGGTCCTCCATCAGCAAGTCGAGCACTGCCACCTGACACACAGCCTGCTGAAAGATCAGATT
CTCTCCCTGGGCCAAGACCATAACGAGCTCCTGGACCGCCTGGTGAGGTCCATCATGCGCCTGGACTAACACTGGGACTC
CACAGAGCAGCATCACCAGCTCCAGCACTGCCACCAAATGGGGAGAAAGCTGGAAAATGAGATTCTTATTCTGGGCTACA
TTCAGAGCTGGCTCCTGGGCCACCGGCTGATGTCAACCCTGCTCCTGTACCTCTACCAACACCAGGGCTGAAGATACCAC
ACCGCCGTCCATCTCCATCTCTGGCCCCGGCACCAGGAGAAGAGCCTACTGGAGGGCTCGATTCCCAACCTGGGCCACCT
ACAGAAATGATTCCTCAACCACCTGCTCCTGCACCAACACCG

Alignment

ORF - retro_lafr_868 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.84 %
• Parental protein coverage: 81.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VDPSPGSPPEMAPGPQADVNPAPAAAPTPELQTAPAIPSPAPSLPPDPELPEGWDSYPGPPPEPAPVPPG
          .D..PG..PE...GP......A.A...T.EL.T....PS....LPPD....E..DS.PGP.P..AP.PPG
Retrocopy LDFFPGQLPEHTQGPLPESDLALAG--TLELGTTTGPPSASRALPPDTQPAERSDSLPGPRP*RAPGPPG

Parental  EVDPAPAPKPELHRAPLIPSPAPTVEPDEEPAGGSDSYPGPPPEPVPGPPAD-EPPPKPDPGPPADV-NP
          EV..AP.....LHRA....SPAP...P..E.AG..DSY.G...E..PGPPAD..P.P.P.P.P.......
Retrocopy EVHHAPGLTLGLHRAA---SPAPALPPNGEKAGK*DSYSGLHSELAPGPPADVNPAPVPLPTPGLKIPHR

Parental  APAPT-QEEPGEEPAGGPDSHPGPPTEMVPQPPAPAPTP
          .P.P.....PGEEP.GG.DS.PGPPTEM.PQPPAPAPTP
Retrocopy RPSPSLAPAPGEEPTGGLDSQPGPPTEMIPQPPAPAPTP

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_868 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,