RetrogeneDB ID: retro_lafr_151

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_0:116778194..116778518(+)
• Located in intron of: ENSLAFG00000015950

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSA
• Ensembl ID: ENSLAFG00000011261
• Aliases: None
• Description: None

Sequence

>retro_lafr_151
CCTGTTTCCGCTCCCCCTTCCCTTCTCTGGTGGACTCCTGGGCCCACCACATCTCAGAAACAGGAAGAGGGGAACCCCTC
GGAGGAGACTGGCTAGGAGAAACAGAACACACAGGAAAAGGAAGGTATTCTCTCTGAGAGAGCTAAGGAGGCAAAGCTAA
AGGCCAAATGTCCATGCCTAGGACAAAAGCCTGGAGGGCTCAACTTCCTTCTGAAGAGACTCCAGAAAGGACAAAAGTAC
TTTGACTCGGAAGACTACAACATGGCCAAAACCAAGATGAATAAGCAGCTGCCAAGTGCAGGACCAGACAAGAACCTGGT
GACT

Alignment

ORF - retro_lafr_151 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.9 %
• Parental protein coverage: 69.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PVDFPGPTLH-SPGPAMSQKQEEENPSEETGEEKQDTQEKEGILPERAEEAKLKAKYPSLGQKPGGSDFL
          PV..P...L...PGP..SQKQEE.NPSEETG.EKQ.TQEKEGIL.ERA.EAKLKAK.P.LGQKPGG..FL
Retrocopy PVSAPPSLLWWTPGPTTSQKQEEGNPSEETG*EKQNTQEKEGILSERAKEAKLKAKCPCLGQKPGGLNFL

Parental  MKRLQKGQKYFDSGDYNMAKAKMKNKQLPSAGPDKNLVT
          .KRLQKGQKYFDS.DYNMAK.KM.NKQLPSAGPDKNLVT
Retrocopy LKRLQKGQKYFDSEDYNMAKTKM-NKQLPSAGPDKNLVT

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_151 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001375	1 retrocopy	retro_amel_1339,
Canis familiaris	ENSCAFG00000012054	1 retrocopy	retro_cfam_507,
Loxodonta africana	ENSLAFG00000000755	2 retrocopies	retro_lafr_1058, retro_lafr_574,
Loxodonta africana	ENSLAFG00000011261	1 retrocopy	retro_lafr_151 ,
Mustela putorius furo	ENSMPUG00000004647	1 retrocopy	retro_mputfur_299,
Sorex araneus	ENSSARG00000002625	1 retrocopy	retro_sara_621,