RetrogeneDB ID: retro_lafr_449

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_17:22815947..22816682(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS35
• Ensembl ID: ENSLAFG00000010490
• Aliases: None
• Description: None

Sequence

>retro_lafr_449
CCTTTTAAACCATCTGCAGTACCTCTTCCTGTTCGAACGGGTTAGCCAGTAAAAAGGGGAGTGCCCATGGCAAAGGAGGG
AAATCTAGAATGTTTAAAGATGCCCAGTTTTCTGTATTTGACCCCTGTAACAACTAAAAAACACTGTGAAGCTCTTAAAG
ATTTTTGCACTGAGTGGCCAGCTGCACTAGACAGTGATGACAAGTATGAGAAACATTTTTCTAGAGAAATTGACACAGCT
GATTTTGTGTCAGCAGGACCATCTGTTTGAAACCCTGAGGCTCAAATAGTAAACTTAAGGGTTAAACTTTCCAGTCTGAA
TACAGATGATCATGCAAAGAAGAAACTTATTGAACTTGTAGGAAAGTGATACTGCAAGACCACAGATGTGCTTACCATCA
AAACAGGTAGGTGCCCTTTCAAGAGACAGAATTATGATTATACGATTTATCTGCTAACAGTTTTATACCATGAATCTTGG
AAAACTGAAGAACGGGAGAAAAATAAGACTGAAGCAGACATGGAGGAGTACGTATGGAAAAATAGCTCCTCAGAGAAAAA
TATCTTGGAAACGCTTCTCCAGATTAAAGCTGCTGAGAAAAATATGAAAGTGAATAAAGAACAGCTCGTTGGTACTGAAG
AAATTGAAGACTACGAAAAGCCTCTTGTTACTCTTAAGATTGAGGCTGAAAATGAAAATACCATTTCTCAGTACAAAGAA
TCAGTGAAGAGTATT

Alignment

ORF - retro_lafr_449 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.22 %
• Parental protein coverage: 90.07 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PFKPSAVPLPVRMGYPVKRGVPMPKEGNLELLKIPNFLHLTPVAIKKHCEALKDFCTEWPAALDSDEKCE
          PFKPSAVPLPVR.G.PVKRGVPM.KEGNLE.LK.P.FL.LTPV..KKHCEALKDFCTEWPAALDSD.K.E
Retrocopy PFKPSAVPLPVRTG*PVKRGVPMAKEGNLECLKMPSFLYLTPVTTKKHCEALKDFCTEWPAALDSDDKYE

Parental  KHFPIEIDTADYVSAGPSVRNPKARVVTLRVKLSSLNLDDHAKKKLIKLVGERYCKTTDVLTIKTDRCPL
          KHF..EIDTAD.VSAGPSV.NP.A..V.LRVKLSSLN.DDHAKKKLI.LVG..YCKTTDVLTIKT.RCP.
Retrocopy KHFSREIDTADFVSAGPSV*NPEAQIVNLRVKLSSLNTDDHAKKKLIELVGK*YCKTTDVLTIKTGRCPF

Parental  KRQNYDYAMYLLTVLYHESWKTEEWEKNKTEADMEEYVWKNSSSEKNVLETLLRIKAAEKDMEVNKEELL
          KRQNYDY..YLLTVLYHESWKTEE.EKNKTEADMEEYVWKNSSSEKN.LETLL.IKAAEK.M.VNKE.L.
Retrocopy KRQNYDYTIYLLTVLYHESWKTEEREKNKTEADMEEYVWKNSSSEKNILETLLQIKAAEKNMKVNKEQLV

Parental  GAPEVEDYKKSVASLKNEGENENTISQYKESVKRL
          G..E.EDY.K....LK.E.ENENTISQYKESVK..
Retrocopy GTEEIEDYEKPLVTLKIEAENENTISQYKESVKSI

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_449 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000005034	1 retrocopy	retro_etel_2145,
Loxodonta africana	ENSLAFG00000010490	1 retrocopy	retro_lafr_449 ,
Oryctolagus cuniculus	ENSOCUG00000016214	1 retrocopy	retro_ocun_866,
Otolemur garnettii	ENSOGAG00000010630	2 retrocopies	retro_ogar_1121, retro_ogar_2807,