RetrogeneDB ID: retro_lafr_268

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_108:2073328..2073670(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS26
• Ensembl ID: ENSLAFG00000007936
• Aliases: None
• Description: None

Sequence

>retro_lafr_268
GAGGCCGGAGTCGAGGTCCCAGCCTAGTGCAAAGCCCAGGAGGAGGCGGCCAGCACCGAGCCGATGACCTGGAACCAGGC
GGAAAGCCAGCTGCAGCATGAATTGCGGATGGCAAAGCTGCAGCAGGTGAGGGGGCAGGAGCGGCGGCAGGCGGAGGAAC
AGGCCTGCCAGGCCGCACAGGCGCAGGCCTGGGCGCAGGTCAGTGAGCAGGAAGTGCTGCAGCTGTAGGAGTCAGTGACA
AACGTCATCGCCGGAGAAAAACTGGAGGCGTGGGTGGAAGAAGCTTTGGACTTGGGGATGAGCTACAATTGGCTTATCAC
CAGAGAAAGGCTGATGGTCAGG

Alignment

ORF - retro_lafr_268 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.17 %
• Parental protein coverage: 58. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESRVGVLAERRARQKAAEHREMMAWNRAENQRLHELRMARLLQEAREQERLRAEEQALKAQETQAWVQLK
          E..V.V.A...A...AA...E.M.WN.AE.Q..HELRMA.L.Q..R.QER..AEEQA..A...QAW.Q..
Retrocopy EAGVEVPA*CKAQEEAAS-TEPMTWNQAESQLQHELRMAKL-QQVRGQERRQAEEQACQAAQAQAWAQVS

Parental  EREVLQLQEEAKSFITRENLEARVEEALDSPKSYNWAITREGQVVR
          E.EVLQL.E.....I..E.LEA.VEEALD...SYNW.ITRE...VR
Retrocopy EQEVLQL*ESVTNVIAGEKLEAWVEEALDLGMSYNWLITRERLMVR

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_268 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000024910	2 retrocopies	retro_dnov_2149, retro_dnov_780,
Felis catus	ENSFCAG00000028185	1 retrocopy	retro_fcat_843,
Loxodonta africana	ENSLAFG00000007936	1 retrocopy	retro_lafr_268 ,
Mus musculus	ENSMUSG00000037740	1 retrocopy	retro_mmus_978,
Nomascus leucogenys	ENSNLEG00000027041	1 retrocopy	retro_nleu_2813,