RetrogeneDB ID: retro_lafr_542

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_20:7402975..7403268(-)
• Located in intron of: ENSLAFG00000028585

Retrocopy information

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

Parental gene information

• Parental gene symbol: URM1
• Ensembl ID: ENSLAFG00000002178
• Aliases: None
• Description: None

Sequence

>retro_lafr_542
CCGTTGTCAGTGAAGGTGGAGCTCAGAAGTGGCACAGAGCTCCTGTTCGATGGTATGAAGAGGCGTCAGGTCACATTGCT
TGGGCAGGAGGAGCCCTGGGATATCCAGAACCTCCTTGCCTGGACCAAGAAGAATTTGCTAAAAGAACAGCCAGACTTGT
TCACCCAAGGAGACAGTGTGCGGCTGGGAATTGCGTGCTAATGAATGATACTGACTGGGAACTGCCGGGTGAGGCAGACT
ACCAGCATCGGGACCAGGACGGTGTCCTCTTCATGTCCACACTGCATGGAGGC

Alignment

ORF - retro_lafr_542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.29 %
• Parental protein coverage: 97.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PLSVEVEFGGGAELLFNGVKKHQVTLPGQEEPWDIRNLLVWIKKNLLKERPELFIQGDSVRPGI-LVLIN
          PLSV.VE...G.ELLF.G.K..QVTL.GQEEPWDI.NLL.W.KKNLLKE.P.LF.QGDSVR.GI..VL.N
Retrocopy PLSVKVELRSGTELLFDGMKRRQVTLLGQEEPWDIQNLLAWTKKNLLKEQPDLFTQGDSVRLGI<CVLMN

Parental  DADWELLDQGELDYQLQDQDSVLFISTLHGG
          D.DWEL...GE.DYQ..DQD.VLF.STLHGG
Retrocopy DTDWEL--PGEADYQHRDQDGVLFMSTLHGG

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_542 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
Bos taurus	ENSBTAG00000025612	2 retrocopies	retro_btau_1694, retro_btau_570,
Erinaceus europaeus	ENSEEUG00000012945	1 retrocopy	retro_eeur_458,
Loxodonta africana	ENSLAFG00000002178	1 retrocopy	retro_lafr_542 ,
Macropus eugenii	ENSMEUG00000014147	1 retrocopy	retro_meug_1161,