RetrogeneDB ID: retro_lafr_919

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_5:36400790..36401087(+)
• Located in intron of: ENSLAFG00000014919

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM207A
• Ensembl ID: ENSLAFG00000010542
• Aliases: None
• Description: None

Sequence

>retro_lafr_919
ACTAACATCTTTGCCAGGACCAAGATAGACCTCAGCGACTTGGTGCAGAAGCTGGACCTGGTCGCAAGGAGTATCACTTT
CCTCAAGAGAGATGCAGAGACAGAGTCTTTTGCCCAAGAAGGAAAAGCTAAAGCTGAGGTGCAAGAGGTGGCTGCCTAAG
ATAGAAGCCATCCGCTGGCTGAGGAGAAGCACTGGGAGGCATGGTGGCAGAGCGCCGTGGACATAGTGGGGGACCTGTGT
CCACTGATAAAGGCCTTACCTGGGCTGGCAGAGGCTTACAGCAGCCCAGGAGAAAGG

Alignment

ORF - retro_lafr_919 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.76 %
• Parental protein coverage: 57.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TNVFARTKIDLSTLVQKLDLVTRSVTSLKRDAETKNPLPKKEKLK-LRREQWLQKIEAIK-LAEQKRWEA
          TN.FARTKIDLS.LVQKLDLV.RS.T.LKRDAET........K.K.LR...WL.KIEAI..LAE.K.WEA
Retrocopy TNIFARTKIDLSDLVQKLDLVARSITFLKRDAETES-FAQEGKAK>LRCKRWLPKIEAIR<LAEEKHWEA

Parental  RRRRATKVVGDLRPLMEALPELAELESSSSSR
          ....A...VGDL.PL..ALP.LAE..SS...R
Retrocopy WWQSAVDIVGDLCPLIKALPGLAEAYSSPGER

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_919 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000160256	4 retrocopies	retro_hsap_1167, retro_hsap_1916, retro_hsap_2494, retro_hsap_4325,
Gorilla gorilla	ENSGGOG00000014482	1 retrocopy	retro_ggor_1554,
Loxodonta africana	ENSLAFG00000010542	1 retrocopy	retro_lafr_919 ,
Pan troglodytes	ENSPTRG00000013995	3 retrocopies	retro_ptro_1246, retro_ptro_1446, retro_ptro_803,