RetrogeneDB ID: retro_lafr_363

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_13:58250073..58250271(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN6
• Ensembl ID: ENSLAFG00000012967
• Aliases: None
• Description: None

Sequence

>retro_lafr_363
CTAATCTAGAAGAAGCTACAGGGACAAGTGGAGAAATATCAACAGCTACAGAAGGATTTGAGTAAGTCCATGTCAGGGAG
GCAAAAGCTTGAGGCACAACTAACAGAAAATAATGTCGTGAAGGGAGAACTGGCCCTACTGGATGGGTCCAACTTGGCCT
TTAAACTTCTGGGTCCTGTGCTGGTCAAACAGGAGCTG

Alignment

ORF - retro_lafr_363 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.91 %
• Parental protein coverage: 51.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LIQKKLQGEVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQEL
          LI.KKLQG.VEKYQQLQKDLSKSMSGRQKLEAQLTENN.VK.ELALLDGSN..FKLLGPVLVKQEL
Retrocopy LI*KKLQGQVEKYQQLQKDLSKSMSGRQKLEAQLTENNVVKGELALLDGSNLAFKLLGPVLVKQEL

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_363 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011211	2 retrocopies	retro_dnov_1317, retro_dnov_2064,
Loxodonta africana	ENSLAFG00000012967	1 retrocopy	retro_lafr_363 ,
Macropus eugenii	ENSMEUG00000016778	1 retrocopy	retro_meug_1930,
Otolemur garnettii	ENSOGAG00000028341	4 retrocopies	retro_ogar_1185, retro_ogar_2023, retro_ogar_3508, retro_ogar_85,
Ochotona princeps	ENSOPRG00000000983	1 retrocopy	retro_opri_12,
Procavia capensis	ENSPCAG00000006019	1 retrocopy	retro_pcap_226,