RetrogeneDB ID: retro_lafr_1135

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_75:2559093..2559512(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: U2AF1
• Ensembl ID: ENSLAFG00000011460
• Aliases: None
• Description: None

Sequence

>retro_lafr_1135
TTTGGCACTGAGAAAGACAAAGTCAACTGTTCATTTTATTTCAAAATTGGAGCATGTCGTCATGGAAACAGAGGCTCTCA
GTTGCACAATAAACCGATCTTTAGCCAGGCCACTGCCCTCTAGAACATTTACTGTAACCCTCAAAACTCTTCCCAGTCTG
CTGATGGTTTGTGCTGTGCAGAGAGCAATGTAGAGATGCAGAAACAATCTGATGAATTTTTTGAGGAGGTTTTCACAGAA
ATGGAGGAAAAAGTATGAAGTTGAGGAGATGAACATCTGTGATCATTTGGAGACCTTCTAGTTGGAAATGTATATGTCAA
GTTTCACCATGAAGAAGACGCAGAAAGGGCTGTGATTGACTTAAGTAACCTCTGGTTTCATGGACAGCCATTCACGTGGA
GCTCTCCCCTGTTACTGAT

Alignment

ORF - retro_lafr_1135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.56 %
• Parental protein coverage: 62.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FGTEKDKVNCSFYFKIGACRHGDRCSRLHNKPTFSQTIALLNIYRNPQNSSQSADGLRCAVSDVEMQEHY
          FGTEKDKVNCSFYFKIGACRHG.R.S.LHNKP.FSQ..AL.NIY.NPQNSSQSADGL.CA.S.VEMQ...
Retrocopy FGTEKDKVNCSFYFKIGACRHGNRGSQLHNKPIFSQATAL*NIYCNPQNSSQSADGLCCAESNVEMQKQS

Parental  DEFFEEVFTEMEE-KYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQP-IHAELS
          DEFFEEVFTEMEE.KY.EVEEMN.CD.L.GD.LVGNVYVKF..EEDAE.AVIDL.N.WF.GQP.IH.ELS
Retrocopy DEFFEEVFTEMEE>KY-EVEEMNICDHL<GDLLVGNVYVKFHHEEDAERAVIDLSNLWFHGQP<IHVELS

Parental  PVTD
          PVTD
Retrocopy PVTD

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_1135 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015558	1 retrocopy	retro_ecab_1081,
Homo sapiens	ENSG00000160201	2 retrocopies	retro_hsap_1478, retro_hsap_790,
Loxodonta africana	ENSLAFG00000011460	1 retrocopy	retro_lafr_1135 ,
Loxodonta africana	ENSLAFG00000012923	1 retrocopy	retro_lafr_1090,
Macaca mulatta	ENSMMUG00000022769	2 retrocopies	retro_mmul_1071, retro_mmul_2126,
Mus musculus	ENSMUSG00000061613	3 retrocopies	retro_mmus_1602, retro_mmus_1787, retro_mmus_2955,
Nomascus leucogenys	ENSNLEG00000014737	1 retrocopy	retro_nleu_2382,
Otolemur garnettii	ENSOGAG00000016504	1 retrocopy	retro_ogar_241,
Pongo abelii	ENSPPYG00000011463	2 retrocopies	retro_pabe_1227, retro_pabe_703,