RetrogeneDB ID: retro_lafr_361

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_13:47842267..47842548(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2J
• Ensembl ID: ENSLAFG00000021507
• Aliases: None
• Description: None

Sequence

>retro_lafr_361
GAGAACACCAAGGTACCCAATGCCTGTTTGTTCACCATTGACAATGAAGGCCACACTCCAGGAAACATTATGAAATCATG
GCTGTTTAAGGACCCACAGGTACTGTTGCTGGCTACAAAGTCCCTCATCCCTTGTAGCACAGGATCATCATCTGAGTGCA
TGCCACACCCAACTACAGCCCTCAGGAAGCCTTCACCAGTTCCATCACAGACTACATCAGCAAGCTCTCCTAGCTGGAAG
AGTGCTTCTGGGTGGCCATCAAAGACAAGCCAGAAAGAATT

Alignment

ORF - retro_lafr_361 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.63 %
• Parental protein coverage: 80.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLF-AGYKVPHPLEHKIIIRVQTTPDYSPQEAFTNAI
          ..TKVPNACLFTI..E.HT.GNI.KS.L.KDPQVL..AGYKVPHPL.H.III.V..TP.YSPQEAFT..I
Retrocopy ENTKVPNACLFTIDNEGHTPGNIMKSWLFKDPQVLL<AGYKVPHPL*HRIII*VHATPNYSPQEAFTSSI

Parental  TDLISELSLLEERFRVAIKDKQEGI
          TD.IS.LS.LEE.F.VAIKDK.E.I
Retrocopy TDYISKLS*LEECFWVAIKDKPERI

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_361 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
Loxodonta africana	ENSLAFG00000021507	1 retrocopy	retro_lafr_361 ,
Myotis lucifugus	ENSMLUG00000010467	2 retrocopies	retro_mluc_2479, retro_mluc_2499,
Sus scrofa	ENSSSCG00000024080	1 retrocopy	retro_sscr_53,
Ictidomys tridecemlineatus	ENSSTOG00000006377	1 retrocopy	retro_itri_519,