RetrogeneDB ID: retro_lafr_145

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_0:89994304..89994631(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLLP
• Ensembl ID: ENSLAFG00000008636
• Aliases: None
• Description: None

Sequence

>retro_lafr_145
TGGGTAATGTTCATCACTGTCTTCCTCTGACTGGTGACAATCATCATCTTTATCCTGTACCTGTTCCAGCCGCACATGAA
ATTTTACATGGTGTTAATGATCATTAATGTTGGTGCCACTGTTCTCTACATCATGGCCTTCATCACCTGCCCCACTACGG
CTGAGTTGCCAGCCCTGAAGGGCACCCAGATGTATAACCAGCATGCAGCTGCCTCCTCCTTTGCGTGTTTAGTGATGATT
GCCTATGAAGTAAGAACCTTCTTCAGCTTTCAGGCCTGGCGAGGAGTAGGCAACAATGCAGCCACCAGTCAGATGGCTGG
CAGCTAC

Alignment

ORF - retro_lafr_145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.55 %
• Parental protein coverage: 57.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WLVTIIVFV----LYLFQLHMKFYMVPWPLVLMIFNVGATVLYITAFITCSAAVEVTALKGTRPYRQRAA
          W...I.VF........F.L...........VLMI.NVGATVLYI.AFITC....E..ALKGT..Y.Q.AA
Retrocopy WVMFITVFL*LVTIIIFILYLFQPHMKFYMVLMIINVGATVLYIMAFITCPTTAELPALKGTQMYNQHAA

Parental  ASFFACLVMIAYGVSAFFSFRAWRGVGSNAATSQMAGGY
          AS.FACLVMIAY.V..FFSF.AWRGVG.NAATSQMAG.Y
Retrocopy ASSFACLVMIAYEVRTFFSFQAWRGVGNNAATSQMAGSY

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_145 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012103	1 retrocopy	retro_cjac_4155,
Homo sapiens	ENSG00000102934	1 retrocopy	retro_hsap_4816,
Loxodonta africana	ENSLAFG00000008636	1 retrocopy	retro_lafr_145 ,
Macaca mulatta	ENSMMUG00000008924	1 retrocopy	retro_mmul_2569,
Nomascus leucogenys	ENSNLEG00000002825	1 retrocopy	retro_nleu_2191,
Oryctolagus cuniculus	ENSOCUG00000007353	1 retrocopy	retro_ocun_685,
Pongo abelii	ENSPPYG00000007385	1 retrocopy	retro_pabe_3744,
Pan troglodytes	ENSPTRG00000008151	1 retrocopy	retro_ptro_3205,