RetrogeneDB ID: retro_lafr_718

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_32:7007142..7007574(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000031385
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PLA2G12A
• Ensembl ID: ENSLAFG00000000852
• Aliases: None
• Description: None

Sequence

>retro_lafr_718
AATGGCATTCACAAGATAGACACATACCTGAAGGCCGCCTTGGACATCCTGGGAGGCAAGAATGGGCTCTGCCAATGTAA
GTGTGGTGAGGGATCTAAGCCTTACCCACGTTATTGTTATAAACCCTCTCCACCGAATGGGTATGGCTCTCCGCTGTTTG
GGTTCACATTAACACTGGCATCCCTTCCCTGACGAAGTGCTGCAACCAACACGACAGGTGCTACAAGGCCTGTGGCAAAA
GCACGAATGACTGTGACGAGGAGTTCCAGTACTGCCTCTCCAAGATCTGCCGAGATGTGCAGAAAACACTAGGACTCGCT
CAGCGTGTTCAGGCCTGTGAAACAACAATGGAGCTCTTGTTTGACAGTGTTGTGCATTTAAGGCTGTATACCAGACCTGG
ACAGCCAAAAAGCTGCATGTTGGTGTTGCTAC

Alignment

ORF - retro_lafr_718 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.51 %
• Parental protein coverage: 75.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NGVHRIDTYLNAALDLLGGEDGLCQYKCNDGSKPYPRHGYKPSPPNGCGSPLFG-VHLNIGIPSLTKCCN
          NG.H.IDTYL.AALD.LGG..GLCQ.KC..GSKPYPR..YKPSPPNG.GSPLFG.VH.N.GIPSLTKCCN
Retrocopy NGIHKIDTYLKAALDILGGKNGLCQCKCGEGSKPYPRYCYKPSPPNGYGSPLFG<VHINTGIPSLTKCCN

Parental  QHDRCYETCGKSKNDCDEAFQYCLSKICRDVQKTLGLAQHVQACETTVELLFDSVIHL-GCKPYLDSQRA
          QHDRCY..CGKS.NDCDE.FQYCLSKICRDVQKTLGLAQ.VQACETT.ELLFDSV.HL.GC.P.LDSQ.A
Retrocopy QHDRCYKACGKSTNDCDEEFQYCLSKICRDVQKTLGLAQRVQACETTMELLFDSVVHL>GCIPDLDSQKA

Parental  ACWCRY
          ACWC.Y
Retrocopy ACWCCY

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_718 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 14 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015230	1 retrocopy	retro_btau_1557,
Callithrix jacchus	ENSCJAG00000016169	2 retrocopies	retro_cjac_1992, retro_cjac_3936,
Dasypus novemcinctus	ENSDNOG00000016573	7 retrocopies	retro_dnov_1694, retro_dnov_172, retro_dnov_1856, retro_dnov_1930, retro_dnov_2286, retro_dnov_2572, retro_dnov_434,
Homo sapiens	ENSG00000123739	1 retrocopy	retro_hsap_153,
Gorilla gorilla	ENSGGOG00000001082	2 retrocopies	retro_ggor_242, retro_ggor_929,
Loxodonta africana	ENSLAFG00000000852	2 retrocopies	retro_lafr_402, retro_lafr_718 ,
Mustela putorius furo	ENSMPUG00000008637	1 retrocopy	retro_mputfur_964,
Mus musculus	ENSMUSG00000027999	1 retrocopy	retro_mmus_2368,
Otolemur garnettii	ENSOGAG00000004686	1 retrocopy	retro_ogar_670,
Ochotona princeps	ENSOPRG00000014505	2 retrocopies	retro_opri_30, retro_opri_921,
Pan troglodytes	ENSPTRG00000016362	1 retrocopy	retro_ptro_817,
Sus scrofa	ENSSSCG00000009139	3 retrocopies	retro_sscr_622, retro_sscr_623, retro_sscr_670,
Tarsius syrichta	ENSTSYG00000004756	4 retrocopies	retro_tsyr_1366, retro_tsyr_376, retro_tsyr_487, retro_tsyr_493,
Vicugna pacos	ENSVPAG00000009842	1 retrocopy	retro_vpac_466,