RetrogeneDB ID: retro_lafr_132

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_0:13074489..13074912(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX5
• Ensembl ID: ENSLAFG00000025661
• Aliases: None
• Description: None

Sequence

>retro_lafr_132
GGGGAGGGTGTGAACCAGATGAGCCCATCAGAGCTGTACAAAGGCAAGAGGGTAGGCTGCTTGTAGTCTTTGGGGCCTTT
TCCCCAGGCTGTTCCGAGACCCACCTGCTGGGTTTGTGGAGAAGGCTGAGGCTCTGAGGGCCAAGGAGATGCCCATGGTA
CCATGTGTAAATGTCAAAGATGTCTTTGTGACTGGCCAGAGGGGACAAGTTGGCAACACAGAAGGCAAGGTTCAGCTCCT
GGCTGATCCCGCTGCAGCTTTGGGAAGGAGACAGATTTGTTACTAGATGATTCATTGGTGGTGATACTGTTTTAGCATCT
ACGGCCCAAGAAGTTGTCCATGGTGATAGAGGACAGTGTGATGAAGGCCCTGAACCTGGAGCCAGATGGCACAGGCCTCA
CCTGCAGTCTGCTCCCCAATGTT

Alignment

ORF - retro_lafr_132 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.45 %
• Parental protein coverage: 89.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GEPGNKVNLAELYKGKK-GVLFGVPGAFTPGCSKTHL-PGFVEQAGALKAKGAQVVACLSVNDVFVTGEW
          GE..N.....ELYKGK..G.L..V.GAF.PGCS.THL..GFVE.A.AL.AK....V.C..V.DVFVTG..
Retrocopy GEGVNQMSPSELYKGKR<GRLLVVFGAFSPGCSETHL<AGFVEKAEALRAKEMPMVPCVNVKDVFVTGQR

Parental  GKAHHAEGKVRLLADPTGA-FGKATDLLLDDSLVP-LFGNHRLKRFSMVIEDGVVKALNVEPDGTGLTCS
          G.....EGKV.LLADP..A.FGK.TDLLLDDSLV..LF...R.K..SMVIED.V.KALN.EPDGTGLTCS
Retrocopy GQVGNTEGKVQLLADPAAA<FGKETDLLLDDSLVVILF*HLRPKKLSMVIEDSVMKALNLEPDGTGLTCS

Parental  LAPNI
          L.PN.
Retrocopy LLPNV

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_132 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 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017959	1 retrocopy	retro_amel_753,
Bos taurus	ENSBTAG00000008648	1 retrocopy	retro_btau_1364,
Callithrix jacchus	ENSCJAG00000018014	1 retrocopy	retro_cjac_3013,
Dasypus novemcinctus	ENSDNOG00000004647	1 retrocopy	retro_dnov_2664,
Equus caballus	ENSECAG00000017747	2 retrocopies	retro_ecab_823, retro_ecab_844,
Echinops telfairi	ENSETEG00000000264	3 retrocopies	retro_etel_1821, retro_etel_662, retro_etel_740,
Felis catus	ENSFCAG00000028856	3 retrocopies	retro_fcat_1189, retro_fcat_410, retro_fcat_727,
Homo sapiens	ENSG00000126432	1 retrocopy	retro_hsap_408,
Gorilla gorilla	ENSGGOG00000001337	1 retrocopy	retro_ggor_404,
Loxodonta africana	ENSLAFG00000025661	2 retrocopies	retro_lafr_132 , retro_lafr_250,
Macaca mulatta	ENSMMUG00000013397	1 retrocopy	retro_mmul_504,
Mustela putorius furo	ENSMPUG00000012907	1 retrocopy	retro_mputfur_1360,
Nomascus leucogenys	ENSNLEG00000005003	2 retrocopies	retro_nleu_1007, retro_nleu_2228,
Procavia capensis	ENSPCAG00000010811	1 retrocopy	retro_pcap_144,
Pongo abelii	ENSPPYG00000003106	1 retrocopy	retro_pabe_310,
Pan troglodytes	ENSPTRG00000003835	1 retrocopy	retro_ptro_313,
Sus scrofa	ENSSSCG00000013030	2 retrocopies	retro_sscr_1041, retro_sscr_888,