RetrogeneDB ID: retro_lafr_226

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_10:35884397..35884789(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000027158
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUDT5
• Ensembl ID: ENSLAFG00000012052
• Aliases: None
• Description: None

Sequence

>retro_lafr_226
AAAAAAAAAAATTACATGGATCCTACTGGTAAAACTAGAACCTGGGATACTGTGAAATGTACAACCAGGAAAAGACAGTC
TGTCTGTGGTGTGGCAATTATCCCAGTGCTGCAAAGAATTCTTCATTATGAATGTACTGTTCTGATGAAACAGCTTAGAT
CACCAAGGGGTGGCTACTGCACAGAATTCTCTGCAGGCCTCATGGACGATAATGAGAGCCCAGAAGTAGCTGCTCTTCCA
GAGCTTGAGGAAGGAACTGGTTATAAATGTGACATTGTTGAATGTTCTCCAGTTGTATGTATGGATCCAGGTTTGTCAAA
TTGTACGGTGCATATCATAGCAGTATCATTAATGGGGATGATCATGAAAATGTAAGACCTAAGCCAAAGCCC

Alignment

ORF - retro_lafr_226 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.27 %
• Parental protein coverage: 59.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ERTTYMDPTGKTRTWETVKRTTRKGQSADGVAVIPVLQRTLHYECIVLVKQFRPPIGGYCLEFPAGLIDD
          ....YMDPTGKTRTW.TVK.TTRK.QS..GVA.IPVLQR.LHYEC.VL.KQ.R.P.GGYC.EF.AGL.DD
Retrocopy KKKNYMDPTGKTRTWDTVKCTTRKRQSVCGVAIIPVLQRILHYECTVLMKQLRSPRGGYCTEFSAGLMDD

Parental  NESPEAAALRELEEETGYKGDIAECSPVLCMDPGLSNCTVHIVTVT-INGDDAENVRPKPKP
          NESPE.AAL.ELEE.TGYK.DI.ECSPV.CMDPGLSNCTVHI..V..INGDD.ENVRPKPKP
Retrocopy NESPEVAALPELEEGTGYKCDIVECSPVVCMDPGLSNCTVHIIAVS<INGDDHENVRPKPKP

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_226 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 18 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019509	2 retrocopies	retro_btau_1326, retro_btau_1438,
Canis familiaris	ENSCAFG00000004794	2 retrocopies	retro_cfam_435, retro_cfam_612,
Equus caballus	ENSECAG00000023658	1 retrocopy	retro_ecab_647,
Echinops telfairi	ENSETEG00000006403	1 retrocopy	retro_etel_946,
Felis catus	ENSFCAG00000025093	1 retrocopy	retro_fcat_350,
Homo sapiens	ENSG00000165609	1 retrocopy	retro_hsap_3580,
Gorilla gorilla	ENSGGOG00000006325	1 retrocopy	retro_ggor_2415,
Loxodonta africana	ENSLAFG00000012052	1 retrocopy	retro_lafr_226 ,
Myotis lucifugus	ENSMLUG00000010453	2 retrocopies	retro_mluc_1263, retro_mluc_2073,
Macaca mulatta	ENSMMUG00000017141	1 retrocopy	retro_mmul_1828,
Nomascus leucogenys	ENSNLEG00000012298	1 retrocopy	retro_nleu_2838,
Oryctolagus cuniculus	ENSOCUG00000009308	1 retrocopy	retro_ocun_862,
Otolemur garnettii	ENSOGAG00000005816	2 retrocopies	retro_ogar_2071, retro_ogar_2988,
Pongo abelii	ENSPPYG00000002091	2 retrocopies	retro_pabe_2949, retro_pabe_3040,
Pan troglodytes	ENSPTRG00000002294	1 retrocopy	retro_ptro_2427,
Rattus norvegicus	ENSRNOG00000017741	1 retrocopy	retro_rnor_1672,
Sus scrofa	ENSSSCG00000011113	1 retrocopy	retro_sscr_143,
Tursiops truncatus	ENSTTRG00000007394	2 retrocopies	retro_ttru_209, retro_ttru_495,