RetrogeneDB ID: retro_lafr_198

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_1:11389035..11389331(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TXNL4A
• Ensembl ID: ENSLAFG00000003190
• Aliases: None
• Description: None

Sequence

>retro_lafr_198
GGACACGATTGGGATCTTACTTGTATGAAAATAGATGAATTTCTATATAGCATAGCTGAAAAGGTTAAAAATTTTGTAGT
TATTTATCTTGTGGATATTACAGAAGTACCTGACTTCAAGGAAATGTATCAGTTATACAATCTTTGCACTGTCATGTTTT
TCTTCGGGAACAACCACATAATGATTGATTTGGGGACTGGTAACAACAAGAAGATTAAGTGGGCCATCAGGACAAACAGG
AGATGATCTGATCGACATCATAGATCTACCACGGAGCATGCAAGAGCCGGGGGCTG

Alignment

ORF - retro_lafr_198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 69.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGNNN
          GHDWD.TCMK.DE.LYSIAEKVKNF.VIYLVDITEVPDF..MY.LY..CTVMFFF.N.HIMIDLGTGNN.
Retrocopy GHDWDLTCMKIDEFLYSIAEKVKNFVVIYLVDITEVPDFKEMYQLYNLCTVMFFFGNNHIMIDLGTGNNK

Parental  KINWAM-EDKQEMIDIIETVYRGARKGRGL
          KI.WA...DKQEMI......Y.GA.K.RGL
Retrocopy KIKWAI<QDKQEMI*STS*IYHGACKSRGL

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_198 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010130	2 retrocopies	retro_cjac_2805, retro_cjac_3659,
Homo sapiens	ENSG00000141759	2 retrocopies	retro_hsap_2185, retro_hsap_4900,
Gorilla gorilla	ENSGGOG00000005285	2 retrocopies	retro_ggor_1731, retro_ggor_3060,
Loxodonta africana	ENSLAFG00000003190	1 retrocopy	retro_lafr_198 ,
Myotis lucifugus	ENSMLUG00000009188	1 retrocopy	retro_mluc_562,
Macaca mulatta	ENSMMUG00000001613	2 retrocopies	retro_mmul_2636, retro_mmul_913,
Nomascus leucogenys	ENSNLEG00000008378	2 retrocopies	retro_nleu_1268, retro_nleu_314,
Otolemur garnettii	ENSOGAG00000034753	1 retrocopy	retro_ogar_1751,
Pan troglodytes	ENSPTRG00000010136	1 retrocopy	retro_ptro_1663,
Rattus norvegicus	ENSRNOG00000017596	2 retrocopies	retro_rnor_1358, retro_rnor_2458,
Ictidomys tridecemlineatus	ENSSTOG00000022277	1 retrocopy	retro_itri_1063,
Tarsius syrichta	ENSTSYG00000009428	1 retrocopy	retro_tsyr_240,