RetrogeneDB ID: retro_lafr_149

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_0:105215378..105216088(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM183A
• Ensembl ID: ENSLAFG00000018443
• Aliases: None
• Description: None

Sequence

>retro_lafr_149
ATGGCCCGGAGGCTCAGCCCATTAGGCCATCCTCACTCTGACACAGTCACTATGCCCAAGAGAAGGAAGTGACTCAAGTT
TCAGGCCCACGATGTCTGCTCCAGTCGAGTGACCTTGGCAGATTTTGCCAACTCCGGTTCAGCCTTCGTGAAGTCTGGAT
GGGACAAGAAAGCCATCCTAAATGCTGTTCAGCAAGAAGTACAATCTATTTGTGGCTTGGAAGCCTCCCAGTTTCTTCCA
CAGGAAGCTCTCTCTGGGGCTGGTGAGCCCTATGACATCATCGATAGCAGTGTTGAGATGGATGCCCAAGAGGAAAGCAT
TTATGCCAGAACCGTTTCCAGAAAAAAGAAAAGCAAGAAACACAAAGAAGACCCGGACAGGGCTGGAGGAGAAGAGTATC
CCACGGATATTTGGCTCTTGCTGGCCTCCTATATCCATCCTGAGGACATTGTGAATTTTCCCCTGATTCATAAGAATGCC
TGGACTGTCACTTGCACTGCTGCCTTTTGGACCAGGTCGTACTGAAGGCACTACATGCTGGATGCCTCTCTGCCTCTGCA
CCTGCGACCAGAGTCAACGGGGAAGCTGCGCTGTCTCCCGGCTTGTGTGATCCAATACTTTACCATATTCGTAAGCCATT
TGCTGCTCGAATCTCCAAGAATCCAGCCCTTGCAGAAAAGACTCCTGGTGCACTAAAGAATTCCAAATGC

Alignment

ORF - retro_lafr_149 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.31 %
• Parental protein coverage: 62.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MARGLGPLG-PRSDTVAMPKRGKRLKFRAHDACSGRVTVADFANSDPAVVKSGRVKKAVANAVQQEVKSL
          MAR.L.PLG.P.SDTV.MPKR.K.LKF.AHD.CS.RVT.ADFANS..A.VKSG..KKA..NAVQQEV.S.
Retrocopy MARRLSPLGHPHSDTVTMPKRRK*LKFQAHDVCSSRVTLADFANSGSAFVKSGWDKKAILNAVQQEVQSI

Parental  CGLEASQVPAEEALSGVGEPCDIIDSSDEMDAQEESIYERTVSRKKKSKRHREDLDRAGGEEYPMDIWLL
          CGLEASQ....EALSG.GEP.DIIDSS.EMDAQEESIY.RTVSRKKKSK.H.ED.DRAGGEEYP.DIWLL
Retrocopy CGLEASQFLPQEALSGAGEPYDIIDSSVEMDAQEESIYARTVSRKKKSKKHKEDPDRAGGEEYPTDIWLL

Parental  LASYIRPEDIVNFSLICKNAWTVTCTAAFWTRLYRRHYTLDASLPFRLRPESMEKLRCLRACVIR-SLYH
          LASYI.PEDIVNF.LI.KNAWTVTCTAAFWTR.Y.RHY.LDASLP..LRPES..KLRCL.ACVI...LYH
Retrocopy LASYIHPEDIVNFPLIHKNAWTVTCTAAFWTRSY*RHYMLDASLPLHLRPESTGKLRCLPACVIQ<ILYH

Parental  MYEPFAARISKNPAIPESTPSTLKNSKC
          ...PFAARISKNPA..E.TP..LKNSKC
Retrocopy IRKPFAARISKNPALAEKTPGALKNSKC

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_149 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000008318	1 retrocopy	retro_etel_1835,
Felis catus	ENSFCAG00000013106	1 retrocopy	retro_fcat_3,
Homo sapiens	ENSG00000163444	3 retrocopies	retro_hsap_2808, retro_hsap_2863, retro_hsap_3157,
Gorilla gorilla	ENSGGOG00000009834	2 retrocopies	retro_ggor_1358, retro_ggor_2533,
Loxodonta africana	ENSLAFG00000018443	1 retrocopy	retro_lafr_149 ,
Macaca mulatta	ENSMMUG00000000801	1 retrocopy	retro_mmul_1532,
Nomascus leucogenys	ENSNLEG00000018106	2 retrocopies	retro_nleu_2541, retro_nleu_2663,
Otolemur garnettii	ENSOGAG00000000911	1 retrocopy	retro_ogar_3209,
Pongo abelii	ENSPPYG00000000340	2 retrocopies	retro_pabe_1333, retro_pabe_2627,
Pan troglodytes	ENSPTRG00000001864	2 retrocopies	retro_ptro_1902, retro_ptro_2278,
Rattus norvegicus	ENSRNOG00000003594	2 retrocopies	retro_rnor_1954, retro_rnor_2386,
Sus scrofa	ENSSSCG00000015473	1 retrocopy	retro_sscr_879,
Ictidomys tridecemlineatus	ENSSTOG00000012466	1 retrocopy	retro_itri_421,
Tarsius syrichta	ENSTSYG00000007009	1 retrocopy	retro_tsyr_717,