RetrogeneDB ID: retro_lafr_1023

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_6:18025785..18026015(-)
• Located in intron of: ENSLAFG00000007066

Retrocopy information

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

Parental gene information

• Parental gene symbol: BET1
• Ensembl ID: ENSLAFG00000000587
• Aliases: None
• Description: None

Sequence

>retro_lafr_1023
CTCACTGAAAGTCTGAGCGCAAAGCAACTGCTATAAAATTTCTCTCCATTGAAATAGGCCGTGAAGTTAGAAATCAAAAT
AAATTATTAGCCGAAATGGATTTACAATCTGATTCTACAACTGGATTTTGGGGTGAAACTACAGGGAACCTGAAGATTTT
ATCTAGAGGGAGTCAAATCAAGCTGCTGTGCTATATGATGCTGTTTTCATTGTCTTTTTTGTCATTTATT

Alignment

ORF - retro_lafr_1023 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.64 %
• Parental protein coverage: 64.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LTESLRSK-VTAIKSLSIEIGHEVKNQNKLLAEMDSEFDSTTGFLGKTMGKLKILSRGSQTKLLCYMMLF
          LTESL..K..TAIK.LSIEIG.EV.NQNKLLAEMD...DSTTGF.G.T.G.LKILSRGSQ.KLLCYMMLF
Retrocopy LTESLSAK<ATAIKFLSIEIGREVRNQNKLLAEMDLQSDSTTGFWGETTGNLKILSRGSQIKLLCYMMLF

Parental  SL-FVFFV
          SL.F..F.
Retrocopy SLSFLSFI

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_1023 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 16 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003424	1 retrocopy	retro_btau_1054,
Choloepus hoffmanni	ENSCHOG00000001276	1 retrocopy	retro_chof_2211,
Callithrix jacchus	ENSCJAG00000013720	3 retrocopies	retro_cjac_1411, retro_cjac_2019, retro_cjac_3155,
Dasypus novemcinctus	ENSDNOG00000001012	3 retrocopies	retro_dnov_1683, retro_dnov_393, retro_dnov_60,
Homo sapiens	ENSG00000105829	1 retrocopy	retro_hsap_3809,
Gorilla gorilla	ENSGGOG00000002176	1 retrocopy	retro_ggor_2560,
Loxodonta africana	ENSLAFG00000000587	1 retrocopy	retro_lafr_1023 ,
Macaca mulatta	ENSMMUG00000000007	1 retrocopy	retro_mmul_1656,
Nomascus leucogenys	ENSNLEG00000015441	1 retrocopy	retro_nleu_2151,
Oryctolagus cuniculus	ENSOCUG00000017029	2 retrocopies	retro_ocun_1116, retro_ocun_355,
Ochotona princeps	ENSOPRG00000004536	4 retrocopies	retro_opri_201, retro_opri_249, retro_opri_388, retro_opri_880,
Pan troglodytes	ENSPTRG00000019408	1 retrocopy	retro_ptro_2584,
Rattus norvegicus	ENSRNOG00000011008	2 retrocopies	retro_rnor_2195, retro_rnor_2196,
Sus scrofa	ENSSSCG00000015325	2 retrocopies	retro_sscr_455, retro_sscr_516,
Tupaia belangeri	ENSTBEG00000000765	2 retrocopies	retro_tbel_3115, retro_tbel_4272,
Tarsius syrichta	ENSTSYG00000009729	2 retrocopies	retro_tsyr_136, retro_tsyr_1843,