RetrogeneDB ID: retro_lafr_729

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_33:22230838..22231469(-)
• Located in intron of: ENSLAFG00000017227

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPE
• Ensembl ID: ENSLAFG00000014127
• Aliases: None
• Description: Ribulose-phosphate 3-epimerase [Source:UniProtKB/TrEMBL;Acc:G3TCM6]

Sequence

>retro_lafr_729
GATTTAAGGGCCATGTACCTCTGGATGCTGGGCTCCGGGGCCAATTATCTACACCTGTATGTAATGGATGAGTGTTTTGT
TCCCAGCATCACCTTTGATCACCCTGTGAGAAAGCCTCTGAAAGCACTAGGCCAGGACCCTTTCTTTGACAGGCACGTGA
TGGTGTCCAGGCTGTAATAGTGGGTAAAGCCAATGACTGTAGCAGGTGCCAATCAATATATGCCTTTCAACTTGAGGCTA
CTGAGAACCCAGGGGCTTTGATTAAAGACATTGAGGAGGATGGGATGAAGGTTGATCTTGCCATCAAACCAGGAACTACA
GTTGAGTGTTCGGTGCCATGGGCTAATCAGATAGATACAGGCTTTGATATGACAGTGGAACCTGGCCTTGGAGGGCAGAA
ATTCATGGACAACATGATGCCAAAGGTTCACTGGTCGAGGACCTAGTTCTTGTCTTTGGACATAGAGGTTGATGGCAGAG
TATGTCCTGACACTGTCCATGAGTGTGCAGAGGCAGGAGCTAACATGATTGTGTCTGACACTGCCATTAGGAGGAGTGAA
GAGCTGGATCTGTGATCAACTGGTTAAGAAATGTTCGCTCAGAAGCTGCTCAGAAATGTTCTCTTGATAGA

Alignment

ORF - retro_lafr_729 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.36 %
• Parental protein coverage: 92.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NLGAECLRMLDSGADYLHLDVMDGHFVPNITFGHPVVESLRKQLGQDPFFDMHMMVSRPEQWVKPMAVAG
          .L.A..L.ML.SGA.YLHL.VMD..FVP.ITF.HPV...L.K.LGQDPFFD.H.MVSR...WVKPM.VAG
Retrocopy DLRAMYLWMLGSGANYLHLYVMDECFVPSITFDHPVRKPL-KALGQDPFFDRHVMVSRL**WVKPMTVAG

Parental  ANQY-TFHL-EATENPGALIKDIRENGMKVGLAIKPGTTVEYLAPWANQIDMALVMTVEPGFGGQKFMED
          ANQY..F.L.EATENPGALIKDI.E.GMKV.LAIKPGTTVE...PWANQID....MTVEPG.GGQKFM..
Retrocopy ANQYMPFNL<EATENPGALIKDIEEDGMKVDLAIKPGTTVECSVPWANQIDTGFDMTVEPGLGGQKFMDN

Parental  MMPKVHWLRTQFPSLDIEVDGGVGPDTVHKCAEAGANMIVSGSAIMRSED-PRSVINLLRNVCSEAAQKR
          MMPKVHW.RT.F.SLDIEVDG.V.PDTVH.CAEAGANMIVS..AI.RSE....SVIN.LRNV.SEAAQK.
Retrocopy MMPKVHWSRT*FLSLDIEVDGRVCPDTVHECAEAGANMIVSDTAIRRSEE<AGSVINWLRNVRSEAAQKC

Parental  CLDR
          .LDR
Retrocopy SLDR

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_729 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 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004965	3 retrocopies	retro_amel_1327, retro_amel_1363, retro_amel_827,
Bos taurus	ENSBTAG00000047806	2 retrocopies	retro_btau_343, retro_btau_815,
Canis familiaris	ENSCAFG00000013811	3 retrocopies	retro_cfam_1441, retro_cfam_1596, retro_cfam_1623,
Choloepus hoffmanni	ENSCHOG00000001110	5 retrocopies	retro_chof_1534, retro_chof_2386, retro_chof_392, retro_chof_492, retro_chof_574,
Dasypus novemcinctus	ENSDNOG00000003193	1 retrocopy	retro_dnov_789,
Equus caballus	ENSECAG00000000002	3 retrocopies	retro_ecab_245, retro_ecab_446, retro_ecab_562,
Latimeria chalumnae	ENSLACG00000002800	1 retrocopy	retro_lcha_21,
Loxodonta africana	ENSLAFG00000014127	2 retrocopies	retro_lafr_675, retro_lafr_729 ,
Macaca mulatta	ENSMMUG00000010513	2 retrocopies	retro_mmul_366, retro_mmul_618,
Monodelphis domestica	ENSMODG00000015827	6 retrocopies	retro_mdom_1181, retro_mdom_1676, retro_mdom_449, retro_mdom_490, retro_mdom_505, retro_mdom_667,
Mustela putorius furo	ENSMPUG00000007948	2 retrocopies	retro_mputfur_1066, retro_mputfur_1280,
Oryctolagus cuniculus	ENSOCUG00000016995	1 retrocopy	retro_ocun_768,
Pongo abelii	ENSPPYG00000013132	4 retrocopies	retro_pabe_1052, retro_pabe_1878, retro_pabe_2340, retro_pabe_555,
Pteropus vampyrus	ENSPVAG00000014452	2 retrocopies	retro_pvam_217, retro_pvam_636,
Sus scrofa	ENSSSCG00000016152	1 retrocopy	retro_sscr_825,
Ictidomys tridecemlineatus	ENSSTOG00000010322	1 retrocopy	retro_itri_1750,
Tursiops truncatus	ENSTTRG00000000908	1 retrocopy	retro_ttru_158,
Vicugna pacos	ENSVPAG00000011585	1 retrocopy	retro_vpac_91,