RetrogeneDB ID: retro_lafr_1014

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_6:57804772..57805279(+)
• Located in intron of: ENSLAFG00000011313

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP3R1
• Ensembl ID: ENSLAFG00000022682
• Aliases: None
• Description: None

Sequence

>retro_lafr_1014
GGAAACGAGGCGAGTTACCCCGCGGAGATGTGCTCCCACTTTGACCAGGATGAAATTAAAAGGCTGGGAAAGCGCTTCAA
AAAGCTGGACTTGGACAAGTCGGGCTCGCTGAGCGTGGAGGAGTTCCTGTCCATGCCCGAGCTGCGGTACAACCCCTTGC
TGCGGCGAGTGATCGACATCTTCGACACCGACGGGAGTGGCGAAGTGGACTTCAAGGAATTCATCGTGGGGGCTTCCCAA
TTCAGTGTCAAAGGAAACGAGGAGCAGAAATTGAGGTTTGCTTTCAACATCTACGACATGGATAAAGACGGCTACATTTC
CAACGGCGAGCTCTTCCAGGTGTTGAGGATGATGGTGGGGAGCAACCTGAAAGACTGGCAGTTACAGCAGCTTGTGGACA
AAACCATCATCATCCTGGACAGGGATGGCGACGGGAAAATATCCTTCGAGGAGTTCTCTGCTGTGGTCCGGGGCCTGGAG
ATCCACAAGAAGCTGGTGCTAATTGTG

Alignment

ORF - retro_lafr_1014 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.84 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GNEASYPLEMCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEVD
          GNEASYP.EMCSHFD.DEIKRLGKRFKKLDLD.SGSLSVEEF.S.PEL..NPL..RVIDIFDTDG.GEVD
Retrocopy GNEASYPAEMCSHFDQDEIKRLGKRFKKLDLDKSGSLSVEEFLSMPELRYNPLLRRVIDIFDTDGSGEVD

Parental  FKEFIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINAD
          FKEFI.G.SQFSVKG..EQKLRFAF.IYDMDKDGYISNGELFQVL.MMVG.NLKD.QLQQ.VDKTII..D
Retrocopy FKEFIVGASQFSVKGNEEQKLRFAFNIYDMDKDGYISNGELFQVLRMMVGSNLKDWQLQQLVDKTIIILD

Parental  KDGDGRISFEEFCAVVGGLDIHKKMVVDV
          .DGDG.ISFEEF.AVV.GL.IHKK.V..V
Retrocopy RDGDGKISFEEFSAVVRGLEIHKKLVLIV

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_1014 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 22 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010619	1 retrocopy	retro_btau_1660,
Choloepus hoffmanni	ENSCHOG00000002893	1 retrocopy	retro_chof_2602,
Callithrix jacchus	ENSCJAG00000006498	1 retrocopy	retro_cjac_624,
Dipodomys ordii	ENSDORG00000019760	1 retrocopy	retro_dord_404,
Equus caballus	ENSECAG00000009627	1 retrocopy	retro_ecab_651,
Felis catus	ENSFCAG00000028482	1 retrocopy	retro_fcat_1639,
Homo sapiens	ENSG00000221823	1 retrocopy	retro_hsap_3,
Loxodonta africana	ENSLAFG00000014743	3 retrocopies	retro_lafr_221, retro_lafr_795, retro_lafr_838,
Loxodonta africana	ENSLAFG00000022682	1 retrocopy	retro_lafr_1014 ,
Macaca mulatta	ENSMMUG00000017460	1 retrocopy	retro_mmul_1141,
Mustela putorius furo	ENSMPUG00000006250	1 retrocopy	retro_mputfur_537,
Nomascus leucogenys	ENSNLEG00000026538	1 retrocopy	retro_nleu_1049,
Oryctolagus cuniculus	ENSOCUG00000027562	1 retrocopy	retro_ocun_272,
Otolemur garnettii	ENSOGAG00000034876	1 retrocopy	retro_ogar_1011,
Pan troglodytes	ENSPTRG00000041941	1 retrocopy	retro_ptro_2909,
Rattus norvegicus	ENSRNOG00000043210	1 retrocopy	retro_rnor_1932,
Sus scrofa	ENSSSCG00000022362	1 retrocopy	retro_sscr_86,
Ictidomys tridecemlineatus	ENSSTOG00000025985	1 retrocopy	retro_itri_1569,
Tarsius syrichta	ENSTSYG00000019531	2 retrocopies	retro_tsyr_326, retro_tsyr_41,
Tursiops truncatus	ENSTTRG00000021395	1 retrocopy	retro_ttru_382,
Vicugna pacos	ENSVPAG00000015522	1 retrocopy	retro_vpac_3,
Drosophila melanogaster	FBgn0015614	1 retrocopy	retro_dmel_53,