RetrogeneDB ID: retro_rnor_1175

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:6718729..6719269(+)
• Located in intron of: ENSRNOG00000016645

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fdps
• Ensembl ID: ENSRNOG00000043377
• Aliases: Fdps, Ac2-125, FPS
• Description: farnesyl pyrophosphate synthase [Source:RefSeq peptide;Acc:NP_114028]

Sequence

>retro_rnor_1175
GAAGCCATCAACAATTCTCTGCTCCTGGAGCCTCCATCTACTGCCTGCTGAAGTTCTGCTGCAGGGAGCAGCCCTACTCC
CTGAACCTGCTGGAGCGCTGTCTACGGAGCTGCTATCAGGCTGAGACATGGCAGTCTGTGGACCTCATCACAGCACCCCA
GGGCCATGGGCATCTTGGTGGATACACTGAAAAGAGGTACAAATATGTTGTCAAGAACAAGGCCGCCTCTACTCTTTCCA
CCTGCCTACACAGCTGCCGTGTACATGGCCGGAATTGATGGGGAGGAGGAGCATGCTAATGCCTTGAAGATCCTGCTGGA
GATGGGCGAGTTCTTTCAGGTCCAGGATGACTACCTTGATCTCTTTGCAGACCCCAGTGTGACCGGAAAGGTCAGCACTG
ACATCCAGGACAACAAATGCAGCTGGCTGGTGGTTCAGTGTCTGCTATGAGCCACTCCTCAGCAGCGCCAGATCTCAGAG
GAGAATTTCGGGCAGAGGGACCCAGTGGATCTGCAGACTGTGTTCTTCAGGTACGAGGAA

Alignment

ORF - retro_rnor_1175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.91 %
• Parental protein coverage: 51.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DAINDALLLE-AAIYRLLKFYCREQPYYLNLLELFLQSSYQTEIGQTLDLITAPQGQVDLGRYTEKRYKS
          .AIN..LLLE.A.IY.LLKF.CREQPY.LNLLE..L.S.YQ.E..Q..DLITAPQG...LG.YTEKRYK.
Retrocopy EAINNSLLLE<ASIYCLLKFCCREQPYSLNLLERCLRSCYQAETWQSVDLITAPQGHGHLGGYTEKRYKY

Parental  IVKYKTA-FYSFYLPI-AAAMYMAGIDGEKEHANALKILLEMGEFFQIQDDYLDLFGDPSVTGKVGTDIQ
          .VK.K.A..YSF.LP...AA.YMAGIDGE.EHANALKILLEMGEFFQ.QDDYLDLF.DPSVTGKV.TDIQ
Retrocopy VVKNKAA<LYSFHLPT<TAAVYMAGIDGEEEHANALKILLEMGEFFQVQDDYLDLFADPSVTGKVSTDIQ

Parental  DNKCSWLVVQCLLRATPQQRQILEENYGQKDPEKVARVKALYEE
          DNKCSWLVVQCLL.ATPQQRQI.EEN.GQ.DP.....V...YEE
Retrocopy DNKCSWLVVQCLL*ATPQQRQISEENFGQRDPVDLQTVFFRYEE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	133.15 RPM
SRP017611_kidney	0.07 RPM	47.24 RPM
SRP017611_liver	0.07 RPM	215.03 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1175 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1175 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1175 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030749	2 retrocopies	retro_cfam_1822, retro_cfam_1888,
Callithrix jacchus	ENSCJAG00000008364	11 retrocopies	retro_cjac_1066, retro_cjac_1217, retro_cjac_1395, retro_cjac_157, retro_cjac_2011, retro_cjac_2081, retro_cjac_2161, retro_cjac_299, retro_cjac_4154, retro_cjac_44, retro_cjac_70,
Echinops telfairi	ENSETEG00000001154	6 retrocopies	retro_etel_1770, retro_etel_1818, retro_etel_2179, retro_etel_730, retro_etel_743, retro_etel_990,
Homo sapiens	ENSG00000160752	6 retrocopies	retro_hsap_1519, retro_hsap_1558, retro_hsap_1560, retro_hsap_3871, retro_hsap_3872, retro_hsap_502,
Microcebus murinus	ENSMICG00000007468	1 retrocopy	retro_mmur_1148,
Macaca mulatta	ENSMMUG00000023144	3 retrocopies	retro_mmul_1190, retro_mmul_2152, retro_mmul_565,
Mus musculus	ENSMUSG00000059743	5 retrocopies	retro_mmus_1028, retro_mmus_1552, retro_mmus_2802, retro_mmus_3625, retro_mmus_590,
Nomascus leucogenys	ENSNLEG00000012099	6 retrocopies	retro_nleu_1486, retro_nleu_1727, retro_nleu_2301, retro_nleu_2405, retro_nleu_2595, retro_nleu_2692,
Pongo abelii	ENSPPYG00000000747	3 retrocopies	retro_pabe_1290, retro_pabe_1329, retro_pabe_235,
Pan troglodytes	ENSPTRG00000001422	9 retrocopies	retro_ptro_1028, retro_ptro_1048, retro_ptro_1049, retro_ptro_2637, retro_ptro_2638, retro_ptro_2639, retro_ptro_2940, retro_ptro_2995, retro_ptro_377,
Rattus norvegicus	ENSRNOG00000043377	3 retrocopies	retro_rnor_1175 , retro_rnor_153, retro_rnor_2897,
Ictidomys tridecemlineatus	ENSSTOG00000004475	1 retrocopy	retro_itri_488,
Tursiops truncatus	ENSTTRG00000013326	1 retrocopy	retro_ttru_689,