Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000007

Orthogroup ID

OG0003823

Physical Location & Seq

Genomic Coordinates Reverse (-)

47987922 .. 47992002

Gene Structure 4081 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_7G00200610.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 762 bp

ATGAATGTGTTAAGCTTCTCCTCCATCTGTTGCCAGCCTTCGTTTCCTTTTCCTTTCGGAATGAGCAGATCACAAGAGCCTTCAGCCCTTAAATGGAAGCGCTCGAACTCGCAATCTGGGTCTTTGACAGAGCATGAAAGCAAACTCTATGATGCCATCCGCAGCAAGGCAGATATGGGCATGTCTGTACAAGACTTGAGGCGAGAAACAGGACTCCAGAACAATTTATTTACCAAGGCCATCAAAACACTTCAAGCCAAACAACTGATAAAAGAGGATAAAAATTTTGAAAACAAGACGAGGAAACATTACATGGCTACAGAGTTTGAGCCCTCAAAGGAGATAACCGGTGGTGCTTGGTATGATAATGGACAGTTGGATACTGAGTTTATAAAGGTTGTAAAACGTGGGGTTGTGAAGGTCATCCATGATCAGGGGATTGCTACCTTGGAGGAAATTTCACACGCAATTAGTATGAAGAAGTTACTAACTGTTAACTTATCCGCACAGGAATTGAAACAGGTTCTTGGGGCTTTGGTTTTGGACAATGCGGTCCAGAGGGTGGAGAGCACTGATACGGGGGACTTTGTCGGTGCTAAAGCTAGGAAAGATTGTTATAAGTGCTGCAAGAGAGGGGAACCAAACTTAGCATCCATGGCTTCCATTCCATGCGGAGTCTGTCTGCGTATTAATCAATGTACCCCAGATGGCATTATTTCCCCAACCACCTGTGAATACTTCAAAAAATGGTTGGATTTCTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0001817 GO:0001819 GO:0002682 GO:0002684 GO:0003674 GO:0003676 GO:0003677 GO:0003690 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0008150 GO:0030880 GO:0031347 GO:0031349 GO:0031974 GO:0031981 GO:0032479 GO:0032481 GO:0032648 GO:0032728 GO:0032991 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044464 GO:0045088 GO:0045089 GO:0048518 GO:0048583 GO:0048584 GO:0050776 GO:0050778 GO:0050789 GO:0051239 GO:0051240 GO:0055029 GO:0061695 GO:0065007 GO:0070013 GO:0080134 GO:0097159 GO:1901363 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko04623 ko05169 map00230 map00240 map01100 map03020 map04623 map05169

Pfam Domains

Protein Families

RNA_pol_Rpc34

Protein Analysis

253

Amino Acids

28.33

Weight (kDa)

8.78

Isoelectric Point (pI)

52.39

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpc34	PF05158	30 - 144	4.3e-29	RNA polymerase Rpc34 subunit
RNA_pol_Rpc34	PF05158	146 - 252	3e-11	RNA polymerase Rpc34 subunit

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Align Labels (Cladogram)

Image

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Publication-ready

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Orthologous Genes (Group: OG0003823)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G23710
fragaria_vesca	FvH4_6g29950 FvH4_6g29950 FvH4_6g41460
malus_domestica	MD08G1239800.v1.1 MD15G1431400.v1.1
prunus_persica	Prupe.1G576300_v2.0.a1 Prupe.5G067300_v2.0.a1
pyrus_communis	pycom08g20810 pycom15g38120
rosa_chinensis	RchiOBHm_Chr2g0135951 RchiOBHm_Chr6g0271261 RchiOBHm_Chr6g0271271
rosa_laevigata	RLG00000019491 RLG00000020962
rosa_multiflora	Rmu_sc0004866.1_g000010 Rmu_ssc0000343.1_g000019
rosa_roxburghii	Rroxscaffold_2G00108750 Rroxscaffold_7G00200610
rosa_rugosa	Rorug02G0327000 Rorug02G0457600 Rorug06G0035800 Rorug06G0036000
rosa_samantha	Rh2BG385300 Rh2CG364400 Rh2DG401600 Rh6AG179300 Rh6BG182300 Rh6CG179200 Rh6DG170900
rosa_wichuraiana	Rw2G030860 Rw2G031070 Rw2G043270 Rw6G015420

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	2 cut(s)	392, 618
AasI	GACNNNNNNGTC	1 cut(s)	551
AccB7I	CCANNNNNTGG	1 cut(s)	562
AciI	CCGC	4 cut(s)	160, 504, 551, 672
AcsI	RAATTY	2 cut(s)	283, 456
AcuI	CTGAAG	1 cut(s)	66
AfaI	GTAC	2 cut(s)	189, 700
AfeI	AGCGCT	1 cut(s)	101
AfiI	CCNNNNNNNGG	4 cut(s)	93, 166, 433, 562
AgeI	ACCGGT	1 cut(s)	347
AgsI	TTSAA	4 cut(s)	254, 290, 517, 742
AluBI	AGCT	2 cut(s)	15, 602
AluI	AGCT	2 cut(s)	15, 602
Alw21I	GWGCWC	1 cut(s)	572
Aor51HI	AGCGCT	1 cut(s)	101
AoxI	GGCC	1 cut(s)	237
ApeKI	GCWGC	2 cut(s)	162, 624
ApoI	RAATTY	2 cut(s)	283, 456
AseI	ATTAAT	1 cut(s)	690
AsiGI	ACCGGT	1 cut(s)	347
AspLEI	GCGC	1 cut(s)	102
AspS9I	GGNCC	1 cut(s)	553
AvaII	GGWCC	1 cut(s)	553
BanII	GRGCYC	1 cut(s)	333
Bbv12I	GWGCWC	1 cut(s)	572
BbvI	GCAGC	2 cut(s)	174, 611
BccI	CCATC	4 cut(s)	32, 164, 248, 701
BciVI	GTATCC	1 cut(s)	373
BclI	TGATCA	1 cut(s)	430
BfaI	CTAG	1 cut(s)	603
BfmI	CTRYAG	1 cut(s)	318
BfoI	RGCGCY	1 cut(s)	103
BfuI	GTATCC	1 cut(s)	373
BisI	GCNGC	2 cut(s)	163, 625
BlsI	GCNGC	2 cut(s)	164, 626
Bme18I	GGWCC	1 cut(s)	553
BmgT120I	GGNCC	1 cut(s)	553
BmiI	GGNNCC	1 cut(s)	639
BmsI	GCATC	2 cut(s)	142, 659
BpmI	CTGGAG	1 cut(s)	200
BpuEI	CTTGAG	1 cut(s)	217
BsaJI	CCNNGG	3 cut(s)	234, 447, 654
BsaWI	WCCGGW	1 cut(s)	347
Bsc4I	CCNNNNNNNGG	4 cut(s)	93, 166, 433, 562
Bse118I	RCCGGY	1 cut(s)	347
BseDI	CCNNGG	3 cut(s)	234, 447, 654
BseGI	GGATG	3 cut(s)	156, 423, 650
BseLI	CCNNNNNNNGG	4 cut(s)	93, 166, 433, 562
BseMII	CTCAG	1 cut(s)	375
BseRI	GAGGAG	1 cut(s)	10
BseXI	GCAGC	2 cut(s)	174, 611
BshFI	GGCC	1 cut(s)	239
BshTI	ACCGGT	1 cut(s)	347
BsiHKAI	GWGCWC	1 cut(s)	572
BsiSI	CCGG	1 cut(s)	348
BslFI	GGGAC	1 cut(s)	596
BslI	CCNNNNNNNGG	4 cut(s)	93, 166, 433, 562
BsmFI	GGGAC	1 cut(s)	596
BsnI	GGCC	1 cut(s)	239
Bsp1286I	GDGCHC	2 cut(s)	333, 572
Bsp1407I	TGTACA	1 cut(s)	187
Bsp143I	GATC	2 cut(s)	68, 430
Bsp19I	CCATGG	1 cut(s)	654
BspACI	CCGC	4 cut(s)	160, 504, 551, 672
BspANI	GGCC	1 cut(s)	239
BspCNI	CTCAG	1 cut(s)	376
BspLI	GGNNCC	1 cut(s)	639
BsrFI	RCCGGY	1 cut(s)	347
BsrGI	TGTACA	1 cut(s)	187
BssAI	RCCGGY	1 cut(s)	347
BssECI	CCNNGG	3 cut(s)	234, 447, 654
BssMI	GATC	2 cut(s)	68, 430
BssT1I	CCWWGG	3 cut(s)	234, 447, 654
Bst4CI	ACNGT	2 cut(s)	375, 493
BstAUI	TGTACA	1 cut(s)	187
BstC8I	GCNNGC	1 cut(s)	35
BstDEI	CTNAG	2 cut(s)	384, 646
BstDSI	CCRYGG	1 cut(s)	654
BstF5I	GGATG	3 cut(s)	156, 423, 650
BstH2I	RGCGCY	1 cut(s)	103
BstHHI	GCGC	1 cut(s)	102
BstKTI	GATC	2 cut(s)	71, 433
BstMBI	GATC	2 cut(s)	68, 430
BstMWI	GCNNNNNNNGC	1 cut(s)	656
BstNSI	RCATGY	1 cut(s)	184
BstSFI	CTRYAG	1 cut(s)	318
BstV1I	GCAGC	2 cut(s)	174, 611
BsuI	GTATCC	1 cut(s)	373
BsuRI	GGCC	1 cut(s)	239
BtgI	CCRYGG	1 cut(s)	654
BtsCI	GGATG	3 cut(s)	156, 423, 650
BtsIMutI	CAGTG	1 cut(s)	570
Cac8I	GCNNGC	1 cut(s)	35
CfoI	GCGC	1 cut(s)	102
Cfr10I	RCCGGY	1 cut(s)	347
Cfr13I	GGNCC	1 cut(s)	553
Csp6I	GTAC	2 cut(s)	188, 699
CspAI	ACCGGT	1 cut(s)	347
CviAII	CATG	6 cut(s)	134, 181, 313, 428, 655, 669
CviQI	GTAC	2 cut(s)	188, 699
DdeI	CTNAG	2 cut(s)	384, 646
DpnI	GATC	2 cut(s)	70, 432
DpnII	GATC	2 cut(s)	68, 430
DrdI	GACNNNNNNGTC	1 cut(s)	551
DseDI	GACNNNNNNGTC	1 cut(s)	551
Eco130I	CCWWGG	3 cut(s)	234, 447, 654
Eco24I	GRGCYC	1 cut(s)	333
Eco47I	GGWCC	1 cut(s)	553
Eco47III	AGCGCT	1 cut(s)	101
Eco57I	CTGAAG	1 cut(s)	66
EcoT14I	CCWWGG	3 cut(s)	234, 447, 654
EcoT38I	GRGCYC	1 cut(s)	333
ErhI	CCWWGG	3 cut(s)	234, 447, 654
FaeI	CATG	6 cut(s)	137, 184, 316, 431, 658, 672
FaqI	GGGAC	1 cut(s)	596
FatI	CATG	6 cut(s)	133, 180, 312, 427, 654, 668
FbaI	TGATCA	1 cut(s)	430
Fnu4HI	GCNGC	2 cut(s)	163, 625
FokI	GGATG	3 cut(s)	143, 410, 637
FriOI	GRGCYC	1 cut(s)	333
Fsp4HI	GCNGC	2 cut(s)	163, 625
FspBI	CTAG	1 cut(s)	603
GlaI	GCGC	1 cut(s)	101
GluI	GCNGC	2 cut(s)	163, 625
GsuI	CTGGAG	1 cut(s)	200
HaeII	RGCGCY	1 cut(s)	103
HaeIII	GGCC	1 cut(s)	239
HapII	CCGG	1 cut(s)	348
HhaI	GCGC	1 cut(s)	102
Hin1II	CATG	6 cut(s)	137, 184, 316, 431, 658, 672
Hin6I	GCGC	1 cut(s)	100
HinP1I	GCGC	1 cut(s)	100
HincII	GTYRAC	1 cut(s)	496
HindII	GTYRAC	1 cut(s)	496
HindIII	AAGCTT	1 cut(s)	13
HinfI	GANTC	2 cut(s)	213, 675
HpaI	GTTAAC	1 cut(s)	496
HpaII	CCGG	1 cut(s)	348
Hpy166II	GTNNAC	1 cut(s)	496
Hpy188I	TCNGA	2 cut(s)	59, 761
Hpy188III	TCNNGA	2 cut(s)	217, 556
Hpy8I	GTNNAC	1 cut(s)	496
HpyAV	CCTTC	3 cut(s)	48, 90, 412
HpyCH4III	ACNGT	2 cut(s)	375, 493
HpyCH4IV	ACGT	1 cut(s)	406
HpyCH4V	TGCA	1 cut(s)	627
HpyF10VI	GCNNNNNNNGC	1 cut(s)	656
HpyF3I	CTNAG	2 cut(s)	384, 646
HpySE526I	ACGT	1 cut(s)	406
Hsp92II	CATG	6 cut(s)	137, 184, 316, 431, 658, 672
HspAI	GCGC	1 cut(s)	100
Ksp22I	TGATCA	1 cut(s)	430
KspAI	GTTAAC	1 cut(s)	496
Kzo9I	GATC	2 cut(s)	68, 430
Lsp1109I	GCAGC	2 cut(s)	174, 611
LweI	GCATC	2 cut(s)	142, 659
MaeI	CTAG	1 cut(s)	603
MaeII	ACGT	1 cut(s)	406
MaeIII	GTNAC	1 cut(s)	483
MalI	GATC	2 cut(s)	70, 432
MboI	GATC	2 cut(s)	68, 430
MboII	GAAGA	1 cut(s)	490
MhlI	GDGCHC	2 cut(s)	333, 572
MluCI	AATT	5 cut(s)	223, 283, 456, 468, 512
MlyI	GAGTC	2 cut(s)	207, 684
MmeI	TCCRAC	2 cut(s)	357, 732
MnlI	CCTC	8 cut(s)	31, 192, 268, 294, 343, 445, 552, 626
MseI	TTAA	4 cut(s)	11, 90, 495, 690
MspI	CCGG	1 cut(s)	348
MwoI	GCNNNNNNNGC	1 cut(s)	656
NcoI	CCATGG	1 cut(s)	654
NdeII	GATC	2 cut(s)	68, 430
NlaIII	CATG	6 cut(s)	137, 184, 316, 431, 658, 672
NlaIV	GGNNCC	1 cut(s)	639
NspI	RCATGY	1 cut(s)	184
PflFI	GACNNNGTC	1 cut(s)	587
PflMI	CCANNNNNTGG	1 cut(s)	562
PinAI	ACCGGT	1 cut(s)	347
PkrI	GCNGC	2 cut(s)	164, 626
PleI	GAGTC	2 cut(s)	207, 683
PpsI	GAGTC	2 cut(s)	207, 683
PshBI	ATTAAT	1 cut(s)	690
PsiI	TTATAA	2 cut(s)	392, 618
PspN4I	GGNNCC	1 cut(s)	639
PspPI	GGNCC	1 cut(s)	553
PsyI	GACNNNGTC	1 cut(s)	587
RsaI	GTAC	2 cut(s)	189, 700
RsaNI	GTAC	2 cut(s)	188, 699
SaqAI	TTAA	4 cut(s)	11, 90, 495, 690
SatI	GCNGC	2 cut(s)	163, 625
Sau3AI	GATC	2 cut(s)	68, 430
Sau96I	GGNCC	1 cut(s)	553
SchI	GAGTC	2 cut(s)	207, 684
SduI	GDGCHC	2 cut(s)	333, 572
SetI	ASST	8 cut(s)	17, 399, 409, 423, 449, 525, 604, 731
SfaNI	GCATC	2 cut(s)	142, 659
SfcI	CTRYAG	1 cut(s)	318
SinI	GGWCC	1 cut(s)	553
SmlI	CTYRAG	1 cut(s)	196
SmoI	CTYRAG	1 cut(s)	196
Sse9I	AATT	5 cut(s)	223, 283, 456, 468, 512
SsiI	CCGC	4 cut(s)	160, 504, 551, 672
SspMI	CTAG	1 cut(s)	603
StyI	CCWWGG	3 cut(s)	234, 447, 654
TaaI	ACNGT	2 cut(s)	375, 493
TaiI	ACGT	1 cut(s)	409
TaqI	TCGA	1 cut(s)	104
TasI	AATT	5 cut(s)	223, 283, 456, 468, 512
TatI	WGTACW	1 cut(s)	187
Tru1I	TTAA	4 cut(s)	11, 90, 495, 690
Tru9I	TTAA	4 cut(s)	11, 90, 495, 690
TscAI	CASTG	1 cut(s)	577
TseI	GCWGC	2 cut(s)	162, 624
TspDTI	ATGAA	3 cut(s)	17, 150, 491
TspRI	CASTG	1 cut(s)	577
Tth111I	GACNNNGTC	1 cut(s)	587
Van91I	CCANNNNNTGG	1 cut(s)	562
VpaK11BI	GGWCC	1 cut(s)	553
VspI	ATTAAT	1 cut(s)	690
XapI	RAATTY	2 cut(s)	283, 456
XceI	RCATGY	1 cut(s)	184
XspI	CTAG	1 cut(s)	603

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.