Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000005

Orthogroup ID

OG0001508

Physical Location & Seq

Genomic Coordinates Reverse (-)

14190535 .. 14199497

Gene Structure 8963 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_5G00344210.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 645 bp

ATGAGGCGGCTTCGTGAATGTGGTTATCAAAAATATGGTGTAGAAAAGATGAATAGCGGTCATACAGGCCGGATGTTGTGTGTTGATAAAAGGGAGTCTAACATCACCGTTGGTGTGGTGTATTACCAAAGACTGAAGCACATGGTAGCCGACAAGATTCATTCTTGTGGGCCGGGTCCTGTGCAGCCTTTCACAAGGCAACCTACTAAAGGACAGGCTCACAATGGTGGTCTACGGGTTAGAGAAATGGAACGAGATTGTGTTATTGCACACGGTGCTGCTCATTTTTTGAAAGAGAGGTTGTTTAACCTCAGTGATCCTTATAGGATTCATAAAATAAAGAGTGTGTTGAAGGAAAAATACATTATGTGCTTTCGTCAAGTAACCGATGAAGAGGGAATCAAGGAATTACAAATCACAGCTCAATCAGCATTTAGTATCATTATTCTAGATCGATATGCCTACCTTGCAAAAATTCAAGCTCCTCGCCACTCAATGTCCCGTCATCGCTTGAAGCCCCACGCGCAGCCCATCCGCCAGCCCGGTCATCCACCTCCGCCGCAGCAAAACCCTCAAATTGTTCCTCACCCGCCCCGACCTCCGCCGATTGCCTCGCCGGAGTACTTCGTCCGATGCTCCCACTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0003674 GO:0003824 GO:0003899 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005665 GO:0005737 GO:0005829 GO:0005911 GO:0006139 GO:0006396 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009506 GO:0009892 GO:0009987 GO:0010033 GO:0010467 GO:0010468 GO:0010605 GO:0010608 GO:0010629 GO:0014070 GO:0016070 GO:0016441 GO:0016458 GO:0016591 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019222 GO:0019438 GO:0030054 GO:0030880 GO:0031047 GO:0031050 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0034062 GO:0034641 GO:0034654 GO:0035194 GO:0035195 GO:0035196 GO:0040029 GO:0042221 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0043331 GO:0044237 GO:0044238 GO:0044249 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044451 GO:0044464 GO:0046483 GO:0048519 GO:0050789 GO:0050896 GO:0051716 GO:0055029 GO:0055044 GO:0060255 GO:0061695 GO:0065007 GO:0070013 GO:0070887 GO:0070918 GO:0071310 GO:0071359 GO:0071407 GO:0071704 GO:0090304 GO:0097747 GO:0140098 GO:1901360 GO:1901362 GO:1901576 GO:1901698 GO:1901699 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko05016 ko05169 map00230 map00240 map01100 map03020 map05016 map05169

Pfam Domains

Protein Families

RNA_pol_Rpb2_1 RNA_pol_Rpb2_2 RNA_pol_Rpb2_3 RNA_pol_Rpb2_4 RNA_pol_Rpb2_5 RNA_pol_Rpb2_6 RNA_pol_Rpb2_7

Protein Analysis

214

Amino Acids

24.63

Weight (kDa)

9.92

Isoelectric Point (pI)

45.19

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb2_6	PF00562	3 - 73	1.2e-19	RNA polymerase Rpb2, domain 6
RNA_pol_Rpb2_7	PF04560	76 - 139	7e-13	RNA polymerase Rpb2, domain 7

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: OG0001508)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT4G37020 AT4G37020
fragaria_vesca	FvH4_1g15950 FvH4_1g15950 FvH4_1g15950 FvH4_1g15950 FvH4_1g15950
malus_domestica	MD02G1301600.v1.1 MD02G1301800.v1.1 MD07G1022300.v1.1 MD17G1282900.v1.1
prunus_persica	Prupe.7G134300_v2.0.a1 Prupe.7G134300_v2.0.a1 Prupe.7G134300_v2.0.a1 Prupe.7G134300_v2.0.a1
pyrus_communis	pycom02g25340 pycom02g25350 pycom02g25400
rosa_chinensis	RchiOBHm_Chr2g0105351 RchiOBHm_Chr3g0472951
rosa_laevigata	RLG00000017419
rosa_multiflora	Rmu_co8381435.1_g000001 Rmu_sc0001407.1_g000022
rosa_roxburghii	Rroxscaffold_1G00022310 Rroxscaffold_2G00114060 Rroxscaffold_2G00126470 Rroxscaffold_2G00138270 Rroxscaffold_4G00312150 Rroxscaffold_4G00329030 Rroxscaffold_5G00344210 Rroxscaffold_5G00351740 Rroxscaffold_6G00388800 Rroxscaffold_6G00408610
rosa_rugosa	Rorug02G0127800 Rorug03G0292600
rosa_samantha	Rh1BG139100 Rh2AG178500 Rh2AG329700 Rh2BG186900 Rh2CG183000 Rh2DG184400 Rh3BG143700 Rh3BG208100 Rh3CG145000 Rh3DG145000 Rh3DG167900 Rh5DG241200 Rh5DG275600 Rh6DG097100 Rh6DG389000
rosa_wichuraiana	Rw2G014010

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	1 cut(s)	232
AccII	CGCG	1 cut(s)	524
AciI	CCGC	7 cut(s)	7, 57, 535, 557, 560, 590, 602
AclWI	GGATC	1 cut(s)	311
AcsI	RAATTY	1 cut(s)	474
AcuI	CTGAAG	1 cut(s)	155
AdeI	CACNNNGTG	1 cut(s)	275
AfaI	GTAC	1 cut(s)	623
AfiI	CCNNNNNNNGG	1 cut(s)	209
AgsI	TTSAA	4 cut(s)	292, 352, 479, 514
AleI	CACNNNNGTG	1 cut(s)	225
AluBI	AGCT	2 cut(s)	422, 482
AluI	AGCT	2 cut(s)	422, 482
AlwI	GGATC	1 cut(s)	311
AoxI	GGCC	2 cut(s)	67, 170
ApeKI	GCWGC	4 cut(s)	184, 278, 526, 562
ApoI	RAATTY	1 cut(s)	474
AspLEI	GCGC	1 cut(s)	526
AspS9I	GGNCC	2 cut(s)	170, 176
AsuC2I	CCSGG	2 cut(s)	174, 543
AsuHPI	GGTGA	2 cut(s)	97, 578
AvaII	GGWCC	1 cut(s)	176
BarI	GAAGNNNNNNTAC	2 cut(s)	344, 376
BbvI	GCAGC	4 cut(s)	196, 265, 538, 574
BccI	CCATC	1 cut(s)	539
BcnI	CCSGG	2 cut(s)	174, 543
BfaI	CTAG	1 cut(s)	449
BisI	GCNGC	6 cut(s)	8, 185, 279, 527, 560, 563
BlsI	GCNGC	6 cut(s)	9, 186, 280, 528, 561, 564
BmcAI	AGTACT	1 cut(s)	623
Bme1390I	CCNGG	2 cut(s)	174, 543
Bme18I	GGWCC	1 cut(s)	176
BmgT120I	GGNCC	2 cut(s)	170, 176
BmiI	GGNNCC	1 cut(s)	177
BmrFI	CCNGG	2 cut(s)	174, 543
BmsI	GCATC	1 cut(s)	623
BpuMI	CCSGG	2 cut(s)	174, 543
Bsa29I	ATCGAT	1 cut(s)	454
Bsc4I	CCNNNNNNNGG	1 cut(s)	209
BseCI	ATCGAT	1 cut(s)	454
BseGI	GGATG	3 cut(s)	78, 531, 547
BseLI	CCNNNNNNNGG	1 cut(s)	209
BseMII	CTCAG	1 cut(s)	325
BseRI	GAGGAG	1 cut(s)	474
BseXI	GCAGC	4 cut(s)	196, 265, 538, 574
BsgI	GTGCAG	1 cut(s)	203
Bsh1236I	CGCG	1 cut(s)	524
BshFI	GGCC	2 cut(s)	69, 172
BshVI	ATCGAT	1 cut(s)	454
BsiSI	CCGG	4 cut(s)	70, 173, 543, 617
BslFI	GGGAC	1 cut(s)	484
BslI	CCNNNNNNNGG	1 cut(s)	209
BsmFI	GGGAC	1 cut(s)	484
BsnI	GGCC	2 cut(s)	69, 172
Bsp143I	GATC	2 cut(s)	316, 451
BspACI	CCGC	7 cut(s)	7, 57, 535, 557, 560, 590, 602
BspANI	GGCC	2 cut(s)	69, 172
BspCNI	CTCAG	1 cut(s)	324
BspDI	ATCGAT	1 cut(s)	454
BspFNI	CGCG	1 cut(s)	524
BspLI	GGNNCC	1 cut(s)	177
BspPI	GGATC	1 cut(s)	311
BssMI	GATC	2 cut(s)	316, 451
Bst4CI	ACNGT	2 cut(s)	109, 275
Bst6I	CTCTTC	1 cut(s)	387
BstAPI	GCANNNNNTGC	1 cut(s)	275
BstC8I	GCNNGC	1 cut(s)	539
BstDEI	CTNAG	1 cut(s)	311
BstENI	CCTNNNNNAGG	1 cut(s)	207
BstF5I	GGATG	3 cut(s)	78, 531, 547
BstFNI	CGCG	1 cut(s)	524
BstHHI	GCGC	1 cut(s)	526
BstKTI	GATC	2 cut(s)	319, 454
BstMBI	GATC	2 cut(s)	316, 451
BstMWI	GCNNNNNNNGC	4 cut(s)	275, 428, 467, 523
BstSCI	CCNGG	2 cut(s)	172, 541
BstUI	CGCG	1 cut(s)	524
BstV1I	GCAGC	4 cut(s)	196, 265, 538, 574
Bsu15I	ATCGAT	1 cut(s)	454
BsuRI	GGCC	2 cut(s)	69, 172
BsuTUI	ATCGAT	1 cut(s)	454
BtgZI	GCGATG	1 cut(s)	491
BtsCI	GGATG	3 cut(s)	78, 531, 547
BtsIMutI	CAGTG	1 cut(s)	319
Cac8I	GCNNGC	1 cut(s)	539
CfoI	GCGC	1 cut(s)	526
Cfr13I	GGNCC	2 cut(s)	170, 176
ClaI	ATCGAT	1 cut(s)	454
Csp6I	GTAC	1 cut(s)	622
CviAII	CATG	1 cut(s)	142
CviQI	GTAC	1 cut(s)	622
DdeI	CTNAG	1 cut(s)	311
DpnI	GATC	2 cut(s)	318, 453
DpnII	GATC	2 cut(s)	316, 451
DraIII	CACNNNGTG	1 cut(s)	275
Eam1104I	CTCTTC	1 cut(s)	387
EarI	CTCTTC	1 cut(s)	387
EciI	GGCGGA	3 cut(s)	524, 546, 591
Eco47I	GGWCC	1 cut(s)	176
Eco57I	CTGAAG	1 cut(s)	155
EcoNI	CCTNNNNNAGG	1 cut(s)	207
EcoO109I	RGGNCCY	1 cut(s)	176
FaeI	CATG	1 cut(s)	145
FaiI	YATR	7 cut(s)	36, 63, 143, 324, 333, 368, 459
FaqI	GGGAC	1 cut(s)	484
FatI	CATG	1 cut(s)	141
FauI	CCCGC	1 cut(s)	597
FblI	GTMKAC	1 cut(s)	232
Fnu4HI	GCNGC	6 cut(s)	8, 185, 279, 527, 560, 563
FokI	GGATG	3 cut(s)	85, 518, 534
Fsp4HI	GCNGC	6 cut(s)	8, 185, 279, 527, 560, 563
FspBI	CTAG	1 cut(s)	449
GlaI	GCGC	1 cut(s)	525
GluI	GCNGC	6 cut(s)	8, 185, 279, 527, 560, 563
HaeIII	GGCC	2 cut(s)	69, 172
HapII	CCGG	4 cut(s)	70, 173, 543, 617
HhaI	GCGC	1 cut(s)	526
Hin1II	CATG	1 cut(s)	145
Hin6I	GCGC	1 cut(s)	524
HinP1I	GCGC	1 cut(s)	524
HinfI	GANTC	4 cut(s)	95, 157, 328, 399
HpaII	CCGG	4 cut(s)	70, 173, 543, 617
HphI	GGTGA	2 cut(s)	97, 578
Hpy166II	GTNNAC	1 cut(s)	233
Hpy188I	TCNGA	1 cut(s)	632
Hpy188III	TCNNGA	2 cut(s)	14, 449
Hpy8I	GTNNAC	1 cut(s)	233
HpyAV	CCTTC	1 cut(s)	346
HpyCH4III	ACNGT	2 cut(s)	109, 275
HpyCH4V	TGCA	3 cut(s)	184, 269, 470
HpyF10VI	GCNNNNNNNGC	4 cut(s)	275, 428, 467, 523
HpyF3I	CTNAG	1 cut(s)	311
Hsp92II	CATG	1 cut(s)	145
HspAI	GCGC	1 cut(s)	524
Kzo9I	GATC	2 cut(s)	316, 451
LmnI	GCTCC	2 cut(s)	487, 641
LpnPI	CCDG	8 cut(s)	51, 83, 186, 192, 200, 551, 556, 630
Lsp1109I	GCAGC	4 cut(s)	196, 265, 538, 574
LweI	GCATC	1 cut(s)	623
MaeI	CTAG	1 cut(s)	449
MaeIII	GTNAC	1 cut(s)	382
MalI	GATC	2 cut(s)	318, 453
MboI	GATC	2 cut(s)	316, 451
MboII	GAAGA	1 cut(s)	404
MluCI	AATT	3 cut(s)	407, 474, 576
MlyI	GAGTC	1 cut(s)	104
MnlI	CCTC	9 cut(s)	291, 320, 388, 495, 564, 582, 594, 609, 622
MseI	TTAA	1 cut(s)	306
MslI	CAYNNNNRTG	2 cut(s)	165, 225
MspI	CCGG	4 cut(s)	70, 173, 543, 617
MspR9I	CCNGG	2 cut(s)	174, 543
MvnI	CGCG	1 cut(s)	524
MwoI	GCNNNNNNNGC	4 cut(s)	275, 428, 467, 523
NciI	CCSGG	2 cut(s)	174, 543
NdeII	GATC	2 cut(s)	316, 451
NlaIII	CATG	1 cut(s)	145
NlaIV	GGNNCC	1 cut(s)	177
OliI	CACNNNNGTG	1 cut(s)	225
PfeI	GAWTC	3 cut(s)	157, 328, 399
PkrI	GCNGC	6 cut(s)	9, 186, 280, 528, 561, 564
PleI	GAGTC	1 cut(s)	103
PpsI	GAGTC	1 cut(s)	103
PpuMI	RGGWCCY	1 cut(s)	176
Psp5II	RGGWCCY	1 cut(s)	176
PspN4I	GGNNCC	1 cut(s)	177
PspPI	GGNCC	2 cut(s)	170, 176
PspPPI	RGGWCCY	1 cut(s)	176
RsaI	GTAC	1 cut(s)	623
RsaNI	GTAC	1 cut(s)	622
RseI	CAYNNNNRTG	2 cut(s)	165, 225
SaqAI	TTAA	1 cut(s)	306
SatI	GCNGC	6 cut(s)	8, 185, 279, 527, 560, 563
Sau3AI	GATC	2 cut(s)	316, 451
Sau96I	GGNCC	2 cut(s)	170, 176
ScaI	AGTACT	1 cut(s)	623
SchI	GAGTC	1 cut(s)	104
ScrFI	CCNGG	2 cut(s)	174, 543
SetI	ASST	8 cut(s)	205, 302, 312, 424, 468, 484, 556, 601
SfaNI	GCATC	1 cut(s)	623
SinI	GGWCC	1 cut(s)	176
SmiMI	CAYNNNNRTG	2 cut(s)	165, 225
Sse9I	AATT	3 cut(s)	407, 474, 576
SsiI	CCGC	7 cut(s)	7, 57, 535, 557, 560, 590, 602
SspMI	CTAG	1 cut(s)	449
StyD4I	CCNGG	2 cut(s)	172, 541
TaaI	ACNGT	2 cut(s)	109, 275
TaqI	TCGA	1 cut(s)	454
TasI	AATT	3 cut(s)	407, 474, 576
TatI	WGTACW	1 cut(s)	621
TauI	GCSGC	2 cut(s)	10, 562
TfiI	GAWTC	3 cut(s)	157, 328, 399
Tru1I	TTAA	1 cut(s)	306
Tru9I	TTAA	1 cut(s)	306
TscAI	CASTG	1 cut(s)	319
TseI	GCWGC	4 cut(s)	184, 278, 526, 562
TspDTI	ATGAA	4 cut(s)	65, 149, 320, 405
TspRI	CASTG	1 cut(s)	319
VpaK11BI	GGWCC	1 cut(s)	176
XagI	CCTNNNNNAGG	1 cut(s)	207
XapI	RAATTY	1 cut(s)	474
XbaI	TCTAGA	1 cut(s)	448
XmiI	GTMKAC	1 cut(s)	232
XspI	CTAG	1 cut(s)	449
ZrmI	AGTACT	1 cut(s)	623

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