Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1B

Orthogroup ID

OG0000701

Physical Location & Seq

Genomic Coordinates Forward (+)

26055698 .. 26083233

Gene Structure 27536 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1BG161500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 858 bp

ATGGAGCAGAGGAAAACAGAGGAGCCAAGCTCTCTCCGCGACAACTCAGTCTTTCTCCCCCAGTCCCTCGCCACTTTACACGGACCAGTCACACAGATTTATGTGTTCTTCCCTGACGAACCAAAAATAGGGGTCAAGACGATCAAGAATTACATCAAACGCTTGGTTCAGGATGATACGGACAAAGCCATCGTGCTTATTCAACAAAATCTGACTCCGTTTGCAAAGCGCTTCATAAGTGAGATGAGATCAAAGTACAACTTGGAGGGTTTTCCAGGAAATATGGTTTTGACAGAAGAAGAAATTATGAGGCTCTATAGAGTTCGAAAGACAGTGATGCAAATGCTGAAAGATCGGGACTATCTAATTGTTGATCATGATCTCAACATGACAATGTCGCAGTTTAAAAACAAACATGGAGAGAACATGAAGAGGGAGGACCGTACTATCAATAGAAGGAAGAGAGATGACGAGTCTGATCAGATTTATGTGTTTTTCCCTGACGAACCAAAAGTTGGGGCCAAGACAATGAAGAGTTACATCACACGCATGAATCAGGAGAATCTAATTAGAGCAATCTTAGTTGTTCAACAAAATCTGAGTCCTTTTGCAGAGACCTCCATTAGTGAGATGGGTTCAAAGTACCACCTGGAGATTTTCCAGGAGGCAGAATTGTTGAGGTACACTGTGAAAGAAACACAGCTACCTCTTATTCAGCTGATTGATCCAATTGCAAGATATTACGGGCTTAAGCGTGGACAAGTTGTGAAGATAATCCGGCCAAGTGAGACTGCAGGGCGATATGTCACCTACCGTTACGTTATCCAAGTACAGCAGCAGAAACCTGGATTGCATTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000418 GO:0000428 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005665 GO:0005666 GO:0005730 GO:0005736 GO:0006139 GO:0006351 GO:0006366 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0010467 GO:0016070 GO:0016591 GO:0018130 GO:0019438 GO:0030880 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044452 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0090304 GO:0097659 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko04623 ko05016 ko05169 map00230 map00240 map01100 map03020 map04623 map05016 map05169

Pfam Domains

Protein Families

RNA_pol_Rpb5_C RNA_pol_Rpb5_N

Protein Analysis

285

Amino Acids

33.56

Weight (kDa)

9.38

Isoelectric Point (pI)

39.7

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	99 - 184	1.9e-29	RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_C	PF01191	225 - 274	2.4e-21	RNA polymerase Rpb5, C-terminal domain

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

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0000701)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G22320
fragaria_vesca	FvH4_5g21560 FvH4_7g09301 FvH4_7g09301
malus_domestica	MD02G1080800.v1.1 MD02G1093900.v1.1 MD15G1208600.v1.1
prunus_persica	Prupe.2G121300_v2.0.a1 Prupe.2G121300_v2.0.a1 Prupe.2G121400_v2.0.a1 Prupe.2G121400_v2.0.a1
pyrus_communis	pycom02g06410 pycom02g07430 pycom15g18470
rosa_chinensis	RchiOBHm_Chr1g0332791 RchiOBHm_Chr1g0344101 RchiOBHm_Chr1g0344151 RchiOBHm_Chr1g0344171 RchiOBHm_Chr1g0345361 RchiOBHm_Chr1g0345421 RchiOBHm_Chr1g0345561 RchiOBHm_Chr1g0345591 RchiOBHm_Chr1g0345671 RchiOBHm_Chr1g0345701 RchiOBHm_Chr1g0345711 RchiOBHm_Chr1g0345721 RchiOBHm_Chr1g0345801 RchiOBHm_Chr1g0345851 RchiOBHm_Chr1g0345901 RchiOBHm_Chr1g0345921 RchiOBHm_Chr1g0345931 RchiOBHm_Chr1g0345951 RchiOBHm_Chr1g0345961 RchiOBHm_Chr7g0208981
rosa_laevigata	RLG00000003175 RLG00000029644
rosa_multiflora	Rmu_co8382943.1_g000001 Rmu_sc0000532.1_g000035 Rmu_sc0001292.1_g000003 Rmu_sc0001349.1_g000004 Rmu_sc0001692.1_g000006 Rmu_sc0001692.1_g000027 Rmu_sc0002329.1_g000024 Rmu_sc0002329.1_g000032 Rmu_sc0004239.1_g000023 Rmu_sc0008115.1_g000011
rosa_roxburghii	Rroxscaffold_3G00238160 Rroxscaffold_3G00249920 Rroxscaffold_4G00310020 Rroxscaffold_4G00317980 Rroxscaffold_5G00344600
rosa_rugosa	Rorug01G0103700 Rorug01G0103800 Rorug01G0103900 Rorug01G0171800 Rorug07G0107800
rosa_samantha	Rh1BG097500 Rh1BG161500 Rh1CG122000 Rh1CG173900 Rh1CG180700 Rh1CG181100 Rh1DG133900 Rh1DG191900 Rh7AG242600 Rh7BG237400 Rh7DG249500
rosa_wichuraiana	Rw1G010510 Rw1G016120 Rw1G016200 Rw1G016220 Rw1G016430 Rw1G016490 Rw7G020550

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AasI	GACNNNNNNGTC	1 cut(s)	47
AccB7I	CCANNNNNTGG	1 cut(s)	515
AccII	CGCG	1 cut(s)	39
AciI	CCGC	1 cut(s)	37
AclWI	GGATC	1 cut(s)	719
AcoI	YGGCCR	1 cut(s)	779
AfaI	GTAC	5 cut(s)	257, 445, 644, 683, 831
AfeI	AGCGCT	1 cut(s)	230
AfiI	CCNNNNNNNGG	2 cut(s)	128, 515
AflII	CTTAAG	1 cut(s)	749
AgsI	TTSAA	3 cut(s)	203, 590, 639
AjnI	CCWGG	4 cut(s)	274, 648, 660, 844
AjuI	GAANNNNNNNTTGG	2 cut(s)	498, 530
AluBI	AGCT	3 cut(s)	30, 703, 718
AluI	AGCT	3 cut(s)	30, 703, 718
Alw26I	GTCTC	2 cut(s)	608, 782
AlwI	GGATC	1 cut(s)	719
Aor51HI	AGCGCT	1 cut(s)	230
AoxI	GGCC	2 cut(s)	519, 779
ApeKI	GCWGC	1 cut(s)	835
ArsI	GACNNNNNNTTYG	2 cut(s)	586, 618
AspLEI	GCGC	1 cut(s)	231
AspS9I	GGNCC	3 cut(s)	83, 439, 519
AsuHPI	GGTGA	1 cut(s)	799
AsuII	TTCGAA	1 cut(s)	325
AvaII	GGWCC	2 cut(s)	83, 439
BbvI	GCAGC	1 cut(s)	847
BccI	CCATC	2 cut(s)	197, 625
BciT130I	CCWGG	4 cut(s)	276, 650, 662, 846
BclI	TGATCA	2 cut(s)	373, 478
BcoDI	GTCTC	2 cut(s)	608, 782
BfmI	CTRYAG	2 cut(s)	316, 792
BfoI	RGCGCY	1 cut(s)	232
BfrI	CTTAAG	1 cut(s)	749
BisI	GCNGC	1 cut(s)	836
BlsI	GCNGC	1 cut(s)	837
Bme1390I	CCNGG	4 cut(s)	276, 650, 662, 846
Bme18I	GGWCC	2 cut(s)	83, 439
BmgT120I	GGNCC	3 cut(s)	83, 439, 519
BmiI	GGNNCC	2 cut(s)	24, 520
BmrFI	CCNGG	4 cut(s)	276, 650, 662, 846
BmrI	ACTGGG	1 cut(s)	55
BmsI	GCATC	1 cut(s)	327
BmuI	ACTGGG	1 cut(s)	55
BplI	GAGNNNNNCTC	2 cut(s)	14, 46
BpmI	CTGGAG	1 cut(s)	671
Bpu14I	TTCGAA	1 cut(s)	325
BsaBI	GATNNNNATC	1 cut(s)	378
BsaI	GGTCTC	1 cut(s)	608
Bsc4I	CCNNNNNNNGG	2 cut(s)	128, 515
Bse1I	ACTGG	2 cut(s)	61, 86
Bse8I	GATNNNNATC	1 cut(s)	378
BseBI	CCWGG	4 cut(s)	276, 650, 662, 846
BseGI	GGATG	1 cut(s)	178
BseJI	GATNNNNATC	1 cut(s)	378
BseLI	CCNNNNNNNGG	2 cut(s)	128, 515
BseMII	CTCAG	2 cut(s)	60, 590
BseNI	ACTGG	2 cut(s)	61, 86
BseRI	GAGGAG	1 cut(s)	35
BseXI	GCAGC	1 cut(s)	847
Bsh1236I	CGCG	1 cut(s)	39
BshFI	GGCC	2 cut(s)	521, 781
BsiSI	CCGG	1 cut(s)	778
BslFI	GGGAC	2 cut(s)	49, 371
BslI	CCNNNNNNNGG	2 cut(s)	128, 515
BsmAI	GTCTC	2 cut(s)	608, 782
BsmFI	GGGAC	2 cut(s)	49, 371
BsnI	GGCC	2 cut(s)	521, 781
Bso31I	GGTCTC	1 cut(s)	608
Bsp119I	TTCGAA	1 cut(s)	325
Bsp143I	GATC	7 cut(s)	141, 248, 352, 373, 379, 478, 724
BspACI	CCGC	1 cut(s)	37
BspANI	GGCC	2 cut(s)	521, 781
BspCNI	CTCAG	2 cut(s)	59, 591
BspFNI	CGCG	1 cut(s)	39
BspHI	TCATGA	1 cut(s)	376
BspLI	GGNNCC	2 cut(s)	24, 520
BspMAI	CTGCAG	1 cut(s)	796
BspPI	GGATC	1 cut(s)	719
BspT104I	TTCGAA	1 cut(s)	325
BspTI	CTTAAG	1 cut(s)	749
BspTNI	GGTCTC	1 cut(s)	608
BsrI	ACTGG	2 cut(s)	61, 86
BssMI	GATC	7 cut(s)	141, 248, 352, 373, 379, 478, 724
Bst2UI	CCWGG	4 cut(s)	276, 650, 662, 846
Bst4CI	ACNGT	4 cut(s)	334, 443, 688, 815
Bst6I	CTCTTC	3 cut(s)	425, 455, 527
BstAFI	CTTAAG	1 cut(s)	749
BstBI	TTCGAA	1 cut(s)	325
BstDEI	CTNAG	3 cut(s)	46, 580, 599
BstF5I	GGATG	1 cut(s)	178
BstFNI	CGCG	1 cut(s)	39
BstH2I	RGCGCY	1 cut(s)	232
BstHHI	GCGC	1 cut(s)	231
BstKTI	GATC	7 cut(s)	144, 251, 355, 376, 382, 481, 727
BstMAI	GTCTC	2 cut(s)	608, 782
BstMBI	GATC	7 cut(s)	141, 248, 352, 373, 379, 478, 724
BstMWI	GCNNNNNNNGC	1 cut(s)	36
BstNI	CCWGG	4 cut(s)	276, 650, 662, 846
BstSCI	CCNGG	4 cut(s)	274, 648, 660, 844
BstSFI	CTRYAG	2 cut(s)	316, 792
BstUI	CGCG	1 cut(s)	39
BstV1I	GCAGC	1 cut(s)	847
BsuRI	GGCC	2 cut(s)	521, 781
BtsCI	GGATG	1 cut(s)	178
BtsIMutI	CAGTG	2 cut(s)	339, 684
CciI	TCATGA	1 cut(s)	376
CfoI	GCGC	1 cut(s)	231
Cfr13I	GGNCC	3 cut(s)	83, 439, 519
Csp6I	GTAC	5 cut(s)	256, 444, 643, 682, 830
CviAII	CATG	5 cut(s)	377, 388, 416, 427, 550
CviJI	RGCY	9 cut(s)	25, 30, 188, 313, 521, 703, 718, 748, 781
CviKI_1	RGCY	9 cut(s)	25, 30, 188, 313, 521, 703, 718, 748, 781
CviQI	GTAC	5 cut(s)	256, 444, 643, 682, 830
DdeI	CTNAG	3 cut(s)	46, 580, 599
DpnI	GATC	7 cut(s)	143, 250, 354, 375, 381, 480, 726
DpnII	GATC	7 cut(s)	141, 248, 352, 373, 379, 478, 724
DraI	TTTAAA	1 cut(s)	406
DrdI	GACNNNNNNGTC	1 cut(s)	47
DseDI	GACNNNNNNGTC	1 cut(s)	47
EaeI	YGGCCR	1 cut(s)	779
Eam1104I	CTCTTC	3 cut(s)	425, 455, 527
EarI	CTCTTC	3 cut(s)	425, 455, 527
Eco31I	GGTCTC	1 cut(s)	608
Eco47I	GGWCC	2 cut(s)	83, 439
Eco47III	AGCGCT	1 cut(s)	230
EcoRII	CCWGG	4 cut(s)	274, 648, 660, 844
FaeI	CATG	5 cut(s)	380, 391, 419, 430, 553
FalI	AAGNNNNNCTT	2 cut(s)	245, 277
FaqI	GGGAC	2 cut(s)	49, 371
FatI	CATG	5 cut(s)	376, 387, 415, 426, 549
FbaI	TGATCA	2 cut(s)	373, 478
Fnu4HI	GCNGC	1 cut(s)	836
FokI	GGATG	1 cut(s)	185
Fsp4HI	GCNGC	1 cut(s)	836
GlaI	GCGC	1 cut(s)	230
GluI	GCNGC	1 cut(s)	836
GsuI	CTGGAG	1 cut(s)	671
HaeII	RGCGCY	1 cut(s)	232
HaeIII	GGCC	2 cut(s)	521, 781
HapII	CCGG	1 cut(s)	778
HhaI	GCGC	1 cut(s)	231
Hin1II	CATG	5 cut(s)	380, 391, 419, 430, 553
Hin6I	GCGC	1 cut(s)	229
HinP1I	GCGC	1 cut(s)	229
HinfI	GANTC	5 cut(s)	214, 473, 553, 562, 601
HpaII	CCGG	1 cut(s)	778
HphI	GGTGA	1 cut(s)	799
Hpy166II	GTNNAC	2 cut(s)	684, 758
Hpy188I	TCNGA	4 cut(s)	213, 478, 483, 600
Hpy188III	TCNNGA	6 cut(s)	136, 145, 170, 356, 377, 557
Hpy8I	GTNNAC	2 cut(s)	684, 758
HpyAV	CCTTC	1 cut(s)	450
HpyCH4III	ACNGT	4 cut(s)	334, 443, 688, 815
HpyCH4IV	ACGT	1 cut(s)	819
HpyCH4V	TGCA	6 cut(s)	224, 340, 611, 734, 794, 853
HpyF10VI	GCNNNNNNNGC	1 cut(s)	36
HpyF3I	CTNAG	3 cut(s)	46, 580, 599
HpySE526I	ACGT	1 cut(s)	819
Hsp92II	CATG	5 cut(s)	380, 391, 419, 430, 553
HspAI	GCGC	1 cut(s)	229
Ksp22I	TGATCA	2 cut(s)	373, 478
Kzo9I	GATC	7 cut(s)	141, 248, 352, 373, 379, 478, 724
LmnI	GCTCC	2 cut(s)	4, 22
Lsp1109I	GCAGC	1 cut(s)	847
LweI	GCATC	1 cut(s)	327
MaeII	ACGT	1 cut(s)	819
MaeIII	GTNAC	4 cut(s)	88, 536, 805, 815
MalI	GATC	7 cut(s)	143, 250, 354, 375, 381, 480, 726
MboI	GATC	7 cut(s)	141, 248, 352, 373, 379, 478, 724
MboII	GAAGA	7 cut(s)	100, 308, 311, 442, 472, 544, 781
MfeI	CAATTG	1 cut(s)	729
MluCI	AATT	6 cut(s)	148, 303, 366, 567, 671, 729
MlyI	GAGTC	3 cut(s)	208, 482, 610
MseI	TTAA	2 cut(s)	405, 750
MslI	CAYNNNNRTG	2 cut(s)	392, 548
MspA1I	CMGCKG	1 cut(s)	718
MspCI	CTTAAG	1 cut(s)	749
MspI	CCGG	1 cut(s)	778
MspR9I	CCNGG	4 cut(s)	276, 650, 662, 846
MunI	CAATTG	1 cut(s)	729
MvaI	CCWGG	4 cut(s)	276, 650, 662, 846
MvnI	CGCG	1 cut(s)	39
MwoI	GCNNNNNNNGC	1 cut(s)	36
NdeII	GATC	7 cut(s)	141, 248, 352, 373, 379, 478, 724
NlaIII	CATG	5 cut(s)	380, 391, 419, 430, 553
NlaIV	GGNNCC	2 cut(s)	24, 520
NmuCI	GTSAC	2 cut(s)	88, 805
NspV	TTCGAA	1 cut(s)	325
PagI	TCATGA	1 cut(s)	376
PfeI	GAWTC	2 cut(s)	553, 562
PflFI	GACNNNGTC	1 cut(s)	394
PflMI	CCANNNNNTGG	1 cut(s)	515
PfoI	TCCNGGA	2 cut(s)	274, 660
PkrI	GCNGC	1 cut(s)	837
PleI	GAGTC	3 cut(s)	208, 481, 609
PpsI	GAGTC	3 cut(s)	208, 481, 609
Psp6I	CCWGG	4 cut(s)	274, 648, 660, 844
PspGI	CCWGG	4 cut(s)	274, 648, 660, 844
PspN4I	GGNNCC	2 cut(s)	24, 520
PspPI	GGNCC	3 cut(s)	83, 439, 519
PstI	CTGCAG	1 cut(s)	796
PsyI	GACNNNGTC	1 cut(s)	394
PvuII	CAGCTG	1 cut(s)	718
RsaI	GTAC	5 cut(s)	257, 445, 644, 683, 831
RsaNI	GTAC	5 cut(s)	256, 444, 643, 682, 830
RseI	CAYNNNNRTG	2 cut(s)	392, 548
SaqAI	TTAA	2 cut(s)	405, 750
SatI	GCNGC	1 cut(s)	836
Sau3AI	GATC	7 cut(s)	141, 248, 352, 373, 379, 478, 724
Sau96I	GGNCC	3 cut(s)	83, 439, 519
SchI	GAGTC	3 cut(s)	208, 482, 610
ScrFI	CCNGG	4 cut(s)	276, 650, 662, 846
SfaNI	GCATC	1 cut(s)	327
SfcI	CTRYAG	2 cut(s)	316, 792
SfuI	TTCGAA	1 cut(s)	325
SinI	GGWCC	2 cut(s)	83, 439
SmiMI	CAYNNNNRTG	2 cut(s)	392, 548
SmlI	CTYRAG	1 cut(s)	749
SmoI	CTYRAG	1 cut(s)	749
Sse9I	AATT	6 cut(s)	148, 303, 366, 567, 671, 729
SsiI	CCGC	1 cut(s)	37
StyD4I	CCNGG	4 cut(s)	274, 648, 660, 844
TaaI	ACNGT	4 cut(s)	334, 443, 688, 815
TaiI	ACGT	1 cut(s)	822
TaqI	TCGA	1 cut(s)	325
TasI	AATT	6 cut(s)	148, 303, 366, 567, 671, 729
TatI	WGTACW	2 cut(s)	255, 829
TfiI	GAWTC	2 cut(s)	553, 562
Tru1I	TTAA	2 cut(s)	405, 750
Tru9I	TTAA	2 cut(s)	405, 750
TscAI	CASTG	2 cut(s)	339, 691
TseFI	GTSAC	2 cut(s)	88, 805
TseI	GCWGC	1 cut(s)	835
Tsp45I	GTSAC	2 cut(s)	88, 805
TspDTI	ATGAA	4 cut(s)	223, 443, 545, 566
TspGWI	ACGGA	3 cut(s)	96, 194, 207
TspRI	CASTG	2 cut(s)	339, 691
Tth111I	GACNNNGTC	1 cut(s)	394
Van91I	CCANNNNNTGG	1 cut(s)	515
Vha464I	CTTAAG	1 cut(s)	749
VpaK11BI	GGWCC	2 cut(s)	83, 439
XcmI	CCANNNNNNNNNTGG	1 cut(s)	628

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