Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1D

Orthogroup ID

OG0000701

Physical Location & Seq

Genomic Coordinates Forward (+)

38244289 .. 38247339

Gene Structure 3051 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1DG191900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 936 bp

ATGGATCTAACTGAAGGAGAAATTACTAGGCTCTATAGAGTTCGAAAGACAGTGATGCAAATGGTGAAAGATTGGGACTATATAATTGTAGATCATGATCTCAACATGACAATGTCGCAGTTCAAAAACAAATATGGAGAGAACATGAAAAGAGATGATCTATCAATAGAAGGAAGCGAGATTTATGTGTTCTTCCCTGACGAACCAAAAATAGGGGTCAAGACGATCAAGAATTACATCAAACGCTTGGTTCAGGATGATACGGACAAAGCCATCGTGCTTATTCAACAAAATCTGACTCCGTTTGCAAAGCGCTTCATAAGTGAGATGAGATCAAAGTACAACTTGGAGGGTTTTCCAGGAAATATGGTTTTGACAGAAGAAGAAATTATGAGGCTCTATAGAGTTCGAAAGACAGTGATGCAAATGCTGAAAGATCGGGACTATCTAATTGTTGATCATGATCTCAACATGACAATGTCGCAGTTTAAAAACAAACATGGAGAGAACATGAAGAGGGAGGACCGTACTATCAATAGAAGGAAGAGAGATGACGAGTCTGATCAGATTTATGTGTTTTTCCCTGACGAACCAAAAGTTGGGGCCAAGACAATGAAGAGTTACATCACACGCATGAATCAGGAGAATCTAATTAGAGCAATCTTAGTTGTTCAACAAAATCTGAGTCCTTTTGCAGAGACCTCCATTAGTGAGATGGGTTCAAAGTACCACCTGGAGATTTTCCAGGAGGCAGAATTGTACACTGTGAAAGAAACACAGCTACCTCTTATTCAGCTGATTGATCCAATTGCAAGATATTACGGGCTTAAGCGTGGACAAGTTGTGAAGATAATCCGGCCAAGTGAGACTGCAGGGCGATATGTCACCTACCGTTACGTTATCCAAGTACAGCAGCAGAAACCTGGATTGCATTAG

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

311

Amino Acids

36.91

Weight (kDa)

9.01

Isoelectric Point (pI)

34.18

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	6 - 82	9.4e-23	RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_N	PF03871	127 - 212	2.2e-29	RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_C	PF01191	254 - 300	2.1e-20	RNA polymerase Rpb5, C-terminal domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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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)
AccB7I	CCANNNNNTGG	1 cut(s)	599
AclWI	GGATC	2 cut(s)	12, 797
AcoI	YGGCCR	1 cut(s)	857
AcuI	CTGAAG	1 cut(s)	33
AfaI	GTAC	5 cut(s)	341, 529, 728, 761, 909
AfeI	AGCGCT	1 cut(s)	314
AfiI	CCNNNNNNNGG	2 cut(s)	212, 599
AflII	CTTAAG	1 cut(s)	827
AgsI	TTSAA	4 cut(s)	124, 287, 674, 723
AjnI	CCWGG	4 cut(s)	358, 732, 744, 922
AjuI	GAANNNNNNNTTGG	2 cut(s)	582, 614
AluBI	AGCT	2 cut(s)	781, 796
AluI	AGCT	2 cut(s)	781, 796
Alw26I	GTCTC	2 cut(s)	692, 860
AlwI	GGATC	2 cut(s)	12, 797
Aor51HI	AGCGCT	1 cut(s)	314
AoxI	GGCC	2 cut(s)	603, 857
ApeKI	GCWGC	1 cut(s)	913
ArsI	GACNNNNNNTTYG	2 cut(s)	670, 702
AspLEI	GCGC	1 cut(s)	315
AspS9I	GGNCC	2 cut(s)	523, 603
AsuHPI	GGTGA	2 cut(s)	76, 877
AsuII	TTCGAA	2 cut(s)	43, 409
AvaII	GGWCC	1 cut(s)	523
BbvI	GCAGC	1 cut(s)	925
BccI	CCATC	2 cut(s)	281, 709
BciT130I	CCWGG	4 cut(s)	360, 734, 746, 924
BclI	TGATCA	2 cut(s)	457, 562
BcoDI	GTCTC	2 cut(s)	692, 860
BfaI	CTAG	1 cut(s)	27
BfmI	CTRYAG	3 cut(s)	34, 400, 870
BfoI	RGCGCY	1 cut(s)	316
BfrI	CTTAAG	1 cut(s)	827
BisI	GCNGC	1 cut(s)	914
BlsI	GCNGC	1 cut(s)	915
Bme1390I	CCNGG	4 cut(s)	360, 734, 746, 924
Bme18I	GGWCC	1 cut(s)	523
BmgT120I	GGNCC	2 cut(s)	523, 603
BmiI	GGNNCC	1 cut(s)	604
BmrFI	CCNGG	4 cut(s)	360, 734, 746, 924
BmsI	GCATC	2 cut(s)	45, 411
BpmI	CTGGAG	1 cut(s)	755
Bpu14I	TTCGAA	2 cut(s)	43, 409
BsaBI	GATNNNNATC	2 cut(s)	96, 462
BsaI	GGTCTC	1 cut(s)	692
Bsc4I	CCNNNNNNNGG	2 cut(s)	212, 599
Bse8I	GATNNNNATC	2 cut(s)	96, 462
BseBI	CCWGG	4 cut(s)	360, 734, 746, 924
BseGI	GGATG	1 cut(s)	262
BseJI	GATNNNNATC	2 cut(s)	96, 462
BseLI	CCNNNNNNNGG	2 cut(s)	212, 599
BseMII	CTCAG	1 cut(s)	674
BseXI	GCAGC	1 cut(s)	925
BshFI	GGCC	2 cut(s)	605, 859
BsiSI	CCGG	1 cut(s)	856
BslFI	GGGAC	2 cut(s)	89, 455
BslI	CCNNNNNNNGG	2 cut(s)	212, 599
BsmAI	GTCTC	2 cut(s)	692, 860
BsmFI	GGGAC	2 cut(s)	89, 455
BsnI	GGCC	2 cut(s)	605, 859
Bso31I	GGTCTC	1 cut(s)	692
Bsp119I	TTCGAA	2 cut(s)	43, 409
Bsp1407I	TGTACA	1 cut(s)	759
BspANI	GGCC	2 cut(s)	605, 859
BspCNI	CTCAG	1 cut(s)	675
BspHI	TCATGA	2 cut(s)	94, 460
BspLI	GGNNCC	1 cut(s)	604
BspMAI	CTGCAG	1 cut(s)	874
BspPI	GGATC	2 cut(s)	12, 797
BspT104I	TTCGAA	2 cut(s)	43, 409
BspTI	CTTAAG	1 cut(s)	827
BspTNI	GGTCTC	1 cut(s)	692
BsrGI	TGTACA	1 cut(s)	759
Bst2UI	CCWGG	4 cut(s)	360, 734, 746, 924
Bst4CI	ACNGT	5 cut(s)	52, 418, 527, 766, 893
Bst6I	CTCTTC	3 cut(s)	509, 539, 611
BstAFI	CTTAAG	1 cut(s)	827
BstAUI	TGTACA	1 cut(s)	759
BstBI	TTCGAA	2 cut(s)	43, 409
BstDEI	CTNAG	2 cut(s)	664, 683
BstF5I	GGATG	1 cut(s)	262
BstH2I	RGCGCY	1 cut(s)	316
BstHHI	GCGC	1 cut(s)	315
BstMAI	GTCTC	2 cut(s)	692, 860
BstNI	CCWGG	4 cut(s)	360, 734, 746, 924
BstSCI	CCNGG	4 cut(s)	358, 732, 744, 922
BstSFI	CTRYAG	3 cut(s)	34, 400, 870
BstV1I	GCAGC	1 cut(s)	925
BstX2I	RGATCY	1 cut(s)	4
BstYI	RGATCY	1 cut(s)	4
BsuRI	GGCC	2 cut(s)	605, 859
BtsCI	GGATG	1 cut(s)	262
BtsIMutI	CAGTG	3 cut(s)	57, 423, 762
CciI	TCATGA	2 cut(s)	94, 460
CfoI	GCGC	1 cut(s)	315
Cfr13I	GGNCC	2 cut(s)	523, 603
Csp6I	GTAC	5 cut(s)	340, 528, 727, 760, 908
CviAII	CATG	8 cut(s)	95, 106, 145, 461, 472, 500, 511, 634
CviJI	RGCY	8 cut(s)	31, 272, 397, 605, 781, 796, 826, 859
CviKI_1	RGCY	8 cut(s)	31, 272, 397, 605, 781, 796, 826, 859
CviQI	GTAC	5 cut(s)	340, 528, 727, 760, 908
DdeI	CTNAG	2 cut(s)	664, 683
DraI	TTTAAA	1 cut(s)	490
EaeI	YGGCCR	1 cut(s)	857
Eam1104I	CTCTTC	3 cut(s)	509, 539, 611
EarI	CTCTTC	3 cut(s)	509, 539, 611
Eco31I	GGTCTC	1 cut(s)	692
Eco47I	GGWCC	1 cut(s)	523
Eco47III	AGCGCT	1 cut(s)	314
Eco57I	CTGAAG	1 cut(s)	33
EcoRII	CCWGG	4 cut(s)	358, 732, 744, 922
FaeI	CATG	8 cut(s)	98, 109, 148, 464, 475, 503, 514, 637
FalI	AAGNNNNNCTT	2 cut(s)	329, 361
FaqI	GGGAC	2 cut(s)	89, 455
FatI	CATG	8 cut(s)	94, 105, 144, 460, 471, 499, 510, 633
FbaI	TGATCA	2 cut(s)	457, 562
Fnu4HI	GCNGC	1 cut(s)	914
FokI	GGATG	1 cut(s)	269
Fsp4HI	GCNGC	1 cut(s)	914
FspBI	CTAG	1 cut(s)	27
GlaI	GCGC	1 cut(s)	314
GluI	GCNGC	1 cut(s)	914
GsuI	CTGGAG	1 cut(s)	755
HaeII	RGCGCY	1 cut(s)	316
HaeIII	GGCC	2 cut(s)	605, 859
HapII	CCGG	1 cut(s)	856
HhaI	GCGC	1 cut(s)	315
Hin1II	CATG	8 cut(s)	98, 109, 148, 464, 475, 503, 514, 637
Hin6I	GCGC	1 cut(s)	313
HinP1I	GCGC	1 cut(s)	313
HinfI	GANTC	5 cut(s)	298, 557, 637, 646, 685
HpaII	CCGG	1 cut(s)	856
HphI	GGTGA	2 cut(s)	76, 877
Hpy166II	GTNNAC	2 cut(s)	762, 836
Hpy188I	TCNGA	4 cut(s)	297, 562, 567, 684
Hpy188III	TCNNGA	7 cut(s)	95, 220, 229, 254, 440, 461, 641
Hpy8I	GTNNAC	2 cut(s)	762, 836
HpyAV	CCTTC	3 cut(s)	8, 164, 534
HpyCH4III	ACNGT	5 cut(s)	52, 418, 527, 766, 893
HpyCH4IV	ACGT	1 cut(s)	897
HpyCH4V	TGCA	7 cut(s)	58, 308, 424, 695, 812, 872, 931
HpyF3I	CTNAG	2 cut(s)	664, 683
HpySE526I	ACGT	1 cut(s)	897
Hsp92II	CATG	8 cut(s)	98, 109, 148, 464, 475, 503, 514, 637
HspAI	GCGC	1 cut(s)	313
Ksp22I	TGATCA	2 cut(s)	457, 562
Lsp1109I	GCAGC	1 cut(s)	925
LweI	GCATC	2 cut(s)	45, 411
MaeI	CTAG	1 cut(s)	27
MaeII	ACGT	1 cut(s)	897
MaeIII	GTNAC	3 cut(s)	620, 883, 893
MboII	GAAGA	7 cut(s)	184, 392, 395, 526, 556, 628, 859
MfeI	CAATTG	1 cut(s)	807
MflI	RGATCY	1 cut(s)	4
MluCI	AATT	8 cut(s)	21, 84, 232, 387, 450, 651, 755, 807
MlyI	GAGTC	3 cut(s)	292, 566, 694
MnlI	CCTC	7 cut(s)	343, 387, 510, 514, 712, 742, 795
MseI	TTAA	2 cut(s)	489, 828
MslI	CAYNNNNRTG	3 cut(s)	110, 476, 632
MspA1I	CMGCKG	1 cut(s)	796
MspCI	CTTAAG	1 cut(s)	827
MspI	CCGG	1 cut(s)	856
MspR9I	CCNGG	4 cut(s)	360, 734, 746, 924
MunI	CAATTG	1 cut(s)	807
MvaI	CCWGG	4 cut(s)	360, 734, 746, 924
NlaIII	CATG	8 cut(s)	98, 109, 148, 464, 475, 503, 514, 637
NlaIV	GGNNCC	1 cut(s)	604
NmuCI	GTSAC	1 cut(s)	883
NspV	TTCGAA	2 cut(s)	43, 409
PagI	TCATGA	2 cut(s)	94, 460
PfeI	GAWTC	2 cut(s)	637, 646
PflFI	GACNNNGTC	2 cut(s)	112, 478
PflMI	CCANNNNNTGG	1 cut(s)	599
PfoI	TCCNGGA	2 cut(s)	358, 744
PkrI	GCNGC	1 cut(s)	915
PleI	GAGTC	3 cut(s)	292, 565, 693
PpsI	GAGTC	3 cut(s)	292, 565, 693
Psp6I	CCWGG	4 cut(s)	358, 732, 744, 922
PspGI	CCWGG	4 cut(s)	358, 732, 744, 922
PspN4I	GGNNCC	1 cut(s)	604
PspPI	GGNCC	2 cut(s)	523, 603
PstI	CTGCAG	1 cut(s)	874
PsuI	RGATCY	1 cut(s)	4
PsyI	GACNNNGTC	2 cut(s)	112, 478
PvuII	CAGCTG	1 cut(s)	796
RsaI	GTAC	5 cut(s)	341, 529, 728, 761, 909
RsaNI	GTAC	5 cut(s)	340, 528, 727, 760, 908
RseI	CAYNNNNRTG	3 cut(s)	110, 476, 632
SaqAI	TTAA	2 cut(s)	489, 828
SatI	GCNGC	1 cut(s)	914
Sau96I	GGNCC	2 cut(s)	523, 603
SchI	GAGTC	3 cut(s)	292, 566, 694
ScrFI	CCNGG	4 cut(s)	360, 734, 746, 924
SetI	ASST	8 cut(s)	704, 735, 783, 787, 798, 890, 900, 925
SfaNI	GCATC	2 cut(s)	45, 411
SfcI	CTRYAG	3 cut(s)	34, 400, 870
SfuI	TTCGAA	2 cut(s)	43, 409
SinI	GGWCC	1 cut(s)	523
SmiMI	CAYNNNNRTG	3 cut(s)	110, 476, 632
SmlI	CTYRAG	1 cut(s)	827
SmoI	CTYRAG	1 cut(s)	827
Sse9I	AATT	8 cut(s)	21, 84, 232, 387, 450, 651, 755, 807
SspMI	CTAG	1 cut(s)	27
StyD4I	CCNGG	4 cut(s)	358, 732, 744, 922
TaaI	ACNGT	5 cut(s)	52, 418, 527, 766, 893
TaiI	ACGT	1 cut(s)	900
TaqI	TCGA	2 cut(s)	43, 409
TasI	AATT	8 cut(s)	21, 84, 232, 387, 450, 651, 755, 807
TatI	WGTACW	3 cut(s)	339, 759, 907
TfiI	GAWTC	2 cut(s)	637, 646
Tru1I	TTAA	2 cut(s)	489, 828
Tru9I	TTAA	2 cut(s)	489, 828
TscAI	CASTG	3 cut(s)	57, 423, 769
TseFI	GTSAC	1 cut(s)	883
TseI	GCWGC	1 cut(s)	913
Tsp45I	GTSAC	1 cut(s)	883
TspDTI	ATGAA	5 cut(s)	161, 307, 527, 629, 650
TspGWI	ACGGA	2 cut(s)	278, 291
TspRI	CASTG	3 cut(s)	57, 423, 769
Tth111I	GACNNNGTC	2 cut(s)	112, 478
Van91I	CCANNNNNTGG	1 cut(s)	599
Vha464I	CTTAAG	1 cut(s)	827
VpaK11BI	GGWCC	1 cut(s)	523
XcmI	CCANNNNNNNNNTGG	1 cut(s)	712
XspI	CTAG	1 cut(s)	27

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