Rh7DG216500

a DNA repair protein and transcription factor. Arabidopsis thaliana has duplicated XPB gene (AtXPB1 and AtXPB2, with high similarity to each other). XPB proteins are involved in both DNA repair and transcription, they are component of the transcription factor IIH (TFIIH) and are responsible for DNA helicase activity during nucleotide (nt) excision repair (NER). Complementation assays in yeast rad25 mutant strains suggest the involvement of AtXPB2 in DNA repair. Although both genes are expressed in a constitutive manner during the plant life cycle, Northern blot analyses suggest that light modulates the expression level of both XPB copies

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr7D
OG0001033
Physical Location & Seq
Reverse (-)
20874378 .. 20875436
1059 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh7DG216500.1

Sequence Viewer

Length: 1059 bp
ATGTTAATCCGCCGCAAAAGCAATGCTGCTGGGGTGGTGGTTGTGACTACATATAGCATGCTTGGCTGTGGTGGCAATAGGTCCCAACAGTCTACAAACATTATTGAGGAAATAAAAAATAGAAAATGGGGGTTGATTCTCATGGATGAGGTTCATGTAACTCCTGCTAAATCGTTTCAAAATGTCATCCGAATCACCAAATCACACTGCAAGCTTGGCCTCACGACGACGCTCTTGAGAGAAGATGACAAGATATCAGATCTCAACTTCCTCATTGGACCCAAATTATATGAAGCAAACTGGTTGGATTTGGCGAAACGAGGATACATTGCAAATGTGCTCTGTGCTGAAGTAAGGTGTCAGATGACAAAGGAGTTCTTTGCCGAGTATAAGAAAGAAAACTCCTACAAAAGAAAGCAAGCACTTTATTTGATGAATCCAAACAAGTTTAGGATATGCGAGTATCTTATACAGTTTCATGAGCAGCAGCGCCGTGGTGATAAGATCATAGTCTTTTCCGACAACCTCTTCACCCTCACTGAATATGCCACCAAGCTCCGAAAACCTATGTTTTATGGTGCCACCACGCAGGCTGAGACGACAAAAGTTCTAGAAGAGTTCAAAACAAACCCGGATGTAAACACCGTATTCATGTCTAAGGTGGGTGATAACTCCTTGGACATTCCCGAGGCAAATGTGATCATTGAGATTTCATGGCATGGCGGTTCGAGACGACAAGAAGCGCAGCGTCTTGGTCGGATTCTAAGGGCCAAGAAAAGTAAAGAGAAGTACAATGCATTCTTCTATTCCCTTGTGTCATCGGATACACGGGAGATGGAATTTGCAGCTAAAAGGCAGCAGTTTTTGGTCGATCAAGGTTATAGTTATAAGATTGTTACAATCTTGCAATTGCCTAATTTTCCTCCACTTGGATCAGGAGCTTTGAGCTATGACAGTCTTCAAGATCAACGCGCACTACTCAAGAAAGTGTTGAGCTTTAATGAGGCTATAGTTGGGGCCGAAGATCCACTAGTAGAAGATGTACATGGCATGCATTGA

Protein Analysis

352

Amino Acids

40.35

Weight (kDa)

9.2

Isoelectric Point (pI)

38.85

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
ResIII PF04851 12 - 78 8.8e-06 Type III restriction enzyme, res subunit
ERCC3_RAD25_C PF16203 104 - 340 1.1e-103 ERCC3/RAD25/XPB C-terminal helicase
Helicase_C PF00271 153 - 257 7e-13 Helicase conserved C-terminal domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 888
AccB1I GGYRCC 1 cut(s) 578
AccI GTMKAC 1 cut(s) 92
AccII CGCG 1 cut(s) 972
AciI CCGC 3 cut(s) 10, 13, 723
AclWI GGATC 2 cut(s) 940, 1019
AcsI RAATTY 1 cut(s) 839
AcuI CTGAAG 1 cut(s) 369
AfaI GTAC 2 cut(s) 791, 1044
AfiI CCNNNNNNNGG 1 cut(s) 929
AgsI TTSAA 3 cut(s) 179, 622, 962
AhlI ACTAGT 1 cut(s) 1030
AluBI AGCT 6 cut(s) 214, 556, 848, 941, 948, 996
AluI AGCT 6 cut(s) 214, 556, 848, 941, 948, 996
Alw21I GWGCWC 1 cut(s) 342
Alw26I GTCTC 2 cut(s) 590, 724
AlwI GGATC 2 cut(s) 940, 1019
Ama87I CYCGRG 1 cut(s) 686
AoxI GGCC 3 cut(s) 217, 768, 1017
ApeKI GCWGC 6 cut(s) 26, 484, 487, 745, 845, 856
ApoI RAATTY 1 cut(s) 839
AspLEI GCGC 3 cut(s) 492, 745, 974
AspS9I GGNCC 4 cut(s) 81, 278, 768, 1017
AsuC2I CCSGG 1 cut(s) 632
AsuHPI GGTGA 4 cut(s) 187, 509, 523, 677
AvaI CYCGRG 1 cut(s) 686
AvaII GGWCC 2 cut(s) 81, 278
BanI GGYRCC 1 cut(s) 578
BbsI GAAGAC 1 cut(s) 950
Bbv12I GWGCWC 1 cut(s) 342
BbvI GCAGC 6 cut(s) 13, 496, 499, 757, 857, 868
BccI CCATC 1 cut(s) 829
BceAI ACGGC 1 cut(s) 477
BciVI GTATCC 2 cut(s) 317, 817
BclI TGATCA 1 cut(s) 699
BcnI CCSGG 1 cut(s) 632
BcoDI GTCTC 2 cut(s) 590, 724
BcuI ACTAGT 1 cut(s) 1030
BfaI CTAG 2 cut(s) 611, 1031
BfmI CTRYAG 1 cut(s) 1008
BfoI RGCGCY 1 cut(s) 493
BfuI GTATCC 2 cut(s) 317, 817
BglII AGATCT 1 cut(s) 259
BisI GCNGC 7 cut(s) 13, 27, 485, 488, 746, 846, 857
BlsI GCNGC 7 cut(s) 14, 28, 486, 489, 747, 847, 858
Bme1390I CCNGG 1 cut(s) 632
Bme18I GGWCC 2 cut(s) 81, 278
BmeT110I CYCGRG 1 cut(s) 686
BmgT120I GGNCC 4 cut(s) 81, 278, 768, 1017
BmiI GGNNCC 4 cut(s) 83, 280, 580, 1018
BmrFI CCNGG 1 cut(s) 632
BpiI GAAGAC 1 cut(s) 950
BpuEI CTTGAG 2 cut(s) 256, 965
BpuMI CCSGG 1 cut(s) 632
BsaJI CCNNGG 3 cut(s) 493, 675, 687
Bsc4I CCNNNNNNNGG 1 cut(s) 929
Bse1I ACTGG 1 cut(s) 305
Bse3DI GCAATG 2 cut(s) 28, 327
BseDI CCNNGG 3 cut(s) 493, 675, 687
BseGI GGATG 3 cut(s) 151, 186, 640
BseLI CCNNNNNNNGG 1 cut(s) 929
BseMI GCAATG 2 cut(s) 28, 327
BseMII CTCAG 1 cut(s) 585
BseNI ACTGG 1 cut(s) 305
BseXI GCAGC 6 cut(s) 13, 496, 499, 757, 857, 868
BseYI CCCAGC 1 cut(s) 29
Bsh1236I CGCG 1 cut(s) 972
BshFI GGCC 3 cut(s) 219, 770, 1019
BshNI GGYRCC 1 cut(s) 578
BsiHKAI GWGCWC 1 cut(s) 342
BsiHKCI CYCGRG 1 cut(s) 686
BsiSI CCGG 1 cut(s) 632
BslFI GGGAC 1 cut(s) 67
BslI CCNNNNNNNGG 1 cut(s) 929
BsmAI GTCTC 2 cut(s) 590, 724
BsmBI CGTCTC 2 cut(s) 590, 724
BsmFI GGGAC 1 cut(s) 67
BsmI GAATGC 1 cut(s) 797
BsnI GGCC 3 cut(s) 219, 770, 1019
BsoBI CYCGRG 1 cut(s) 686
Bsp1286I GDGCHC 1 cut(s) 342
Bsp1407I TGTACA 1 cut(s) 1042
Bsp143I GATC 7 cut(s) 259, 504, 699, 871, 932, 964, 1024
BspACI CCGC 3 cut(s) 10, 13, 723
BspANI GGCC 3 cut(s) 219, 770, 1019
BspCNI CTCAG 1 cut(s) 586
BspFNI CGCG 1 cut(s) 972
BspHI TCATGA 1 cut(s) 478
BspLI GGNNCC 4 cut(s) 83, 280, 580, 1018
BspPI GGATC 2 cut(s) 940, 1019
BspT107I GGYRCC 1 cut(s) 578
BsrDI GCAATG 2 cut(s) 28, 327
BsrGI TGTACA 1 cut(s) 1042
BsrI ACTGG 1 cut(s) 305
BssECI CCNNGG 3 cut(s) 493, 675, 687
BssMI GATC 7 cut(s) 259, 504, 699, 871, 932, 964, 1024
BssT1I CCWWGG 1 cut(s) 675
Bst4CI ACNGT 4 cut(s) 90, 474, 646, 956
Bst6I CTCTTC 2 cut(s) 533, 609
BstAUI TGTACA 1 cut(s) 1042
BstC8I GCNNGC 5 cut(s) 59, 212, 420, 591, 1052
BstDEI CTNAG 3 cut(s) 594, 657, 764
BstDSI CCRYGG 1 cut(s) 493
BstF5I GGATG 3 cut(s) 151, 186, 640
BstFNI CGCG 1 cut(s) 972
BstH2I RGCGCY 1 cut(s) 493
BstHHI GCGC 3 cut(s) 492, 745, 974
BstKTI GATC 7 cut(s) 262, 507, 702, 874, 935, 967, 1027
BstMAI GTCTC 2 cut(s) 590, 724
BstMBI GATC 7 cut(s) 259, 504, 699, 871, 932, 964, 1024
BstMWI GCNNNNNNNGC 4 cut(s) 18, 63, 72, 216
BstNSI RCATGY 2 cut(s) 61, 1054
BstSCI CCNGG 1 cut(s) 630
BstSFI CTRYAG 1 cut(s) 1008
BstUI CGCG 1 cut(s) 972
BstV1I GCAGC 6 cut(s) 13, 496, 499, 757, 857, 868
BstV2I GAAGAC 1 cut(s) 950
BstX2I RGATCY 2 cut(s) 259, 1024
BstYI RGATCY 2 cut(s) 259, 1024
BsuI GTATCC 2 cut(s) 317, 817
BsuRI GGCC 3 cut(s) 219, 770, 1019
BtgI CCRYGG 1 cut(s) 493
BtsCI GGATG 3 cut(s) 151, 186, 640
BtsI GCAGTG 1 cut(s) 205
BtsIMutI CAGTG 2 cut(s) 205, 537
Cac8I GCNNGC 5 cut(s) 59, 212, 420, 591, 1052
CciI TCATGA 1 cut(s) 478
CfoI GCGC 3 cut(s) 492, 745, 974
Cfr13I GGNCC 4 cut(s) 81, 278, 768, 1017
CseI GACGC 2 cut(s) 238, 737
Csp6I GTAC 2 cut(s) 790, 1043
CviAII CATG 9 cut(s) 58, 142, 155, 479, 652, 714, 719, 1046, 1051
CviQI GTAC 2 cut(s) 790, 1043
DdeI CTNAG 3 cut(s) 594, 657, 764
DpnI GATC 7 cut(s) 261, 506, 701, 873, 934, 966, 1026
DpnII GATC 7 cut(s) 259, 504, 699, 871, 932, 964, 1024
Eam1104I CTCTTC 2 cut(s) 533, 609
EarI CTCTTC 2 cut(s) 533, 609
Eco130I CCWWGG 1 cut(s) 675
Eco32I GATATC 1 cut(s) 255
Eco47I GGWCC 2 cut(s) 81, 278
Eco57I CTGAAG 1 cut(s) 369
Eco88I CYCGRG 1 cut(s) 686
EcoO109I RGGNCCY 1 cut(s) 81
EcoRV GATATC 1 cut(s) 255
EcoT14I CCWWGG 1 cut(s) 675
EcoT22I ATGCAT 2 cut(s) 799, 1056
ErhI CCWWGG 1 cut(s) 675
Esp3I CGTCTC 2 cut(s) 590, 724
FaeI CATG 9 cut(s) 61, 145, 158, 482, 655, 717, 722, 1049, 1054
FalI AAGNNNNNCTT 2 cut(s) 362, 394
FaqI GGGAC 1 cut(s) 67
FatI CATG 9 cut(s) 57, 141, 154, 478, 651, 713, 718, 1045, 1050
FbaI TGATCA 1 cut(s) 699
FblI GTMKAC 1 cut(s) 92
Fnu4HI GCNGC 7 cut(s) 13, 27, 485, 488, 746, 846, 857
FokI GGATG 3 cut(s) 158, 173, 647
Fsp4HI GCNGC 7 cut(s) 13, 27, 485, 488, 746, 846, 857
FspBI CTAG 2 cut(s) 611, 1031
GlaI GCGC 3 cut(s) 491, 744, 973
GluI GCNGC 7 cut(s) 13, 27, 485, 488, 746, 846, 857
GsaI CCCAGC 1 cut(s) 33
HaeII RGCGCY 1 cut(s) 493
HaeIII GGCC 3 cut(s) 219, 770, 1019
HapII CCGG 1 cut(s) 632
HgaI GACGC 2 cut(s) 238, 737
HhaI GCGC 3 cut(s) 492, 745, 974
Hin1II CATG 9 cut(s) 61, 145, 158, 482, 655, 717, 722, 1049, 1054
Hin6I GCGC 3 cut(s) 490, 743, 972
HinP1I GCGC 3 cut(s) 490, 743, 972
HindIII AAGCTT 1 cut(s) 212
HinfI GANTC 4 cut(s) 136, 192, 436, 760
HpaII CCGG 1 cut(s) 632
HphI GGTGA 4 cut(s) 187, 509, 523, 677
Hpy166II GTNNAC 2 cut(s) 93, 640
Hpy188I TCNGA 7 cut(s) 191, 259, 363, 520, 560, 759, 823
Hpy188III TCNNGA 9 cut(s) 223, 235, 479, 611, 686, 729, 936, 962, 982
Hpy8I GTNNAC 2 cut(s) 93, 640
Hpy99I CGWCG 2 cut(s) 229, 232
HpyCH4III ACNGT 4 cut(s) 90, 474, 646, 956
HpyCH4V TGCA 6 cut(s) 210, 332, 797, 845, 907, 1054
HpyF10VI GCNNNNNNNGC 4 cut(s) 18, 63, 72, 216
HpyF3I CTNAG 3 cut(s) 594, 657, 764
Hsp92II CATG 9 cut(s) 61, 145, 158, 482, 655, 717, 722, 1049, 1054
HspAI GCGC 3 cut(s) 490, 743, 972
Ksp22I TGATCA 1 cut(s) 699
Kzo9I GATC 7 cut(s) 259, 504, 699, 871, 932, 964, 1024
LmnI GCTCC 2 cut(s) 561, 938
LpnPI CCDG 6 cut(s) 15, 177, 286, 575, 645, 921
Lsp1109I GCAGC 6 cut(s) 13, 496, 499, 757, 857, 868
MaeI CTAG 2 cut(s) 611, 1031
MaeIII GTNAC 3 cut(s) 43, 157, 895
MalI GATC 7 cut(s) 261, 506, 701, 873, 934, 966, 1026
MboI GATC 7 cut(s) 259, 504, 699, 871, 932, 964, 1024
MboII GAAGA 7 cut(s) 254, 520, 626, 793, 950, 1034, 1049
MfeI CAATTG 1 cut(s) 908
MflI RGATCY 2 cut(s) 259, 1024
MhlI GDGCHC 1 cut(s) 342
MluCI AATT 4 cut(s) 284, 839, 908, 916
MmeI TCCRAC 3 cut(s) 285, 543, 737
Mph1103I ATGCAT 2 cut(s) 799, 1056
MseI TTAA 2 cut(s) 5, 999
MspI CCGG 1 cut(s) 632
MspR9I CCNGG 1 cut(s) 632
MunI CAATTG 1 cut(s) 908
Mva1269I GAATGC 1 cut(s) 797
MvnI CGCG 1 cut(s) 972
MwoI GCNNNNNNNGC 4 cut(s) 18, 63, 72, 216
NciI CCSGG 1 cut(s) 632
NdeII GATC 7 cut(s) 259, 504, 699, 871, 932, 964, 1024
NlaIII CATG 9 cut(s) 61, 145, 158, 482, 655, 717, 722, 1049, 1054
NlaIV GGNNCC 4 cut(s) 83, 280, 580, 1018
NmeAIII GCCGAG 1 cut(s) 409
NmuCI GTSAC 1 cut(s) 43
NsiI ATGCAT 2 cut(s) 799, 1056
NspI RCATGY 2 cut(s) 61, 1054
PaeI GCATGC 2 cut(s) 61, 1054
PagI TCATGA 1 cut(s) 478
PctI GAATGC 1 cut(s) 797
PfeI GAWTC 4 cut(s) 136, 192, 436, 760
PkrI GCNGC 7 cut(s) 14, 28, 486, 489, 747, 847, 858
PpuMI RGGWCCY 1 cut(s) 81
PsiI TTATAA 1 cut(s) 888
Psp5II RGGWCCY 1 cut(s) 81
PspFI CCCAGC 1 cut(s) 29
PspN4I GGNNCC 4 cut(s) 83, 280, 580, 1018
PspPI GGNCC 4 cut(s) 81, 278, 768, 1017
PspPPI RGGWCCY 1 cut(s) 81
PsuI RGATCY 2 cut(s) 259, 1024
RsaI GTAC 2 cut(s) 791, 1044
RsaNI GTAC 2 cut(s) 790, 1043
SaqAI TTAA 2 cut(s) 5, 999
SatI GCNGC 7 cut(s) 13, 27, 485, 488, 746, 846, 857
Sau3AI GATC 7 cut(s) 259, 504, 699, 871, 932, 964, 1024
Sau96I GGNCC 4 cut(s) 81, 278, 768, 1017
ScrFI CCNGG 1 cut(s) 632
SduI GDGCHC 1 cut(s) 342
SfcI CTRYAG 1 cut(s) 1008
SinI GGWCC 2 cut(s) 81, 278
SmlI CTYRAG 2 cut(s) 235, 980
SmoI CTYRAG 2 cut(s) 235, 980
SpeI ACTAGT 1 cut(s) 1030
SphI GCATGC 2 cut(s) 61, 1054
Sse9I AATT 4 cut(s) 284, 839, 908, 916
SsiI CCGC 3 cut(s) 10, 13, 723
SspMI CTAG 2 cut(s) 611, 1031
StyD4I CCNGG 1 cut(s) 630
StyI CCWWGG 1 cut(s) 675
TaaI ACNGT 4 cut(s) 90, 474, 646, 956
TaqI TCGA 2 cut(s) 728, 870
TasI AATT 4 cut(s) 284, 839, 908, 916
TatI WGTACW 2 cut(s) 789, 1042
TauI GCSGC 1 cut(s) 15
TfiI GAWTC 4 cut(s) 136, 192, 436, 760
Tru1I TTAA 2 cut(s) 5, 999
Tru9I TTAA 2 cut(s) 5, 999
TscAI CASTG 2 cut(s) 212, 544
TseFI GTSAC 1 cut(s) 43
TseI GCWGC 6 cut(s) 26, 484, 487, 745, 845, 856
Tsp45I GTSAC 1 cut(s) 43
TspDTI ATGAA 6 cut(s) 143, 306, 449, 467, 640, 702
TspRI CASTG 2 cut(s) 212, 544
VpaK11BI GGWCC 2 cut(s) 81, 278
XapI RAATTY 1 cut(s) 839
XbaI TCTAGA 1 cut(s) 610
XceI RCATGY 2 cut(s) 61, 1054
XmiI GTMKAC 1 cut(s) 92
XspI CTAG 2 cut(s) 611, 1031
Zsp2I ATGCAT 2 cut(s) 799, 1056
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.