Rh7AG209400

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
Chr7A
OG0001033
Physical Location & Seq
Reverse (-)
19194179 .. 19194586
408 bp
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UTR
Exon/CDS
Intron
Rh7AG209400.1

Sequence Viewer

Length: 408 bp
ATGTCTAAGGTGGGTGATAACTCCTTGGACATTCCCGAGGCAAATGTGATCATTGAGATTTCATGGCACGGCGGTTCGAGAGGACAAGAAGCGCAGCGTCTTGGTCGGATTCTAAGGGCCAAGAAAAGTAAAGAGAAGTACAATGCATTCTTCTATTCCCTTGTGTCATCGGATACACGGGAGATGGAATTTGCAGCTAAAAGGCAGCAGTTTTTGGTCGATCAAGGTTATAGTTATAAGATTGTTACAATCTTGCAATTGCCTAATTTTCCTCCACTTGGATCAGGAGCTTTGAGCTATGACAGTCTTCAAGATCAACGCGCACTACTCAAGAAAGTGTTGAGCTTTAATGAGGCTATAGTTGGGGCCGAAGATCCACTAGTAGAAGATGTACATGGCATGCATTGA

Protein Analysis

135

Amino Acids

15.12

Weight (kDa)

6.29

Isoelectric Point (pI)

45.05

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
ERCC3_RAD25_C PF16203 1 - 123 1.2e-48 ERCC3/RAD25/XPB C-terminal helicase
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 237
AccII CGCG 1 cut(s) 321
AciI CCGC 1 cut(s) 72
AclWI GGATC 2 cut(s) 289, 368
AcsI RAATTY 1 cut(s) 188
AfaI GTAC 2 cut(s) 140, 393
AfiI CCNNNNNNNGG 1 cut(s) 278
AgsI TTSAA 1 cut(s) 311
AhlI ACTAGT 1 cut(s) 379
AluBI AGCT 4 cut(s) 197, 290, 297, 345
AluI AGCT 4 cut(s) 197, 290, 297, 345
AlwI GGATC 2 cut(s) 289, 368
Ama87I CYCGRG 1 cut(s) 35
AoxI GGCC 2 cut(s) 117, 366
ApeKI GCWGC 3 cut(s) 94, 194, 205
ApoI RAATTY 1 cut(s) 188
AspLEI GCGC 2 cut(s) 94, 323
AspS9I GGNCC 2 cut(s) 117, 366
AsuHPI GGTGA 1 cut(s) 26
AvaI CYCGRG 1 cut(s) 35
BbsI GAAGAC 1 cut(s) 299
BbvI GCAGC 3 cut(s) 106, 206, 217
BccI CCATC 1 cut(s) 178
BceAI ACGGC 1 cut(s) 85
BciVI GTATCC 1 cut(s) 166
BclI TGATCA 1 cut(s) 48
BcuI ACTAGT 1 cut(s) 379
BfaI CTAG 1 cut(s) 380
BfmI CTRYAG 1 cut(s) 357
BfuI GTATCC 1 cut(s) 166
BisI GCNGC 3 cut(s) 95, 195, 206
BlsI GCNGC 3 cut(s) 96, 196, 207
BmeT110I CYCGRG 1 cut(s) 35
BmgT120I GGNCC 2 cut(s) 117, 366
BmiI GGNNCC 1 cut(s) 367
BpiI GAAGAC 1 cut(s) 299
BpuEI CTTGAG 1 cut(s) 314
BsaJI CCNNGG 2 cut(s) 24, 36
Bsc4I CCNNNNNNNGG 1 cut(s) 278
BseDI CCNNGG 2 cut(s) 24, 36
BseLI CCNNNNNNNGG 1 cut(s) 278
BseXI GCAGC 3 cut(s) 106, 206, 217
Bsh1236I CGCG 1 cut(s) 321
BshFI GGCC 2 cut(s) 119, 368
BsiHKCI CYCGRG 1 cut(s) 35
BslI CCNNNNNNNGG 1 cut(s) 278
BsmI GAATGC 1 cut(s) 146
BsnI GGCC 2 cut(s) 119, 368
BsoBI CYCGRG 1 cut(s) 35
Bsp1407I TGTACA 1 cut(s) 391
Bsp143I GATC 5 cut(s) 48, 220, 281, 313, 373
BspACI CCGC 1 cut(s) 72
BspANI GGCC 2 cut(s) 119, 368
BspFNI CGCG 1 cut(s) 321
BspLI GGNNCC 1 cut(s) 367
BspPI GGATC 2 cut(s) 289, 368
BsrGI TGTACA 1 cut(s) 391
BssECI CCNNGG 2 cut(s) 24, 36
BssMI GATC 5 cut(s) 48, 220, 281, 313, 373
BssT1I CCWWGG 1 cut(s) 24
Bst4CI ACNGT 1 cut(s) 305
BstAUI TGTACA 1 cut(s) 391
BstC8I GCNNGC 1 cut(s) 401
BstDEI CTNAG 2 cut(s) 6, 113
BstFNI CGCG 1 cut(s) 321
BstHHI GCGC 2 cut(s) 94, 323
BstKTI GATC 5 cut(s) 51, 223, 284, 316, 376
BstMBI GATC 5 cut(s) 48, 220, 281, 313, 373
BstNSI RCATGY 1 cut(s) 403
BstSFI CTRYAG 1 cut(s) 357
BstUI CGCG 1 cut(s) 321
BstV1I GCAGC 3 cut(s) 106, 206, 217
BstV2I GAAGAC 1 cut(s) 299
BstX2I RGATCY 1 cut(s) 373
BstYI RGATCY 1 cut(s) 373
BsuI GTATCC 1 cut(s) 166
BsuRI GGCC 2 cut(s) 119, 368
Cac8I GCNNGC 1 cut(s) 401
CfoI GCGC 2 cut(s) 94, 323
Cfr13I GGNCC 2 cut(s) 117, 366
CseI GACGC 1 cut(s) 86
Csp6I GTAC 2 cut(s) 139, 392
CviAII CATG 3 cut(s) 63, 395, 400
CviJI RGCY 7 cut(s) 119, 197, 290, 297, 345, 356, 368
CviKI_1 RGCY 7 cut(s) 119, 197, 290, 297, 345, 356, 368
CviQI GTAC 2 cut(s) 139, 392
DdeI CTNAG 2 cut(s) 6, 113
DpnI GATC 5 cut(s) 50, 222, 283, 315, 375
DpnII GATC 5 cut(s) 48, 220, 281, 313, 373
Eco130I CCWWGG 1 cut(s) 24
Eco88I CYCGRG 1 cut(s) 35
EcoT14I CCWWGG 1 cut(s) 24
EcoT22I ATGCAT 2 cut(s) 148, 405
ErhI CCWWGG 1 cut(s) 24
FaeI CATG 3 cut(s) 66, 398, 403
FaiI YATR 7 cut(s) 64, 231, 237, 300, 359, 396, 401
FatI CATG 3 cut(s) 62, 394, 399
FbaI TGATCA 1 cut(s) 48
Fnu4HI GCNGC 3 cut(s) 95, 195, 206
Fsp4HI GCNGC 3 cut(s) 95, 195, 206
FspBI CTAG 1 cut(s) 380
GlaI GCGC 2 cut(s) 93, 322
GluI GCNGC 3 cut(s) 95, 195, 206
HaeIII GGCC 2 cut(s) 119, 368
HgaI GACGC 1 cut(s) 86
HhaI GCGC 2 cut(s) 94, 323
Hin1II CATG 3 cut(s) 66, 398, 403
Hin6I GCGC 2 cut(s) 92, 321
HinP1I GCGC 2 cut(s) 92, 321
HinfI GANTC 1 cut(s) 109
HphI GGTGA 1 cut(s) 26
Hpy188I TCNGA 2 cut(s) 108, 172
Hpy188III TCNNGA 5 cut(s) 35, 78, 285, 311, 331
HpyCH4III ACNGT 1 cut(s) 305
HpyCH4V TGCA 4 cut(s) 146, 194, 256, 403
HpyF3I CTNAG 2 cut(s) 6, 113
Hsp92II CATG 3 cut(s) 66, 398, 403
HspAI GCGC 2 cut(s) 92, 321
Ksp22I TGATCA 1 cut(s) 48
Kzo9I GATC 5 cut(s) 48, 220, 281, 313, 373
LmnI GCTCC 1 cut(s) 287
LpnPI CCDG 1 cut(s) 270
Lsp1109I GCAGC 3 cut(s) 106, 206, 217
MaeI CTAG 1 cut(s) 380
MaeIII GTNAC 1 cut(s) 244
MalI GATC 5 cut(s) 50, 222, 283, 315, 375
MboI GATC 5 cut(s) 48, 220, 281, 313, 373
MboII GAAGA 4 cut(s) 142, 299, 383, 398
MfeI CAATTG 1 cut(s) 257
MflI RGATCY 1 cut(s) 373
MluCI AATT 3 cut(s) 188, 257, 265
MmeI TCCRAC 1 cut(s) 86
MnlI CCTC 4 cut(s) 31, 74, 282, 346
Mph1103I ATGCAT 2 cut(s) 148, 405
MseI TTAA 1 cut(s) 348
MunI CAATTG 1 cut(s) 257
Mva1269I GAATGC 1 cut(s) 146
MvnI CGCG 1 cut(s) 321
NdeII GATC 5 cut(s) 48, 220, 281, 313, 373
NlaIII CATG 3 cut(s) 66, 398, 403
NlaIV GGNNCC 1 cut(s) 367
NsiI ATGCAT 2 cut(s) 148, 405
NspI RCATGY 1 cut(s) 403
PaeI GCATGC 1 cut(s) 403
PctI GAATGC 1 cut(s) 146
PfeI GAWTC 1 cut(s) 109
PkrI GCNGC 3 cut(s) 96, 196, 207
PsiI TTATAA 1 cut(s) 237
PspN4I GGNNCC 1 cut(s) 367
PspPI GGNCC 2 cut(s) 117, 366
PsuI RGATCY 1 cut(s) 373
RsaI GTAC 2 cut(s) 140, 393
RsaNI GTAC 2 cut(s) 139, 392
SaqAI TTAA 1 cut(s) 348
SatI GCNGC 3 cut(s) 95, 195, 206
Sau3AI GATC 5 cut(s) 48, 220, 281, 313, 373
Sau96I GGNCC 2 cut(s) 117, 366
SetI ASST 6 cut(s) 12, 199, 229, 292, 299, 347
SfcI CTRYAG 1 cut(s) 357
SmlI CTYRAG 1 cut(s) 329
SmoI CTYRAG 1 cut(s) 329
SpeI ACTAGT 1 cut(s) 379
SphI GCATGC 1 cut(s) 403
Sse9I AATT 3 cut(s) 188, 257, 265
SsiI CCGC 1 cut(s) 72
SspMI CTAG 1 cut(s) 380
StyI CCWWGG 1 cut(s) 24
TaaI ACNGT 1 cut(s) 305
TaqI TCGA 2 cut(s) 77, 219
TasI AATT 3 cut(s) 188, 257, 265
TatI WGTACW 2 cut(s) 138, 391
TfiI GAWTC 1 cut(s) 109
Tru1I TTAA 1 cut(s) 348
Tru9I TTAA 1 cut(s) 348
TseI GCWGC 3 cut(s) 94, 194, 205
TspDTI ATGAA 1 cut(s) 51
XapI RAATTY 1 cut(s) 188
XceI RCATGY 1 cut(s) 403
XspI CTAG 1 cut(s) 380
Zsp2I ATGCAT 2 cut(s) 148, 405
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.