Rroxscaffold_1G00064580

Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000001
OG0006661
Physical Location & Seq
Forward (+)
86441707 .. 86443110
1404 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_1G00064580.1

Sequence Viewer

Length: 1056 bp
ATGGTGTCCAAAATAATGAAGATTAAGGCTAGCAAGTTTTCATCCATGAATAACCACGACGGCATAAGGCGGCACCACCGCCGCAACTCCTTAGTAAAGAAGGCAGCCGCCGACTCCAAGGTCGTGCTTGCCAGCACTGGCAGCCACAAATGGAGCTTCGAGATCCTAACCCGAACCCAAACTCCAGACCCGGCCTGCCCCGACCCCGGACCTCAAACTACACGCCCCCCACTCCCGCCGTTAACTTCGCCGGAGAAGAGAACCGTGTTTCTCGACCTGGACGAAACACTGGTGCACACTGAGGCCACAGTGCCCCAGCGCTTCAACTTCGTCGTCCGGCCCATTATTCGTGGCACCAAGATGACCTTCTACGTGATCAAACGTCCCGGCGTTGACCAGTTTTTGCAAAGACTGGCAGAGAAGTACGAGGTGGTGGTGTTCACGGCGGGGATGAGAGAGTACGCCACGCTGGTGGTGGACCGACTGGACAGGCAGGGCTTGATATCCCACAGCCTCTACCGCGACTCATGCAAGGAGATGAACGGAAGGTTCGTGAAGGACCTGTCCGGTTTGGGACGTGACTTGCGGCGAGTGGTGATCGTGGACGATAATCCCAACTCGTATTTCCTCCAACAGGAAAATAGGGTTCCGGTCCGGCCGTTCGTCGATGACATGGCAGACGGGGAGCTGGGGAGGTTGTTGGAGTTTTTTGAGGGAGAGGGGTCACGTTGTTCTGAGGACATTAGAGATGCTGTGAGGGAGTATGTTCATGACAAAGGATGGGTTTCCGATGATAATGACGATGACGAGAATGATGAAGATGATGATAATGGTGGTAGTGATAATGATAATGATGATGAGTTGGAGACTGGGAATGGAAAGTCTACTAATATTGCAGTATCAACAACCATTAATTCATCAACACCATGCTGCTTAATTAGTCTGCATGGATATTCTCCATCGGGAAAACCAGTAGCTATGGAGAGTTGGATGAAGATGACCTCGATGAAACAAATAAAAATTAAAGACGTGCATAGCTTGATCACCGGTAACTAG

Protein Analysis

351

Amino Acids

39.53

Weight (kDa)

5.78

Isoelectric Point (pI)

37.58

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
NIF PF03031 88 - 249 3.9e-51 NLI interacting factor-like phosphatase
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)
AasI GACNNNNNNGTC 1 cut(s) 119
AccB1I GGYRCC 2 cut(s) 72, 353
AccI GTMKAC 1 cut(s) 884
AccII CGCG 1 cut(s) 522
AciI CCGC 8 cut(s) 70, 79, 82, 108, 236, 446, 520, 586
AclWI GGATC 1 cut(s) 157
AcoI YGGCCR 1 cut(s) 656
AfaI GTAC 2 cut(s) 425, 461
AfeI AGCGCT 1 cut(s) 320
AfiI CCNNNNNNNGG 2 cut(s) 206, 634
AgeI ACCGGT 1 cut(s) 1046
AgsI TTSAA 1 cut(s) 325
AjiI CACGTC 2 cut(s) 578, 1030
AjnI CCWGG 1 cut(s) 276
AjuI GAANNNNNNNTTGG 4 cut(s) 350, 382, 608, 640
AleI CACNNNNGTG 1 cut(s) 470
AloI GAACNNNNNNTCC 2 cut(s) 166, 198
AluBI AGCT 4 cut(s) 156, 688, 977, 1038
AluI AGCT 4 cut(s) 156, 688, 977, 1038
Alw21I GWGCWC 1 cut(s) 297
Alw26I GTCTC 1 cut(s) 860
Alw44I GTGCAC 1 cut(s) 293
AlwI GGATC 1 cut(s) 157
Aor51HI AGCGCT 1 cut(s) 320
AoxI GGCC 4 cut(s) 192, 303, 338, 656
ApaLI GTGCAC 1 cut(s) 293
ApeKI GCWGC 3 cut(s) 104, 141, 930
AseI ATTAAT 1 cut(s) 912
AsiGI ACCGGT 1 cut(s) 1046
AspLEI GCGC 1 cut(s) 321
AspS9I GGNCC 5 cut(s) 209, 339, 478, 559, 652
AsuC2I CCSGG 3 cut(s) 191, 207, 387
AsuHPI GGTGA 2 cut(s) 607, 1036
AsuNHI GCTAGC 1 cut(s) 29
AvaII GGWCC 4 cut(s) 209, 478, 559, 652
BaeGI GKGCMC 2 cut(s) 297, 315
BanI GGYRCC 2 cut(s) 72, 353
Bbv12I GWGCWC 1 cut(s) 297
BbvI GCAGC 3 cut(s) 116, 153, 917
BccI CCATC 2 cut(s) 774, 967
BceAI ACGGC 4 cut(s) 76, 223, 459, 643
BciT130I CCWGG 1 cut(s) 278
BclI TGATCA 2 cut(s) 375, 1041
BcnI CCSGG 3 cut(s) 191, 207, 387
BcoDI GTCTC 1 cut(s) 860
BfaI CTAG 2 cut(s) 30, 1054
BfoI RGCGCY 1 cut(s) 322
BisI GCNGC 7 cut(s) 71, 82, 105, 108, 142, 587, 931
BlsI GCNGC 7 cut(s) 72, 83, 106, 109, 143, 588, 932
Bme1390I CCNGG 4 cut(s) 191, 207, 278, 387
Bme18I GGWCC 4 cut(s) 209, 478, 559, 652
BmgBI CACGTC 2 cut(s) 578, 1030
BmgT120I GGNCC 5 cut(s) 209, 339, 478, 559, 652
BmiI GGNNCC 3 cut(s) 74, 355, 648
BmrFI CCNGG 4 cut(s) 191, 207, 278, 387
BmrI ACTGGG 1 cut(s) 879
BmsI GCATC 1 cut(s) 739
BmtI GCTAGC 1 cut(s) 33
BmuI ACTGGG 1 cut(s) 879
BpmI CTGGAG 1 cut(s) 168
BpuMI CCSGG 3 cut(s) 191, 207, 387
BsaAI YACGTR 1 cut(s) 373
BsaJI CCNNGG 2 cut(s) 117, 205
BsaWI WCCGGW 3 cut(s) 566, 649, 1046
BsaXI ACNNNNNCTCC 2 cut(s) 166, 196
Bsc4I CCNNNNNNNGG 2 cut(s) 206, 634
Bse118I RCCGGY 1 cut(s) 1046
Bse1I ACTGG 7 cut(s) 142, 294, 397, 417, 489, 874, 971
BseBI CCWGG 1 cut(s) 278
BseDI CCNNGG 2 cut(s) 117, 205
BseGI GGATG 4 cut(s) 41, 456, 785, 996
BseLI CCNNNNNNNGG 2 cut(s) 206, 634
BseMII CTCAG 2 cut(s) 291, 726
BseNI ACTGG 7 cut(s) 142, 294, 397, 417, 489, 874, 971
BseSI GKGCMC 2 cut(s) 297, 315
BseX3I CGGCCG 1 cut(s) 656
BseXI GCAGC 3 cut(s) 116, 153, 917
BseYI CCCAGC 2 cut(s) 315, 688
Bsh1236I CGCG 1 cut(s) 522
Bsh1285I CGRYCG 1 cut(s) 659
BshFI GGCC 4 cut(s) 194, 305, 340, 658
BshNI GGYRCC 2 cut(s) 72, 353
BshTI ACCGGT 1 cut(s) 1046
BsiEI CGRYCG 1 cut(s) 659
BsiHKAI GWGCWC 1 cut(s) 297
BsiSI CCGG 9 cut(s) 191, 207, 251, 337, 387, 567, 650, 655, 1047
BslFI GGGAC 2 cut(s) 369, 588
BslI CCNNNNNNNGG 2 cut(s) 206, 634
BsmAI GTCTC 1 cut(s) 860
BsmFI GGGAC 2 cut(s) 369, 588
BsnI GGCC 4 cut(s) 194, 305, 340, 658
Bsp1286I GDGCHC 2 cut(s) 297, 315
Bsp143I GATC 4 cut(s) 162, 375, 597, 1041
BspACI CCGC 8 cut(s) 70, 79, 82, 108, 236, 446, 520, 586
BspANI GGCC 4 cut(s) 194, 305, 340, 658
BspCNI CTCAG 2 cut(s) 292, 727
BspFNI CGCG 1 cut(s) 522
BspHI TCATGA 1 cut(s) 769
BspLI GGNNCC 3 cut(s) 74, 355, 648
BspOI GCTAGC 1 cut(s) 33
BspPI GGATC 1 cut(s) 157
BspT107I GGYRCC 2 cut(s) 72, 353
BsrFI RCCGGY 1 cut(s) 1046
BsrI ACTGG 7 cut(s) 142, 294, 397, 417, 489, 874, 971
BssAI RCCGGY 1 cut(s) 1046
BssECI CCNNGG 2 cut(s) 117, 205
BssMI GATC 4 cut(s) 162, 375, 597, 1041
BssT1I CCWWGG 1 cut(s) 117
Bst2UI CCWGG 1 cut(s) 278
Bst4CI ACNGT 2 cut(s) 265, 310
Bst6I CTCTTC 1 cut(s) 251
BstBAI YACGTR 1 cut(s) 373
BstC8I GCNNGC 4 cut(s) 31, 129, 133, 196
BstDEI CTNAG 3 cut(s) 91, 300, 735
BstENI CCTNNNNNAGG 1 cut(s) 632
BstF5I GGATG 4 cut(s) 41, 456, 785, 996
BstFNI CGCG 1 cut(s) 522
BstH2I RGCGCY 1 cut(s) 322
BstHHI GCGC 1 cut(s) 321
BstKTI GATC 4 cut(s) 165, 378, 600, 1044
BstMAI GTCTC 1 cut(s) 860
BstMBI GATC 4 cut(s) 162, 375, 597, 1041
BstMCI CGRYCG 1 cut(s) 659
BstMWI GCNNNNNNNGC 3 cut(s) 141, 519, 528
BstNI CCWGG 1 cut(s) 278
BstSCI CCNGG 4 cut(s) 189, 205, 276, 385
BstSLI GKGCMC 2 cut(s) 297, 315
BstUI CGCG 1 cut(s) 522
BstV1I GCAGC 3 cut(s) 116, 153, 917
BstX2I RGATCY 1 cut(s) 162
BstXI CCANNNNNNTGG 1 cut(s) 472
BstYI RGATCY 1 cut(s) 162
BstZI CGGCCG 1 cut(s) 656
BsuRI GGCC 4 cut(s) 194, 305, 340, 658
BtrI CACGTC 2 cut(s) 578, 1030
BtsCI GGATG 4 cut(s) 41, 456, 785, 996
BtsIMutI CAGTG 4 cut(s) 135, 287, 297, 315
Cac8I GCNNGC 4 cut(s) 31, 129, 133, 196
CciI TCATGA 1 cut(s) 769
CfoI GCGC 1 cut(s) 321
Cfr10I RCCGGY 1 cut(s) 1046
Cfr13I GGNCC 5 cut(s) 209, 339, 478, 559, 652
CpoI CGGWCCG 1 cut(s) 652
Csp6I GTAC 2 cut(s) 424, 460
CspAI ACCGGT 1 cut(s) 1046
CspI CGGWCCG 1 cut(s) 652
CviAII CATG 6 cut(s) 46, 528, 673, 770, 927, 947
CviQI GTAC 2 cut(s) 424, 460
DdeI CTNAG 3 cut(s) 91, 300, 735
DpnI GATC 4 cut(s) 164, 377, 599, 1043
DpnII GATC 4 cut(s) 162, 375, 597, 1041
DrdI GACNNNNNNGTC 1 cut(s) 119
DseDI GACNNNNNNGTC 1 cut(s) 119
EaeI YGGCCR 1 cut(s) 656
EagI CGGCCG 1 cut(s) 656
Eam1104I CTCTTC 1 cut(s) 251
EarI CTCTTC 1 cut(s) 251
EclXI CGGCCG 1 cut(s) 656
Eco130I CCWWGG 1 cut(s) 117
Eco32I GATATC 1 cut(s) 504
Eco47I GGWCC 4 cut(s) 209, 478, 559, 652
Eco47III AGCGCT 1 cut(s) 320
Eco52I CGGCCG 1 cut(s) 656
EcoNI CCTNNNNNAGG 1 cut(s) 632
EcoO109I RGGNCCY 1 cut(s) 559
EcoRII CCWGG 1 cut(s) 276
EcoRV GATATC 1 cut(s) 504
EcoT14I CCWWGG 1 cut(s) 117
ErhI CCWWGG 1 cut(s) 117
FaeI CATG 6 cut(s) 49, 531, 676, 773, 930, 950
FalI AAGNNNNNCTT 2 cut(s) 350, 382
FaqI GGGAC 2 cut(s) 369, 588
FatI CATG 6 cut(s) 45, 527, 672, 769, 926, 946
FauI CCCGC 2 cut(s) 243, 439
FbaI TGATCA 2 cut(s) 375, 1041
FblI GTMKAC 1 cut(s) 884
Fnu4HI GCNGC 7 cut(s) 71, 82, 105, 108, 142, 587, 931
FokI GGATG 4 cut(s) 28, 463, 792, 1003
Fsp4HI GCNGC 7 cut(s) 71, 82, 105, 108, 142, 587, 931
FspBI CTAG 2 cut(s) 30, 1054
GlaI GCGC 1 cut(s) 320
GluI GCNGC 7 cut(s) 71, 82, 105, 108, 142, 587, 931
GsaI CCCAGC 2 cut(s) 319, 692
GsuI CTGGAG 1 cut(s) 168
HaeII RGCGCY 1 cut(s) 322
HaeIII GGCC 4 cut(s) 194, 305, 340, 658
HapII CCGG 9 cut(s) 191, 207, 251, 337, 387, 567, 650, 655, 1047
HhaI GCGC 1 cut(s) 321
Hin1II CATG 6 cut(s) 49, 531, 676, 773, 930, 950
Hin6I GCGC 1 cut(s) 319
HinP1I GCGC 1 cut(s) 319
HincII GTYRAC 2 cut(s) 243, 394
HindII GTYRAC 2 cut(s) 243, 394
HinfI GANTC 2 cut(s) 113, 524
HpaI GTTAAC 1 cut(s) 243
HpaII CCGG 9 cut(s) 191, 207, 251, 337, 387, 567, 650, 655, 1047
HphI GGTGA 2 cut(s) 607, 1036
Hpy166II GTNNAC 7 cut(s) 243, 295, 394, 441, 478, 604, 885
Hpy188I TCNGA 2 cut(s) 736, 790
Hpy188III TCNNGA 6 cut(s) 160, 185, 272, 553, 770, 963
Hpy8I GTNNAC 7 cut(s) 243, 295, 394, 441, 478, 604, 885
Hpy99I CGWCG 3 cut(s) 62, 335, 668
HpyAV CCTTC 4 cut(s) 94, 376, 540, 550
HpyCH4III ACNGT 2 cut(s) 265, 310
HpyCH4IV ACGT 5 cut(s) 372, 382, 577, 727, 1029
HpyCH4V TGCA 6 cut(s) 295, 406, 531, 896, 946, 1033
HpyF10VI GCNNNNNNNGC 3 cut(s) 141, 519, 528
HpyF3I CTNAG 3 cut(s) 91, 300, 735
HpySE526I ACGT 5 cut(s) 372, 382, 577, 727, 1029
Hsp92II CATG 6 cut(s) 49, 531, 676, 773, 930, 950
HspAI GCGC 1 cut(s) 319
Ksp22I TGATCA 2 cut(s) 375, 1041
KspAI GTTAAC 1 cut(s) 243
Kzo9I GATC 4 cut(s) 162, 375, 597, 1041
LmnI GCTCC 2 cut(s) 153, 685
Lsp1109I GCAGC 3 cut(s) 116, 153, 917
LweI GCATC 1 cut(s) 739
MaeI CTAG 2 cut(s) 30, 1054
MaeII ACGT 5 cut(s) 372, 382, 577, 727, 1029
MaeIII GTNAC 3 cut(s) 578, 723, 1049
MalI GATC 4 cut(s) 164, 377, 599, 1043
MboI GATC 4 cut(s) 162, 375, 597, 1041
MboII GAAGA 4 cut(s) 31, 268, 830, 1006
MflI RGATCY 1 cut(s) 162
MhlI GDGCHC 2 cut(s) 297, 315
MluCI AATT 3 cut(s) 913, 936, 1020
MlyI GAGTC 2 cut(s) 107, 518
MmeI TCCRAC 4 cut(s) 655, 681, 843, 968
MseI TTAA 5 cut(s) 24, 242, 912, 935, 1023
MslI CAYNNNNRTG 2 cut(s) 359, 470
MspI CCGG 9 cut(s) 191, 207, 251, 337, 387, 567, 650, 655, 1047
MspR9I CCNGG 4 cut(s) 191, 207, 278, 387
MvaI CCWGG 1 cut(s) 278
MvnI CGCG 1 cut(s) 522
MwoI GCNNNNNNNGC 3 cut(s) 141, 519, 528
NciI CCSGG 3 cut(s) 191, 207, 387
NdeII GATC 4 cut(s) 162, 375, 597, 1041
NheI GCTAGC 1 cut(s) 29
NlaIII CATG 6 cut(s) 49, 531, 676, 773, 930, 950
NlaIV GGNNCC 3 cut(s) 74, 355, 648
NmuCI GTSAC 2 cut(s) 578, 723
OliI CACNNNNGTG 1 cut(s) 470
PagI TCATGA 1 cut(s) 769
PcsI WCGNNNNNNNCGW 2 cut(s) 279, 549
PinAI ACCGGT 1 cut(s) 1046
PkrI GCNGC 7 cut(s) 72, 83, 106, 109, 143, 588, 932
PleI GAGTC 2 cut(s) 107, 518
PpsI GAGTC 2 cut(s) 107, 518
Ppu21I YACGTR 1 cut(s) 373
PpuMI RGGWCCY 1 cut(s) 559
PshBI ATTAAT 1 cut(s) 912
Psp5II RGGWCCY 1 cut(s) 559
Psp6I CCWGG 1 cut(s) 276
PspFI CCCAGC 2 cut(s) 315, 688
PspGI CCWGG 1 cut(s) 276
PspN4I GGNNCC 3 cut(s) 74, 355, 648
PspPI GGNCC 5 cut(s) 209, 339, 478, 559, 652
PspPPI RGGWCCY 1 cut(s) 559
PsuI RGATCY 1 cut(s) 162
RsaI GTAC 2 cut(s) 425, 461
RsaNI GTAC 2 cut(s) 424, 460
RseI CAYNNNNRTG 2 cut(s) 359, 470
Rsr2I CGGWCCG 1 cut(s) 652
RsrII CGGWCCG 1 cut(s) 652
SaqAI TTAA 5 cut(s) 24, 242, 912, 935, 1023
SatI GCNGC 7 cut(s) 71, 82, 105, 108, 142, 587, 931
Sau3AI GATC 4 cut(s) 162, 375, 597, 1041
Sau96I GGNCC 5 cut(s) 209, 339, 478, 559, 652
SchI GAGTC 2 cut(s) 107, 518
ScrFI CCNGG 4 cut(s) 191, 207, 278, 387
SduI GDGCHC 2 cut(s) 297, 315
SfaNI GCATC 1 cut(s) 739
SinI GGWCC 4 cut(s) 209, 478, 559, 652
SmiMI CAYNNNNRTG 2 cut(s) 359, 470
Sse9I AATT 3 cut(s) 913, 936, 1020
SsiI CCGC 8 cut(s) 70, 79, 82, 108, 236, 446, 520, 586
SspI AATATT 1 cut(s) 892
SspMI CTAG 2 cut(s) 30, 1054
StyD4I CCNGG 4 cut(s) 189, 205, 276, 385
StyI CCWWGG 1 cut(s) 117
TaaI ACNGT 2 cut(s) 265, 310
TaiI ACGT 5 cut(s) 375, 385, 580, 730, 1032
TaqI TCGA 4 cut(s) 159, 273, 666, 1004
TaqII GACCGA 1 cut(s) 495
TasI AATT 3 cut(s) 913, 936, 1020
TauI GCSGC 4 cut(s) 73, 84, 110, 589
Tru1I TTAA 5 cut(s) 24, 242, 912, 935, 1023
Tru9I TTAA 5 cut(s) 24, 242, 912, 935, 1023
TscAI CASTG 4 cut(s) 142, 294, 304, 315
TseFI GTSAC 2 cut(s) 578, 723
TseI GCWGC 3 cut(s) 104, 141, 930
Tsp45I GTSAC 2 cut(s) 578, 723
TspDTI ATGAA 9 cut(s) 30, 32, 62, 554, 758, 831, 906, 1007, 1022
TspGWI ACGGA 1 cut(s) 558
TspRI CASTG 4 cut(s) 142, 294, 304, 315
VneI GTGCAC 1 cut(s) 293
VpaK11BI GGWCC 4 cut(s) 209, 478, 559, 652
VspI ATTAAT 1 cut(s) 912
XagI CCTNNNNNAGG 1 cut(s) 632
XcmI CCANNNNNNNNNTGG 1 cut(s) 472
XmiI GTMKAC 1 cut(s) 884
XspI CTAG 2 cut(s) 30, 1054
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.