Rorug03G0063700

RNA polymerase II C-terminal domain phosphatase-like

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_rugosa
GWHBQTZ00000003
OG0002842
Physical Location & Seq
Forward (+)
4724578 .. 4728055
3478 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug03G0063700.1

Sequence Viewer

Length: 1200 bp
ATGACCACCCTCTCTCCTCCTCCTCCGAGTTTCAATCCTCTAAAACTCGCTCCCAAATCCCTCATTCCACCCAAACCCGCCTCCGCCTCCGAACCCGACCCGTCCGTTACAGAAACCCCAACCCCAGGCCCAAACCCGACCCAATCCCCCACCACCCTCCTCCACCTCGCTTTCAACCAAGACCACACCTGCTTCTCCGCCGCCACCGACTCCGGCTTCCGCGTCTACACCTGCGACCCCTTCCGCCGCTTCCACAGCGACCCCTCCGGTCCACGCGGCGGCGTCGGATTCGTCCAGATGCTCTTCCACTGCCACTACTTCGCCGTCTTCGGCGGCGGACCCGACCCGTTCTGCCCGCCCAACAAGGTCATGATCTACGACGATCGCCAGTCCCGCTGCGTCAGCGAGCTCTTGTTCCGGTCCGAGGTCAAGTCGGTCAGGCTCCGCCGCGACCGGATCGTCGTCGTTGTTCTCCACAAGATCTTCGTCTACGATTTCAACGCTTTGAAGCTGTTGGATTCGATTGTGACCGTGGAAAACCCTAAGGGACTGTGTGAGGTCTCGCATAAGTCCGGGCCGGCCGTGCTGGCGTGTCCGGGGCTCCACCAGGGGCAAATTCGGGTCGAGCATTACGGGTCGAAGCGGACCAAGTTTATAACGGCACATCGCTCCGGTCTCGCGTGCTTTGCTCTCACTCATGATGGTCAGTTTCTAGCGACGGCGAGTAGTAAAGGGACTCTGGTTAGAGTTTTCAATACTTTGGATGGTACATTGCTCCAAGAGGTGAGGAGAGGAGCAGACAAAGCGGAGATTTACAGTCTTGCTTTCTCTTCCACTGCCCAATGGCTAGCTGTCTCAAGTGACAAGGGTACTGTCCATGTTTTCAGCGTAAAGGTTGACTCAGGATCTTTGGGGAATGATGGATCATGCAGTACATCAGAAATTAGTGGTTCTAATTCATCAGGCATTTCATCTCTGTCTTACATCAAAGCTGTCCTTCCAAGGTATTTTAGTTCAGAATGGTCAGTGGCCAAATTTCGCTTGCAGGAAGGTGTACGGTACATTGTTGCTTTTGGCCACCAGAAGAACACAGTTATCATTGTTGGCATGGATGGGAGCTTCTATCGATGTCAATTTGACCCTGTGAATGGAGGAGAAATGATTCAGCTTGAATATTCCAATTTCCTGAAGGCGGAATAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
NIF dsrm

Protein Analysis

399

Amino Acids

43.6

Weight (kDa)

8.73

Isoelectric Point (pI)

41.23

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PROPPIN PF21032 56 - 390 6.6e-32 PROPPIN
Beta-prop_THOC3 PF25174 121 - 298 5.1e-12 THOC3 beta-propeller domain
Beta-prop_WDR3_1st PF25173 154 - 298 8.5e-07 WDR3 first beta-propeller domain
WD40_WDHD1_1st PF24817 168 - 292 6.1e-06 WDHD1 first WD40 domain
Beta-prop_EML_2 PF23414 202 - 300 3.5e-07 Echinoderm microtubule-associated protein second beta-propeller
Beta-prop_WDR5 PF25175 220 - 299 1e-07 WDR5 beta-propeller domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Publication-ready
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 656
AarI CACCTGC 2 cut(s) 197, 239
AasI GACNNNNNNGTC 1 cut(s) 458
Acc36I ACCTGC 2 cut(s) 197, 239
AccI GTMKAC 2 cut(s) 225, 489
AccII CGCG 4 cut(s) 222, 276, 450, 680
AclWI GGATC 3 cut(s) 464, 913, 931
AcoI YGGCCR 3 cut(s) 579, 1029, 1075
AcsI RAATTY 2 cut(s) 615, 1034
AcyI GRCGYC 1 cut(s) 282
AfaI GTAC 5 cut(s) 769, 871, 934, 1056, 1061
AfiI CCNNNNNNNGG 5 cut(s) 125, 278, 424, 1148, 1192
AgsI TTSAA 6 cut(s) 34, 175, 499, 508, 754, 1172
AjnI CCWGG 2 cut(s) 124, 606
AluBI AGCT 6 cut(s) 409, 511, 851, 992, 1119, 1168
AluI AGCT 6 cut(s) 409, 511, 851, 992, 1119, 1168
Alw21I GWGCWC 1 cut(s) 411
Alw26I GTCTC 3 cut(s) 565, 680, 859
AlwI GGATC 3 cut(s) 464, 913, 931
AoxI GGCC 5 cut(s) 127, 575, 579, 1029, 1075
ApeKI GCWGC 1 cut(s) 396
ApoI RAATTY 2 cut(s) 615, 1034
Asp700I GAANNNNTTC 1 cut(s) 1161
AspS9I GGNCC 6 cut(s) 128, 269, 338, 420, 575, 645
AsuC2I CCSGG 2 cut(s) 574, 597
AsuHPI GGTGA 1 cut(s) 796
AsuNHI GCTAGC 1 cut(s) 847
AvaII GGWCC 4 cut(s) 269, 338, 420, 645
AxyI CCTNAGG 1 cut(s) 543
BalI TGGCCA 2 cut(s) 1031, 1077
BanII GRGCYC 2 cut(s) 411, 603
BbsI GAAGAC 1 cut(s) 319
Bbv12I GWGCWC 1 cut(s) 411
BbvI GCAGC 1 cut(s) 383
BccI CCATC 4 cut(s) 695, 758, 914, 1106
BceAI ACGGC 4 cut(s) 308, 566, 675, 735
BciT130I CCWGG 2 cut(s) 126, 608
BcnI CCSGG 2 cut(s) 574, 597
BcoDI GTCTC 3 cut(s) 565, 680, 859
BfaI CTAG 2 cut(s) 713, 848
BfuAI ACCTGC 2 cut(s) 197, 239
BglI GCCNNNNNGGC 1 cut(s) 587
BglII AGATCT 1 cut(s) 480
BisI GCNGC 7 cut(s) 201, 247, 277, 280, 334, 397, 448
BlsI GCNGC 7 cut(s) 202, 248, 278, 281, 335, 398, 449
Bme1390I CCNGG 4 cut(s) 126, 574, 597, 608
Bme18I GGWCC 4 cut(s) 269, 338, 420, 645
BmgT120I GGNCC 6 cut(s) 128, 269, 338, 420, 575, 645
BmiI GGNNCC 3 cut(s) 340, 443, 602
BmrFI CCNGG 4 cut(s) 126, 574, 597, 608
BmsI GCATC 1 cut(s) 288
BmtI GCTAGC 1 cut(s) 851
BpiI GAAGAC 1 cut(s) 319
BpuEI CTTGAG 1 cut(s) 841
BpuMI CCSGG 2 cut(s) 574, 597
Bsa29I ATCGAT 1 cut(s) 1126
BsaHI GRCGYC 1 cut(s) 282
BsaI GGTCTC 2 cut(s) 565, 680
BsaJI CCNNGG 6 cut(s) 124, 423, 531, 596, 607, 1001
BsaWI WCCGGW 4 cut(s) 266, 417, 453, 671
BsaXI ACNNNNNCTCC 1 cut(s) 28
Bsc4I CCNNNNNNNGG 5 cut(s) 125, 278, 424, 1148, 1192
Bse118I RCCGGY 1 cut(s) 577
Bse1I ACTGG 1 cut(s) 388
Bse21I CCTNAGG 1 cut(s) 543
Bse3DI GCAATG 1 cut(s) 770
BseBI CCWGG 2 cut(s) 126, 608
BseCI ATCGAT 1 cut(s) 1126
BseDI CCNNGG 6 cut(s) 124, 423, 531, 596, 607, 1001
BseGI GGATG 2 cut(s) 769, 1117
BseLI CCNNNNNNNGG 5 cut(s) 125, 278, 424, 1148, 1192
BseMI GCAATG 1 cut(s) 770
BseMII CTCAG 1 cut(s) 915
BseNI ACTGG 1 cut(s) 388
BseRI GAGGAG 7 cut(s) 6, 9, 12, 149, 802, 807, 1167
BseX3I CGGCCG 1 cut(s) 579
BseXI GCAGC 1 cut(s) 383
Bsh1236I CGCG 4 cut(s) 222, 276, 450, 680
Bsh1285I CGRYCG 3 cut(s) 385, 454, 582
BshFI GGCC 5 cut(s) 129, 577, 581, 1031, 1077
BshVI ATCGAT 1 cut(s) 1126
BsiEI CGRYCG 3 cut(s) 385, 454, 582
BsiHKAI GWGCWC 1 cut(s) 411
BsiSI CCGG 8 cut(s) 213, 267, 418, 454, 573, 578, 596, 672
BslFI GGGAC 3 cut(s) 376, 561, 748
BslI CCNNNNNNNGG 5 cut(s) 125, 278, 424, 1148, 1192
BsmAI GTCTC 3 cut(s) 565, 680, 859
BsmFI GGGAC 3 cut(s) 376, 561, 748
BsnI GGCC 5 cut(s) 129, 577, 581, 1031, 1077
Bso31I GGTCTC 2 cut(s) 565, 680
Bsp1286I GDGCHC 2 cut(s) 411, 603
Bsp143I GATC 6 cut(s) 372, 382, 456, 480, 905, 923
BspANI GGCC 5 cut(s) 129, 577, 581, 1031, 1077
BspCNI CTCAG 1 cut(s) 914
BspDI ATCGAT 1 cut(s) 1126
BspFNI CGCG 4 cut(s) 222, 276, 450, 680
BspHI TCATGA 2 cut(s) 369, 697
BspLI GGNNCC 3 cut(s) 340, 443, 602
BspMI ACCTGC 2 cut(s) 197, 239
BspOI GCTAGC 1 cut(s) 851
BspPI GGATC 3 cut(s) 464, 913, 931
BspQI GCTCTTC 1 cut(s) 308
BspTNI GGTCTC 2 cut(s) 565, 680
BsrDI GCAATG 1 cut(s) 770
BsrFI RCCGGY 1 cut(s) 577
BsrI ACTGG 1 cut(s) 388
BssAI RCCGGY 1 cut(s) 577
BssECI CCNNGG 6 cut(s) 124, 423, 531, 596, 607, 1001
BssMI GATC 6 cut(s) 372, 382, 456, 480, 905, 923
BssNI GRCGYC 1 cut(s) 282
BssT1I CCWWGG 1 cut(s) 1001
Bst2UI CCWGG 2 cut(s) 126, 608
Bst4CI ACNGT 6 cut(s) 532, 552, 818, 874, 1059, 1093
Bst6I CTCTTC 2 cut(s) 308, 835
BstACI GRCGYC 1 cut(s) 282
BstC8I GCNNGC 7 cut(s) 356, 407, 579, 588, 682, 849, 1043
BstDEI CTNAG 2 cut(s) 543, 901
BstDSI CCRYGG 1 cut(s) 531
BstF5I GGATG 2 cut(s) 769, 1117
BstFNI CGCG 4 cut(s) 222, 276, 450, 680
BstKTI GATC 6 cut(s) 375, 385, 459, 483, 908, 926
BstMAI GTCTC 3 cut(s) 565, 680, 859
BstMBI GATC 6 cut(s) 372, 382, 456, 480, 905, 923
BstMCI CGRYCG 3 cut(s) 385, 454, 582
BstMWI GCNNNNNNNGC 7 cut(s) 255, 393, 402, 583, 587, 686, 803
BstNI CCWGG 2 cut(s) 126, 608
BstSCI CCNGG 4 cut(s) 124, 572, 595, 606
BstUI CGCG 4 cut(s) 222, 276, 450, 680
BstV1I GCAGC 1 cut(s) 383
BstV2I GAAGAC 1 cut(s) 319
BstX2I RGATCY 2 cut(s) 480, 905
BstYI RGATCY 2 cut(s) 480, 905
BstZI CGGCCG 1 cut(s) 579
Bsu15I ATCGAT 1 cut(s) 1126
Bsu36I CCTNAGG 1 cut(s) 543
BsuRI GGCC 5 cut(s) 129, 577, 581, 1031, 1077
BsuTUI ATCGAT 1 cut(s) 1126
BtgI CCRYGG 1 cut(s) 531
BtgZI GCGATG 1 cut(s) 650
BtsCI GGATG 2 cut(s) 769, 1117
BtsI GCAGTG 2 cut(s) 307, 834
BtsIMutI CAGTG 3 cut(s) 307, 834, 1032
BveI ACCTGC 2 cut(s) 197, 239
Cac8I GCNNGC 7 cut(s) 356, 407, 579, 588, 682, 849, 1043
CciI TCATGA 2 cut(s) 369, 697
Cfr10I RCCGGY 1 cut(s) 577
Cfr13I GGNCC 6 cut(s) 128, 269, 338, 420, 575, 645
ClaI ATCGAT 1 cut(s) 1126
CpoI CGGWCCG 1 cut(s) 420
CseI GACGC 3 cut(s) 211, 271, 388
Csp6I GTAC 5 cut(s) 768, 870, 933, 1055, 1060
CspI CGGWCCG 1 cut(s) 420
CviAII CATG 5 cut(s) 370, 698, 878, 927, 1108
CviQI GTAC 5 cut(s) 768, 870, 933, 1055, 1060
DdeI CTNAG 2 cut(s) 543, 901
DpnI GATC 6 cut(s) 374, 384, 458, 482, 907, 925
DpnII GATC 6 cut(s) 372, 382, 456, 480, 905, 923
DrdI GACNNNNNNGTC 1 cut(s) 458
DseDI GACNNNNNNGTC 1 cut(s) 458
EaeI YGGCCR 3 cut(s) 579, 1029, 1075
EagI CGGCCG 1 cut(s) 579
Eam1104I CTCTTC 2 cut(s) 308, 835
EarI CTCTTC 2 cut(s) 308, 835
EciI GGCGGA 5 cut(s) 73, 187, 233, 351, 434
Ecl136II GAGCTC 1 cut(s) 409
EclXI CGGCCG 1 cut(s) 579
Eco130I CCWWGG 1 cut(s) 1001
Eco24I GRGCYC 2 cut(s) 411, 603
Eco31I GGTCTC 2 cut(s) 565, 680
Eco47I GGWCC 4 cut(s) 269, 338, 420, 645
Eco52I CGGCCG 1 cut(s) 579
Eco53kI GAGCTC 1 cut(s) 409
Eco81I CCTNAGG 1 cut(s) 543
EcoICRI GAGCTC 1 cut(s) 409
EcoRII CCWGG 2 cut(s) 124, 606
EcoT14I CCWWGG 1 cut(s) 1001
EcoT38I GRGCYC 2 cut(s) 411, 603
ErhI CCWWGG 1 cut(s) 1001
FaeI CATG 5 cut(s) 373, 701, 881, 930, 1111
FaiI YATR 7 cut(s) 371, 567, 656, 699, 879, 928, 1109
FalI AAGNNNNNCTT 2 cut(s) 981, 1013
FaqI GGGAC 3 cut(s) 376, 561, 748
FatI CATG 5 cut(s) 369, 697, 877, 926, 1107
FauI CCCGC 3 cut(s) 85, 363, 401
FblI GTMKAC 2 cut(s) 225, 489
Fnu4HI GCNGC 7 cut(s) 201, 247, 277, 280, 334, 397, 448
FokI GGATG 2 cut(s) 776, 1124
FriOI GRGCYC 2 cut(s) 411, 603
FseI GGCCGGCC 1 cut(s) 581
Fsp4HI GCNGC 7 cut(s) 201, 247, 277, 280, 334, 397, 448
FspBI CTAG 2 cut(s) 713, 848
GluI GCNGC 7 cut(s) 201, 247, 277, 280, 334, 397, 448
HaeIII GGCC 5 cut(s) 129, 577, 581, 1031, 1077
HapII CCGG 8 cut(s) 213, 267, 418, 454, 573, 578, 596, 672
HgaI GACGC 3 cut(s) 211, 271, 388
Hin1I GRCGYC 1 cut(s) 282
Hin1II CATG 5 cut(s) 373, 701, 881, 930, 1111
HincII GTYRAC 1 cut(s) 898
HindII GTYRAC 1 cut(s) 898
HinfI GANTC 6 cut(s) 209, 288, 518, 736, 899, 1162
HpaII CCGG 8 cut(s) 213, 267, 418, 454, 573, 578, 596, 672
HphI GGTGA 1 cut(s) 796
Hpy166II GTNNAC 5 cut(s) 226, 272, 490, 898, 1055
Hpy188I TCNGA 6 cut(s) 27, 91, 287, 424, 940, 1018
Hpy188III TCNNGA 5 cut(s) 295, 370, 698, 903, 1186
Hpy8I GTNNAC 5 cut(s) 226, 272, 490, 898, 1055
Hpy99I CGWCG 5 cut(s) 287, 383, 464, 467, 721
HpyAV CCTTC 4 cut(s) 250, 1007, 1043, 1183
HpyCH4III ACNGT 6 cut(s) 532, 552, 818, 874, 1059, 1093
HpyCH4V TGCA 2 cut(s) 930, 1045
HpyF10VI GCNNNNNNNGC 7 cut(s) 255, 393, 402, 583, 587, 686, 803
HpyF3I CTNAG 2 cut(s) 543, 901
Hsp92I GRCGYC 1 cut(s) 282
Hsp92II CATG 5 cut(s) 373, 701, 881, 930, 1111
KroI GCCGGC 1 cut(s) 577
KroNI GCCGGC 1 cut(s) 579
Kzo9I GATC 6 cut(s) 372, 382, 456, 480, 905, 923
LguI GCTCTTC 1 cut(s) 308
LmnI GCTCC 7 cut(s) 55, 447, 606, 674, 780, 794, 1116
Lsp1109I GCAGC 1 cut(s) 383
LweI GCATC 1 cut(s) 288
MaeI CTAG 2 cut(s) 713, 848
MaeIII GTNAC 3 cut(s) 106, 526, 860
MalI GATC 6 cut(s) 374, 384, 458, 482, 907, 925
MboI GATC 6 cut(s) 372, 382, 456, 480, 905, 923
MboII GAAGA 5 cut(s) 295, 319, 475, 822, 1096
MflI RGATCY 2 cut(s) 480, 905
MhlI GDGCHC 2 cut(s) 411, 603
MlsI TGGCCA 2 cut(s) 1031, 1077
MluCI AATT 6 cut(s) 615, 942, 955, 1034, 1133, 1180
MluNI TGGCCA 2 cut(s) 1031, 1077
MlyI GAGTC 3 cut(s) 203, 730, 893
MmeI TCCRAC 2 cut(s) 265, 495
Mox20I TGGCCA 2 cut(s) 1031, 1077
MroNI GCCGGC 1 cut(s) 577
MroXI GAANNNNTTC 1 cut(s) 1161
MscI TGGCCA 2 cut(s) 1031, 1077
Msp20I TGGCCA 2 cut(s) 1031, 1077
MspA1I CMGCKG 1 cut(s) 396
MspI CCGG 8 cut(s) 213, 267, 418, 454, 573, 578, 596, 672
MspR9I CCNGG 4 cut(s) 126, 574, 597, 608
MvaI CCWGG 2 cut(s) 126, 608
MvnI CGCG 4 cut(s) 222, 276, 450, 680
MwoI GCNNNNNNNGC 7 cut(s) 255, 393, 402, 583, 587, 686, 803
NaeI GCCGGC 1 cut(s) 579
NciI CCSGG 2 cut(s) 574, 597
NdeII GATC 6 cut(s) 372, 382, 456, 480, 905, 923
NgoMIV GCCGGC 1 cut(s) 577
NheI GCTAGC 1 cut(s) 847
NlaIII CATG 5 cut(s) 373, 701, 881, 930, 1111
NlaIV GGNNCC 3 cut(s) 340, 443, 602
NmuCI GTSAC 2 cut(s) 526, 860
PagI TCATGA 2 cut(s) 369, 697
PaqCI CACCTGC 2 cut(s) 197, 239
PciSI GCTCTTC 1 cut(s) 308
PdiI GCCGGC 1 cut(s) 579
PdmI GAANNNNTTC 1 cut(s) 1161
PfeI GAWTC 3 cut(s) 288, 518, 1162
PkrI GCNGC 7 cut(s) 202, 248, 278, 281, 335, 398, 449
Ple19I CGATCG 1 cut(s) 385
PleI GAGTC 3 cut(s) 203, 730, 893
PpsI GAGTC 3 cut(s) 203, 730, 893
PsiI TTATAA 1 cut(s) 656
Psp124BI GAGCTC 1 cut(s) 411
Psp6I CCWGG 2 cut(s) 124, 606
PspGI CCWGG 2 cut(s) 124, 606
PspN4I GGNNCC 3 cut(s) 340, 443, 602
PspPI GGNCC 6 cut(s) 128, 269, 338, 420, 575, 645
PsuI RGATCY 2 cut(s) 480, 905
PvuI CGATCG 1 cut(s) 385
RigI GGCCGGCC 1 cut(s) 581
RsaI GTAC 5 cut(s) 769, 871, 934, 1056, 1061
RsaNI GTAC 5 cut(s) 768, 870, 933, 1055, 1060
Rsr2I CGGWCCG 1 cut(s) 420
RsrII CGGWCCG 1 cut(s) 420
SacI GAGCTC 1 cut(s) 411
SapI GCTCTTC 1 cut(s) 308
SatI GCNGC 7 cut(s) 201, 247, 277, 280, 334, 397, 448
Sau3AI GATC 6 cut(s) 372, 382, 456, 480, 905, 923
Sau96I GGNCC 6 cut(s) 128, 269, 338, 420, 575, 645
SchI GAGTC 3 cut(s) 203, 730, 893
ScrFI CCNGG 4 cut(s) 126, 574, 597, 608
SduI GDGCHC 2 cut(s) 411, 603
SfaNI GCATC 1 cut(s) 288
SinI GGWCC 4 cut(s) 269, 338, 420, 645
SmlI CTYRAG 1 cut(s) 856
SmoI CTYRAG 1 cut(s) 856
Sse9I AATT 6 cut(s) 615, 942, 955, 1034, 1133, 1180
SspI AATATT 1 cut(s) 1175
SspMI CTAG 2 cut(s) 713, 848
SstI GAGCTC 1 cut(s) 411
StyD4I CCNGG 4 cut(s) 124, 572, 595, 606
StyI CCWWGG 1 cut(s) 1001
TaaI ACNGT 6 cut(s) 532, 552, 818, 874, 1059, 1093
TaqI TCGA 4 cut(s) 521, 624, 638, 1126
TaqII GACCGA 1 cut(s) 424
TasI AATT 6 cut(s) 615, 942, 955, 1034, 1133, 1180
TatI WGTACW 1 cut(s) 932
TauI GCSGC 6 cut(s) 203, 249, 279, 282, 336, 450
TfiI GAWTC 3 cut(s) 288, 518, 1162
TscAI CASTG 3 cut(s) 314, 841, 1032
TseFI GTSAC 2 cut(s) 526, 860
TseI GCWGC 1 cut(s) 396
Tsp45I GTSAC 2 cut(s) 526, 860
TspDTI ATGAA 2 cut(s) 948, 960
TspGWI ACGGA 1 cut(s) 94
TspRI CASTG 3 cut(s) 314, 841, 1032
VpaK11BI GGWCC 4 cut(s) 269, 338, 420, 645
XapI RAATTY 2 cut(s) 615, 1034
XmiI GTMKAC 2 cut(s) 225, 489
XmnI GAANNNNTTC 1 cut(s) 1161
XspI CTAG 2 cut(s) 713, 848
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.