Rroxscaffold_6G00417040

Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1-like

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000006
OG0002737
Physical Location & Seq
Reverse (-)
38849459 .. 38851972
2514 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_6G00417040.1

Sequence Viewer

Length: 903 bp
ATGGCGTCGGTGGGCCAGGCCGCGGAGGTGTACGAGCCGAAGCCACTCCAAGTCTGGCGAGCTATGATGAACTGGTTGGGCTTCTTCTTCCAGATCATCGTTCAGATCCTCAGAGGCGCCCCTTGCCTCGCTCATTTCCTGTCGTACGTTCCTCTTCTCGCTTCTTCTTCTTCTTCTTCTTTCAGGCCCTTGCCGGTCAGTGAAATCCCTCTCAACGACACGTCGTCCTCCGCTCACGCCAACCTCGAAAACGGCGTCGTAACCGACGATCACCGCCTTCAAAAGCTCACGGTAGTTCTTGACTTAGATGAGACGCTAGTGTGTGCGTACGAAACATCTGGCTTGCCTGCTATTGTTCGGACCCAAGCAGCGGATGCTGGGTTGAAGTGGTTTGAGATAGAATGTGTATCTTCAGACAAGGAGTCTGATGGTAAACCGAAGATCAGTTATGTGACAGTGTTTGAACGTCCTGGTCTGCACGAGTTCTTGAAACGGATTTGTGAATTTGCTGATCTTGTCCTATTTACTGCTGGTCTTGAAGGATATGCTAGACCACTTGTTGACAGAATTGATGTGGAGAACAGATTTAAGCTTCGTCTTTATCGGCCTTCTACAGTTACCACGGAAAACCGGGATCATGTGAAAGATCTGTCTTGTATATCGAAAGATCTCTGTCGAATTGTTATTGTTGACAACAACCCATTTAGTTTTCTGCTGCAACCGGTGAATGGAGTTCCGTGTATTCCATTTTCTGCTGGACATCCATATGATGACCAGCTCTTGGAGGTGCTGCTTCCACTCCTCCAGCACCTCGCCCAGCAAAAGGATGTGAGGCCTGTGCTTTATGAGAGATTCCACATGCCCGAATGGTTTCAAATGCATGGAGTTACTGTTTCTGGTTAG

Protein Analysis

300

Amino Acids

33.74

Weight (kDa)

5.48

Isoelectric Point (pI)

34.96

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
NIF PF03031 96 - 278 4.9e-42 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)
AccB1I GGYRCC 1 cut(s) 116
AccB7I CCANNNNNTGG 1 cut(s) 781
AccBSI CCGCTC 1 cut(s) 233
AccII CGCG 1 cut(s) 23
AciI CCGC 5 cut(s) 21, 23, 231, 274, 371
AclWI GGATC 2 cut(s) 100, 642
AcsI RAATTY 1 cut(s) 503
AcuI CTGAAG 1 cut(s) 396
AcyI GRCGYC 3 cut(s) 5, 117, 255
AfaI GTAC 3 cut(s) 32, 146, 329
AfiI CCNNNNNNNGG 5 cut(s) 22, 370, 728, 781, 823
AflIII ACRYGT 1 cut(s) 219
AgeI ACCGGT 1 cut(s) 721
AgsI TTSAA 6 cut(s) 281, 385, 464, 490, 539, 875
AhdI GACNNNNNGTC 2 cut(s) 223, 421
AjiI CACGTC 1 cut(s) 222
AjnI CCWGG 2 cut(s) 15, 469
AluBI AGCT 4 cut(s) 62, 286, 592, 778
AluI AGCT 4 cut(s) 62, 286, 592, 778
Alw26I GTCTC 1 cut(s) 305
AlwI GGATC 2 cut(s) 100, 642
AoxI GGCC 5 cut(s) 13, 18, 185, 605, 833
ApeKI GCWGC 3 cut(s) 368, 715, 790
ApoI RAATTY 1 cut(s) 503
ArsI GACNNNNNNTTYG 2 cut(s) 240, 272
AsiGI ACCGGT 1 cut(s) 721
Asp700I GAANNNNTTC 1 cut(s) 870
AspLEI GCGC 1 cut(s) 119
AspS9I GGNCC 3 cut(s) 13, 186, 360
AsuC2I CCSGG 1 cut(s) 632
AsuHPI GGTGA 2 cut(s) 263, 736
AvaII GGWCC 1 cut(s) 360
BanI GGYRCC 1 cut(s) 116
BauI CACGAG 1 cut(s) 479
BbvI GCAGC 3 cut(s) 380, 702, 777
BccI CCATC 1 cut(s) 422
BceAI ACGGC 1 cut(s) 268
BciT130I CCWGG 2 cut(s) 17, 471
BcnI CCSGG 1 cut(s) 632
BcoDI GTCTC 1 cut(s) 305
BfaI CTAG 2 cut(s) 317, 549
BfmI CTRYAG 1 cut(s) 612
BfoI RGCGCY 1 cut(s) 120
BglII AGATCT 2 cut(s) 646, 667
BisI GCNGC 4 cut(s) 21, 369, 716, 791
BlsI GCNGC 4 cut(s) 22, 370, 717, 792
Bme1390I CCNGG 3 cut(s) 17, 471, 632
Bme18I GGWCC 1 cut(s) 360
BmeRI GACNNNNNGTC 2 cut(s) 223, 421
BmgBI CACGTC 1 cut(s) 222
BmgT120I GGNCC 3 cut(s) 13, 186, 360
BmiI GGNNCC 2 cut(s) 118, 362
BmrFI CCNGG 3 cut(s) 17, 471, 632
BmsI GCATC 1 cut(s) 364
BpmI CTGGAG 1 cut(s) 788
BpuMI CCSGG 1 cut(s) 632
BsaHI GRCGYC 3 cut(s) 5, 117, 255
BsaJI CCNNGG 2 cut(s) 21, 621
BsaWI WCCGGW 1 cut(s) 721
BsaXI ACNNNNNCTCC 1 cut(s) 876
Bsc4I CCNNNNNNNGG 5 cut(s) 22, 370, 728, 781, 823
Bse118I RCCGGY 2 cut(s) 193, 721
Bse1I ACTGG 1 cut(s) 77
BseBI CCWGG 2 cut(s) 17, 471
BseDI CCNNGG 2 cut(s) 21, 621
BseGI GGATG 3 cut(s) 379, 760, 832
BseLI CCNNNNNNNGG 5 cut(s) 22, 370, 728, 781, 823
BseMII CTCAG 1 cut(s) 124
BseNI ACTGG 1 cut(s) 77
BseRI GAGGAG 1 cut(s) 791
BseXI GCAGC 3 cut(s) 380, 702, 777
BseYI CCCAGC 2 cut(s) 377, 816
BsgI GTGCAG 1 cut(s) 461
Bsh1236I CGCG 1 cut(s) 23
BshFI GGCC 5 cut(s) 15, 20, 187, 607, 835
BshNI GGYRCC 1 cut(s) 116
BshTI ACCGGT 1 cut(s) 721
BsiSI CCGG 3 cut(s) 194, 631, 722
BsiWI CGTACG 2 cut(s) 144, 327
BslI CCNNNNNNNGG 5 cut(s) 22, 370, 728, 781, 823
BsmAI GTCTC 1 cut(s) 305
BsmBI CGTCTC 1 cut(s) 305
BsnI GGCC 5 cut(s) 15, 20, 187, 607, 835
Bsp143I GATC 8 cut(s) 93, 105, 268, 441, 511, 634, 646, 667
BspACI CCGC 5 cut(s) 21, 23, 231, 274, 371
BspANI GGCC 5 cut(s) 15, 20, 187, 607, 835
BspCNI CTCAG 1 cut(s) 123
BspFNI CGCG 1 cut(s) 23
BspLI GGNNCC 2 cut(s) 118, 362
BspPI GGATC 2 cut(s) 100, 642
BspT107I GGYRCC 1 cut(s) 116
BsrBI CCGCTC 1 cut(s) 233
BsrFI RCCGGY 2 cut(s) 193, 721
BsrI ACTGG 1 cut(s) 77
BssAI RCCGGY 2 cut(s) 193, 721
BssECI CCNNGG 2 cut(s) 21, 621
BssMI GATC 8 cut(s) 93, 105, 268, 441, 511, 634, 646, 667
BssNI GRCGYC 3 cut(s) 5, 117, 255
BssSI CACGAG 1 cut(s) 479
Bst2BI CACGAG 1 cut(s) 479
Bst2UI CCWGG 2 cut(s) 17, 471
Bst4CI ACNGT 4 cut(s) 292, 457, 616, 892
Bst6I CTCTTC 1 cut(s) 159
BstACI GRCGYC 3 cut(s) 5, 117, 255
BstAPI GCANNNNNTGC 1 cut(s) 374
BstC8I GCNNGC 3 cut(s) 60, 344, 348
BstDEI CTNAG 2 cut(s) 110, 304
BstDSI CCRYGG 2 cut(s) 21, 621
BstF5I GGATG 3 cut(s) 379, 760, 832
BstFNI CGCG 1 cut(s) 23
BstH2I RGCGCY 1 cut(s) 120
BstHHI GCGC 1 cut(s) 119
BstKTI GATC 8 cut(s) 96, 108, 271, 444, 514, 637, 649, 670
BstMAI GTCTC 1 cut(s) 305
BstMBI GATC 8 cut(s) 93, 105, 268, 441, 511, 634, 646, 667
BstMWI GCNNNNNNNGC 2 cut(s) 123, 374
BstNI CCWGG 2 cut(s) 17, 471
BstNSI RCATGY 1 cut(s) 862
BstSCI CCNGG 3 cut(s) 15, 469, 630
BstSFI CTRYAG 1 cut(s) 612
BstUI CGCG 1 cut(s) 23
BstV1I GCAGC 3 cut(s) 380, 702, 777
BstX2I RGATCY 3 cut(s) 105, 646, 667
BstYI RGATCY 3 cut(s) 105, 646, 667
BsuRI GGCC 5 cut(s) 15, 20, 187, 607, 835
BtgI CCRYGG 2 cut(s) 21, 621
BtrI CACGTC 1 cut(s) 222
BtsCI GGATG 3 cut(s) 379, 760, 832
BtsIMutI CAGTG 2 cut(s) 205, 462
Cac8I GCNNGC 3 cut(s) 60, 344, 348
CfoI GCGC 1 cut(s) 119
Cfr10I RCCGGY 2 cut(s) 193, 721
Cfr13I GGNCC 3 cut(s) 13, 186, 360
Cfr42I CCGCGG 1 cut(s) 24
CseI GACGC 2 cut(s) 244, 322
Csp6I GTAC 3 cut(s) 31, 145, 328
CspAI ACCGGT 1 cut(s) 721
CviAII CATG 3 cut(s) 638, 859, 881
CviQI GTAC 3 cut(s) 31, 145, 328
DdeI CTNAG 2 cut(s) 110, 304
DinI GGCGCC 1 cut(s) 118
DpnI GATC 8 cut(s) 95, 107, 270, 443, 513, 636, 648, 669
DpnII GATC 8 cut(s) 93, 105, 268, 441, 511, 634, 646, 667
DriI GACNNNNNGTC 2 cut(s) 223, 421
Eam1104I CTCTTC 1 cut(s) 159
Eam1105I GACNNNNNGTC 2 cut(s) 223, 421
EarI CTCTTC 1 cut(s) 159
Eco147I AGGCCT 1 cut(s) 835
Eco47I GGWCC 1 cut(s) 360
Eco57I CTGAAG 1 cut(s) 396
EcoO109I RGGNCCY 1 cut(s) 186
EcoRII CCWGG 2 cut(s) 15, 469
EcoT22I ATGCAT 1 cut(s) 882
EgeI GGCGCC 1 cut(s) 118
EheI GGCGCC 1 cut(s) 118
Esp3I CGTCTC 1 cut(s) 305
FaeI CATG 3 cut(s) 641, 862, 884
FatI CATG 3 cut(s) 637, 858, 880
FauNDI CATATG 1 cut(s) 766
Fnu4HI GCNGC 4 cut(s) 21, 369, 716, 791
FokI GGATG 3 cut(s) 386, 747, 839
Fsp4HI GCNGC 4 cut(s) 21, 369, 716, 791
FspBI CTAG 2 cut(s) 317, 549
GlaI GCGC 1 cut(s) 118
GluI GCNGC 4 cut(s) 21, 369, 716, 791
GsaI CCCAGC 2 cut(s) 381, 820
GsuI CTGGAG 1 cut(s) 788
HaeII RGCGCY 1 cut(s) 120
HaeIII GGCC 5 cut(s) 15, 20, 187, 607, 835
HapII CCGG 3 cut(s) 194, 631, 722
HgaI GACGC 2 cut(s) 244, 322
HhaI GCGC 1 cut(s) 119
Hin1I GRCGYC 3 cut(s) 5, 117, 255
Hin1II CATG 3 cut(s) 641, 862, 884
Hin6I GCGC 1 cut(s) 117
HinP1I GCGC 1 cut(s) 117
HincII GTYRAC 2 cut(s) 562, 691
HindII GTYRAC 2 cut(s) 562, 691
HindIII AAGCTT 1 cut(s) 590
HinfI GANTC 2 cut(s) 422, 852
HpaII CCGG 3 cut(s) 194, 631, 722
HphI GGTGA 2 cut(s) 263, 736
Hpy166II GTNNAC 4 cut(s) 31, 434, 562, 691
Hpy188I TCNGA 5 cut(s) 105, 113, 360, 415, 427
Hpy188III TCNNGA 4 cut(s) 91, 299, 487, 536
Hpy8I GTNNAC 4 cut(s) 31, 434, 562, 691
Hpy99I CGWCG 4 cut(s) 10, 226, 260, 269
HpyAV CCTTC 3 cut(s) 287, 533, 618
HpyCH4III ACNGT 4 cut(s) 292, 457, 616, 892
HpyCH4IV ACGT 3 cut(s) 147, 221, 466
HpyCH4V TGCA 3 cut(s) 478, 718, 880
HpyF10VI GCNNNNNNNGC 2 cut(s) 123, 374
HpyF3I CTNAG 2 cut(s) 110, 304
HpySE526I ACGT 3 cut(s) 147, 221, 466
Hsp92I GRCGYC 3 cut(s) 5, 117, 255
Hsp92II CATG 3 cut(s) 641, 862, 884
HspAI GCGC 1 cut(s) 117
KasI GGCGCC 1 cut(s) 116
KspI CCGCGG 1 cut(s) 24
Kzo9I GATC 8 cut(s) 93, 105, 268, 441, 511, 634, 646, 667
Lsp1109I GCAGC 3 cut(s) 380, 702, 777
LweI GCATC 1 cut(s) 364
MaeI CTAG 2 cut(s) 317, 549
MaeII ACGT 3 cut(s) 147, 221, 466
MaeIII GTNAC 4 cut(s) 259, 451, 616, 886
MalI GATC 8 cut(s) 95, 107, 270, 443, 513, 636, 648, 669
MbiI CCGCTC 1 cut(s) 233
MboI GATC 8 cut(s) 93, 105, 268, 441, 511, 634, 646, 667
MflI RGATCY 3 cut(s) 105, 646, 667
MluCI AATT 3 cut(s) 503, 567, 678
Mly113I GGCGCC 1 cut(s) 117
MlyI GAGTC 1 cut(s) 431
Mph1103I ATGCAT 1 cut(s) 882
MroXI GAANNNNTTC 1 cut(s) 870
MseI TTAA 1 cut(s) 588
MslI CAYNNNNRTG 1 cut(s) 765
MspA1I CMGCKG 2 cut(s) 23, 371
MspI CCGG 3 cut(s) 194, 631, 722
MspR9I CCNGG 3 cut(s) 17, 471, 632
MvaI CCWGG 2 cut(s) 17, 471
MvnI CGCG 1 cut(s) 23
MwoI GCNNNNNNNGC 2 cut(s) 123, 374
NarI GGCGCC 1 cut(s) 117
NciI CCSGG 1 cut(s) 632
NdeI CATATG 1 cut(s) 766
NdeII GATC 8 cut(s) 93, 105, 268, 441, 511, 634, 646, 667
NlaIII CATG 3 cut(s) 641, 862, 884
NlaIV GGNNCC 2 cut(s) 118, 362
NmuCI GTSAC 1 cut(s) 451
NsiI ATGCAT 1 cut(s) 882
NspI RCATGY 1 cut(s) 862
PceI AGGCCT 1 cut(s) 835
PcsI WCGNNNNNNNCGW 3 cut(s) 243, 252, 264
PdmI GAANNNNTTC 1 cut(s) 870
PfeI GAWTC 1 cut(s) 852
Pfl23II CGTACG 2 cut(s) 144, 327
PflMI CCANNNNNTGG 1 cut(s) 781
PinAI ACCGGT 1 cut(s) 721
PkrI GCNGC 4 cut(s) 22, 370, 717, 792
PleI GAGTC 1 cut(s) 430
PluTI GGCGCC 1 cut(s) 120
PpsI GAGTC 1 cut(s) 430
Psp6I CCWGG 2 cut(s) 15, 469
PspFI CCCAGC 2 cut(s) 377, 816
PspGI CCWGG 2 cut(s) 15, 469
PspLI CGTACG 2 cut(s) 144, 327
PspN4I GGNNCC 2 cut(s) 118, 362
PspPI GGNCC 3 cut(s) 13, 186, 360
PsuI RGATCY 3 cut(s) 105, 646, 667
RsaI GTAC 3 cut(s) 32, 146, 329
RsaNI GTAC 3 cut(s) 31, 145, 328
RseI CAYNNNNRTG 1 cut(s) 765
SacII CCGCGG 1 cut(s) 24
SaqAI TTAA 1 cut(s) 588
SatI GCNGC 4 cut(s) 21, 369, 716, 791
Sau3AI GATC 8 cut(s) 93, 105, 268, 441, 511, 634, 646, 667
Sau96I GGNCC 3 cut(s) 13, 186, 360
SchI GAGTC 1 cut(s) 431
ScrFI CCNGG 3 cut(s) 17, 471, 632
SfaNI GCATC 1 cut(s) 364
SfcI CTRYAG 1 cut(s) 612
SfoI GGCGCC 1 cut(s) 118
Sfr303I CCGCGG 1 cut(s) 24
SgrBI CCGCGG 1 cut(s) 24
SinI GGWCC 1 cut(s) 360
SmiMI CAYNNNNRTG 1 cut(s) 765
Sse9I AATT 3 cut(s) 503, 567, 678
SseBI AGGCCT 1 cut(s) 835
SsiI CCGC 5 cut(s) 21, 23, 231, 274, 371
SspDI GGCGCC 1 cut(s) 116
SspMI CTAG 2 cut(s) 317, 549
StuI AGGCCT 1 cut(s) 835
StyD4I CCNGG 3 cut(s) 15, 469, 630
TaaI ACNGT 4 cut(s) 292, 457, 616, 892
TaiI ACGT 3 cut(s) 150, 224, 469
TaqI TCGA 3 cut(s) 246, 662, 676
TasI AATT 3 cut(s) 503, 567, 678
TauI GCSGC 1 cut(s) 23
TfiI GAWTC 1 cut(s) 852
Tru1I TTAA 1 cut(s) 588
Tru9I TTAA 1 cut(s) 588
TscAI CASTG 2 cut(s) 205, 462
TseFI GTSAC 1 cut(s) 451
TseI GCWGC 3 cut(s) 368, 715, 790
Tsp45I GTSAC 1 cut(s) 451
TspDTI ATGAA 1 cut(s) 83
TspGWI ACGGA 3 cut(s) 508, 638, 726
TspRI CASTG 2 cut(s) 205, 462
Van91I CCANNNNNTGG 1 cut(s) 781
VpaK11BI GGWCC 1 cut(s) 360
XapI RAATTY 1 cut(s) 503
XceI RCATGY 1 cut(s) 862
XcmI CCANNNNNNNNNTGG 1 cut(s) 51
XmnI GAANNNNTTC 1 cut(s) 870
XspI CTAG 2 cut(s) 317, 549
Zsp2I ATGCAT 1 cut(s) 882
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.