Rw3G010090

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

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr3
OG0002737
Physical Location & Seq
Forward (+)
9690754 .. 9694768
4015 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw3G010090.1

Sequence Viewer

Length: 897 bp
ATGGCGTCGGTGGGCCAGGCCGCGGAGGTGTACGAGCCGAAGCCACTCCAAGTCTGGCGAGCTATGATGAACTGGTTGGGCTTCTTCTTCCAGATCATCGTTCAGATCCTCAGAGGCGCCCCTTGCCTCGCTCATTTCCTGTCGTACGTTCCTCTTCTCGCTTCTTCTTCTTCTTCTTCTTCTTTCAGGCCCTTGCCGGTCAGTGAAATCCCTCTCAACGACACGTCGTCCTCCGCTCACGCCAACCTCGAAAACGGCGTCGTAACCGACGATCTCCGCCTTCAAAAGCTCACGGTAGTTCTTGACTTAGATGAGACGCTGGTGTGTGCGTACGAAACATCTAGCTTGCCTGCTATTGTTCGGACCCAAGCAACAGATGCTGGGTTGAAGTGGTTTGAGATCGAATGTGTATCTTCAGACAAGGAGTCTGATGGTAAACCGAAGATCAGTTATGTGACAGTGTTTGAACGTCCTGGTTTGCACGAGTTCTTGAAACGGATCTGTGAATTTGCTGATCTTGTCCTATTTACTGCTGGTCTTGAAGGTTATGCTAGGCCACTTGTTGACAGAATTGATGTGGAGAACAGATTTAAGCTTCGTCTTTATCGGCCTTCTACAGTTACCACGGAAAACCGGGATCATGTGAAAGATCTGTCTTGTATATCGAAAGATCTCTGTCGAATTGTTATTGTTGACAACAACCCATTTAGTTTTCTGCTGCAACCGGTGAATGGAGTTCCATGTATTCCCTTTTCTGCTGGACATCCATATGATGATCAGCTCTTGGAGGTGCTGCTTCCACTCCTCCAGCACCTCGCCCAGCAAAAGGATCTTCTTCACACAATGATATTGTCTATAGCGTGGGTGCAAGAAAAATATTTTCTTTTGGTTAATTAA

Protein Analysis

298

Amino Acids

33.5

Weight (kDa)

5.28

Isoelectric Point (pI)

34.22

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
NIF PF03031 97 - 278 2.2e-41 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
AccBSI CCGCTC 1 cut(s) 236
AccII CGCG 1 cut(s) 23
AciI CCGC 4 cut(s) 21, 23, 234, 277
AclWI GGATC 4 cut(s) 100, 506, 645, 837
AcsI RAATTY 1 cut(s) 506
AcuI CTGAAG 1 cut(s) 399
AcyI GRCGYC 3 cut(s) 5, 117, 258
AfaI GTAC 3 cut(s) 32, 146, 332
AfiI CCNNNNNNNGG 3 cut(s) 22, 731, 826
AflIII ACRYGT 1 cut(s) 222
AgeI ACCGGT 1 cut(s) 724
AgsI TTSAA 5 cut(s) 284, 388, 467, 493, 542
AhdI GACNNNNNGTC 2 cut(s) 226, 424
AjiI CACGTC 1 cut(s) 225
AjnI CCWGG 2 cut(s) 15, 472
AluBI AGCT 5 cut(s) 62, 289, 345, 595, 781
AluI AGCT 5 cut(s) 62, 289, 345, 595, 781
Alw26I GTCTC 1 cut(s) 308
AlwI GGATC 4 cut(s) 100, 506, 645, 837
AlwNI CAGNNNCTG 1 cut(s) 380
AoxI GGCC 5 cut(s) 13, 18, 188, 554, 608
ApeKI GCWGC 2 cut(s) 718, 793
ApoI RAATTY 1 cut(s) 506
ArsI GACNNNNNNTTYG 2 cut(s) 243, 275
AsiGI ACCGGT 1 cut(s) 724
AspLEI GCGC 1 cut(s) 119
AspS9I GGNCC 3 cut(s) 13, 189, 363
AsuC2I CCSGG 1 cut(s) 635
AsuHPI GGTGA 1 cut(s) 739
AvaII GGWCC 1 cut(s) 363
BanI GGYRCC 1 cut(s) 116
BauI CACGAG 1 cut(s) 482
BbvI GCAGC 2 cut(s) 705, 780
BccI CCATC 1 cut(s) 425
BceAI ACGGC 1 cut(s) 271
BciT130I CCWGG 2 cut(s) 17, 474
BclI TGATCA 1 cut(s) 775
BcnI CCSGG 1 cut(s) 635
BcoDI GTCTC 1 cut(s) 308
BfaI CTAG 2 cut(s) 342, 552
BfmI CTRYAG 2 cut(s) 615, 855
BfoI RGCGCY 1 cut(s) 120
BglII AGATCT 2 cut(s) 649, 670
BisI GCNGC 3 cut(s) 21, 719, 794
BlsI GCNGC 3 cut(s) 22, 720, 795
Bme1390I CCNGG 3 cut(s) 17, 474, 635
Bme18I GGWCC 1 cut(s) 363
BmeRI GACNNNNNGTC 2 cut(s) 226, 424
BmgBI CACGTC 1 cut(s) 225
BmgT120I GGNCC 3 cut(s) 13, 189, 363
BmiI GGNNCC 2 cut(s) 118, 365
BmrFI CCNGG 3 cut(s) 17, 474, 635
BmsI GCATC 1 cut(s) 367
BpmI CTGGAG 1 cut(s) 791
BpuMI CCSGG 1 cut(s) 635
BsaHI GRCGYC 3 cut(s) 5, 117, 258
BsaJI CCNNGG 2 cut(s) 21, 624
BsaWI WCCGGW 1 cut(s) 724
Bsc4I CCNNNNNNNGG 3 cut(s) 22, 731, 826
Bse118I RCCGGY 2 cut(s) 196, 724
Bse1I ACTGG 1 cut(s) 77
BseBI CCWGG 2 cut(s) 17, 474
BseDI CCNNGG 2 cut(s) 21, 624
BseGI GGATG 1 cut(s) 763
BseLI CCNNNNNNNGG 3 cut(s) 22, 731, 826
BseMII CTCAG 1 cut(s) 124
BseNI ACTGG 1 cut(s) 77
BseRI GAGGAG 1 cut(s) 794
BseXI GCAGC 2 cut(s) 705, 780
BseYI CCCAGC 2 cut(s) 380, 819
Bsh1236I CGCG 1 cut(s) 23
BshFI GGCC 5 cut(s) 15, 20, 190, 556, 610
BshNI GGYRCC 1 cut(s) 116
BshTI ACCGGT 1 cut(s) 724
BsiSI CCGG 3 cut(s) 197, 634, 725
BsiWI CGTACG 2 cut(s) 144, 330
BslI CCNNNNNNNGG 3 cut(s) 22, 731, 826
BsmAI GTCTC 1 cut(s) 308
BsmBI CGTCTC 1 cut(s) 308
BsnI GGCC 5 cut(s) 15, 20, 190, 556, 610
BspACI CCGC 4 cut(s) 21, 23, 234, 277
BspANI GGCC 5 cut(s) 15, 20, 190, 556, 610
BspCNI CTCAG 1 cut(s) 123
BspFNI CGCG 1 cut(s) 23
BspLI GGNNCC 2 cut(s) 118, 365
BspPI GGATC 4 cut(s) 100, 506, 645, 837
BspT107I GGYRCC 1 cut(s) 116
BsrBI CCGCTC 1 cut(s) 236
BsrFI RCCGGY 2 cut(s) 196, 724
BsrI ACTGG 1 cut(s) 77
BssAI RCCGGY 2 cut(s) 196, 724
BssECI CCNNGG 2 cut(s) 21, 624
BssNI GRCGYC 3 cut(s) 5, 117, 258
BssSI CACGAG 1 cut(s) 482
Bst2BI CACGAG 1 cut(s) 482
Bst2UI CCWGG 2 cut(s) 17, 474
Bst4CI ACNGT 3 cut(s) 295, 460, 619
Bst6I CTCTTC 1 cut(s) 159
BstACI GRCGYC 3 cut(s) 5, 117, 258
BstAPI GCANNNNNTGC 1 cut(s) 377
BstC8I GCNNGC 3 cut(s) 60, 347, 351
BstDEI CTNAG 2 cut(s) 110, 307
BstDSI CCRYGG 2 cut(s) 21, 624
BstF5I GGATG 1 cut(s) 763
BstFNI CGCG 1 cut(s) 23
BstH2I RGCGCY 1 cut(s) 120
BstHHI GCGC 1 cut(s) 119
BstMAI GTCTC 1 cut(s) 308
BstMWI GCNNNNNNNGC 2 cut(s) 123, 377
BstNI CCWGG 2 cut(s) 17, 474
BstSCI CCNGG 3 cut(s) 15, 472, 633
BstSFI CTRYAG 2 cut(s) 615, 855
BstUI CGCG 1 cut(s) 23
BstV1I GCAGC 2 cut(s) 705, 780
BstX2I RGATCY 5 cut(s) 105, 498, 649, 670, 829
BstYI RGATCY 5 cut(s) 105, 498, 649, 670, 829
BsuRI GGCC 5 cut(s) 15, 20, 190, 556, 610
BtgI CCRYGG 2 cut(s) 21, 624
BtrI CACGTC 1 cut(s) 225
BtsCI GGATG 1 cut(s) 763
BtsIMutI CAGTG 2 cut(s) 208, 465
Cac8I GCNNGC 3 cut(s) 60, 347, 351
CaiI CAGNNNCTG 1 cut(s) 380
CfoI GCGC 1 cut(s) 119
Cfr10I RCCGGY 2 cut(s) 196, 724
Cfr13I GGNCC 3 cut(s) 13, 189, 363
Cfr42I CCGCGG 1 cut(s) 24
CseI GACGC 2 cut(s) 247, 325
Csp6I GTAC 3 cut(s) 31, 145, 331
CspAI ACCGGT 1 cut(s) 724
CviAII CATG 2 cut(s) 641, 741
CviQI GTAC 3 cut(s) 31, 145, 331
DdeI CTNAG 2 cut(s) 110, 307
DinI GGCGCC 1 cut(s) 118
DriI GACNNNNNGTC 2 cut(s) 226, 424
Eam1104I CTCTTC 1 cut(s) 159
Eam1105I GACNNNNNGTC 2 cut(s) 226, 424
EarI CTCTTC 1 cut(s) 159
EciI GGCGGA 1 cut(s) 266
Eco47I GGWCC 1 cut(s) 363
Eco57I CTGAAG 1 cut(s) 399
EcoO109I RGGNCCY 1 cut(s) 189
EcoRII CCWGG 2 cut(s) 15, 472
EgeI GGCGCC 1 cut(s) 118
EheI GGCGCC 1 cut(s) 118
Esp3I CGTCTC 1 cut(s) 308
FaeI CATG 2 cut(s) 644, 744
FaiI YATR 9 cut(s) 65, 453, 549, 642, 662, 742, 769, 771, 857
FatI CATG 2 cut(s) 640, 740
FauNDI CATATG 1 cut(s) 769
FbaI TGATCA 1 cut(s) 775
Fnu4HI GCNGC 3 cut(s) 21, 719, 794
FokI GGATG 1 cut(s) 750
Fsp4HI GCNGC 3 cut(s) 21, 719, 794
FspBI CTAG 2 cut(s) 342, 552
GlaI GCGC 1 cut(s) 118
GluI GCNGC 3 cut(s) 21, 719, 794
GsaI CCCAGC 2 cut(s) 384, 823
GsuI CTGGAG 1 cut(s) 791
HaeII RGCGCY 1 cut(s) 120
HaeIII GGCC 5 cut(s) 15, 20, 190, 556, 610
HapII CCGG 3 cut(s) 197, 634, 725
HgaI GACGC 2 cut(s) 247, 325
HhaI GCGC 1 cut(s) 119
Hin1I GRCGYC 3 cut(s) 5, 117, 258
Hin1II CATG 2 cut(s) 644, 744
Hin6I GCGC 1 cut(s) 117
HinP1I GCGC 1 cut(s) 117
HincII GTYRAC 2 cut(s) 565, 694
HindII GTYRAC 2 cut(s) 565, 694
HindIII AAGCTT 1 cut(s) 593
HinfI GANTC 1 cut(s) 425
HpaII CCGG 3 cut(s) 197, 634, 725
HphI GGTGA 1 cut(s) 739
Hpy166II GTNNAC 4 cut(s) 31, 437, 565, 694
Hpy188I TCNGA 5 cut(s) 105, 113, 363, 418, 430
Hpy188III TCNNGA 4 cut(s) 91, 302, 490, 539
Hpy8I GTNNAC 4 cut(s) 31, 437, 565, 694
Hpy99I CGWCG 4 cut(s) 10, 229, 263, 272
HpyAV CCTTC 3 cut(s) 290, 536, 621
HpyCH4III ACNGT 3 cut(s) 295, 460, 619
HpyCH4IV ACGT 3 cut(s) 147, 224, 469
HpyCH4V TGCA 3 cut(s) 481, 721, 868
HpyF10VI GCNNNNNNNGC 2 cut(s) 123, 377
HpyF3I CTNAG 2 cut(s) 110, 307
HpySE526I ACGT 3 cut(s) 147, 224, 469
Hsp92I GRCGYC 3 cut(s) 5, 117, 258
Hsp92II CATG 2 cut(s) 644, 744
HspAI GCGC 1 cut(s) 117
KasI GGCGCC 1 cut(s) 116
Ksp22I TGATCA 1 cut(s) 775
KspI CCGCGG 1 cut(s) 24
Lsp1109I GCAGC 2 cut(s) 705, 780
LweI GCATC 1 cut(s) 367
MaeI CTAG 2 cut(s) 342, 552
MaeII ACGT 3 cut(s) 147, 224, 469
MaeIII GTNAC 3 cut(s) 262, 454, 619
MbiI CCGCTC 1 cut(s) 236
MflI RGATCY 5 cut(s) 105, 498, 649, 670, 829
MluCI AATT 4 cut(s) 506, 570, 681, 892
Mly113I GGCGCC 1 cut(s) 117
MlyI GAGTC 1 cut(s) 434
MseI TTAA 3 cut(s) 591, 891, 895
MslI CAYNNNNRTG 1 cut(s) 768
MspA1I CMGCKG 1 cut(s) 23
MspI CCGG 3 cut(s) 197, 634, 725
MspR9I CCNGG 3 cut(s) 17, 474, 635
MvaI CCWGG 2 cut(s) 17, 474
MvnI CGCG 1 cut(s) 23
MwoI GCNNNNNNNGC 2 cut(s) 123, 377
NarI GGCGCC 1 cut(s) 117
NciI CCSGG 1 cut(s) 635
NdeI CATATG 1 cut(s) 769
NlaIII CATG 2 cut(s) 644, 744
NlaIV GGNNCC 2 cut(s) 118, 365
NmuCI GTSAC 1 cut(s) 454
PacI TTAATTAA 1 cut(s) 895
PcsI WCGNNNNNNNCGW 3 cut(s) 246, 255, 267
Pfl23II CGTACG 2 cut(s) 144, 330
PinAI ACCGGT 1 cut(s) 724
PkrI GCNGC 3 cut(s) 22, 720, 795
PleI GAGTC 1 cut(s) 433
PluTI GGCGCC 1 cut(s) 120
PpsI GAGTC 1 cut(s) 433
Psp6I CCWGG 2 cut(s) 15, 472
PspFI CCCAGC 2 cut(s) 380, 819
PspGI CCWGG 2 cut(s) 15, 472
PspLI CGTACG 2 cut(s) 144, 330
PspN4I GGNNCC 2 cut(s) 118, 365
PspPI GGNCC 3 cut(s) 13, 189, 363
PstNI CAGNNNCTG 1 cut(s) 380
PsuI RGATCY 5 cut(s) 105, 498, 649, 670, 829
RsaI GTAC 3 cut(s) 32, 146, 332
RsaNI GTAC 3 cut(s) 31, 145, 331
RseI CAYNNNNRTG 1 cut(s) 768
SacII CCGCGG 1 cut(s) 24
SaqAI TTAA 3 cut(s) 591, 891, 895
SatI GCNGC 3 cut(s) 21, 719, 794
Sau96I GGNCC 3 cut(s) 13, 189, 363
SchI GAGTC 1 cut(s) 434
ScrFI CCNGG 3 cut(s) 17, 474, 635
SfaNI GCATC 1 cut(s) 367
SfcI CTRYAG 2 cut(s) 615, 855
SfoI GGCGCC 1 cut(s) 118
Sfr303I CCGCGG 1 cut(s) 24
SgrBI CCGCGG 1 cut(s) 24
SinI GGWCC 1 cut(s) 363
SmiMI CAYNNNNRTG 1 cut(s) 768
Sse9I AATT 4 cut(s) 506, 570, 681, 892
SsiI CCGC 4 cut(s) 21, 23, 234, 277
SspDI GGCGCC 1 cut(s) 116
SspI AATATT 1 cut(s) 878
SspMI CTAG 2 cut(s) 342, 552
StyD4I CCNGG 3 cut(s) 15, 472, 633
TaaI ACNGT 3 cut(s) 295, 460, 619
TaiI ACGT 3 cut(s) 150, 227, 472
TaqI TCGA 4 cut(s) 249, 402, 665, 679
TasI AATT 4 cut(s) 506, 570, 681, 892
TauI GCSGC 1 cut(s) 23
Tru1I TTAA 3 cut(s) 591, 891, 895
Tru9I TTAA 3 cut(s) 591, 891, 895
TscAI CASTG 2 cut(s) 208, 465
TseFI GTSAC 1 cut(s) 454
TseI GCWGC 2 cut(s) 718, 793
Tsp45I GTSAC 1 cut(s) 454
TspDTI ATGAA 1 cut(s) 83
TspGWI ACGGA 2 cut(s) 511, 641
TspRI CASTG 2 cut(s) 208, 465
VpaK11BI GGWCC 1 cut(s) 363
XapI RAATTY 1 cut(s) 506
XcmI CCANNNNNNNNNTGG 1 cut(s) 51
XspI CTAG 2 cut(s) 342, 552
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.