RchiOBHm_Chr3g0463021

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

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
3
OG0002737
Physical Location & Seq
Forward (+)
10525794 .. 10528880
3087 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ42935

Sequence Viewer

Length: 897 bp
ATGGCGTCGGTGGGCCAGGCCGCGGAGGTGTACGAGCCGAAGCCACTCCAAGTCTGGCGAGCTCTGATGAACTGGTTGGGCTTCTTCTTCCAGATCATCGTTCAGATCCTCAGAGGCGCCCCCTGCCTCGCTCATTTCCTGTCGTACGTTCCTCTTCTCGCTTCTTCTTCTTCTTCTTTCAGGCCCTTGCCGGTCAGTGAAATCCCTCTCAACGACACGTCGTCCTCCGCTCACGCCAATCTCGAAAACGGCGTCGTAACCGACGATCACCGCCTTCAAAAGCTCACGGTAGTTCTTGACTTAGATGAGACGCTAGTGTGCGCGTACGAAACATCTAGCTTGCCTGCTATTGTTCGGACCCAAGCAACGGATGCTGGGTTGAAGTGGTTTGAGATAGAATGTGTATCTTCAGACAAGTCTGATGGTAAACCGAAGATCAGTTATGTGACAGTGTTTGAACGTCCTGGTCTGCACGAGTTCTTGAAACGGATTTGTGAATTTGCTGATCTTGTCCTATTTACTGCTGGTCTTGAAGGATATGCTAGACCACTTGTTGACAGAATTGATGTGGAGAGCAGATTTAAGCTTCGTCTTTATCGGCCTTCTACAGTTACCACGGAAAACCGGGATCATGTGAAAGATCTGTCTTGTATATCGAAAGATCTCTGTCGAATTGTTATTGTTGACAACAACCCATTTAGTTTTCTGCTGCAACCGGTGAATGGAGTTCCATGTATTCCCTTTTCTGCTGGACATCCATATGATGATCAGCTCTTGGAGGTGCTGCTTCCACTCCTCCAGCACCTCGCCCAGCAAAAGGATGTGAGGCCTGTGCTTTATGAGAGATTCCACATGCCCGAATGGTTTCAAATGCATGGAGTTACTGTTTCTGGTTAG

Protein Analysis

298

Amino Acids

33.54

Weight (kDa)

5.59

Isoelectric Point (pI)

36.15

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
NIF PF03031 95 - 276 3.4e-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
AccBSI CCGCTC 1 cut(s) 230
AccII CGCG 2 cut(s) 23, 323
AciI CCGC 4 cut(s) 21, 23, 228, 271
AclWI GGATC 2 cut(s) 100, 636
AcsI RAATTY 1 cut(s) 497
AcuI CTGAAG 1 cut(s) 393
AcyI GRCGYC 3 cut(s) 5, 117, 252
AfaI GTAC 3 cut(s) 32, 146, 326
AfiI CCNNNNNNNGG 4 cut(s) 22, 367, 722, 817
AflIII ACRYGT 1 cut(s) 216
AgeI ACCGGT 1 cut(s) 715
AgsI TTSAA 6 cut(s) 278, 382, 458, 484, 533, 869
AhdI GACNNNNNGTC 1 cut(s) 220
AjiI CACGTC 1 cut(s) 219
AjnI CCWGG 2 cut(s) 15, 463
AluBI AGCT 5 cut(s) 62, 283, 339, 586, 772
AluI AGCT 5 cut(s) 62, 283, 339, 586, 772
Alw21I GWGCWC 1 cut(s) 64
Alw26I GTCTC 1 cut(s) 302
AlwI GGATC 2 cut(s) 100, 636
AoxI GGCC 5 cut(s) 13, 18, 182, 599, 827
ApeKI GCWGC 2 cut(s) 709, 784
ApoI RAATTY 1 cut(s) 497
ArsI GACNNNNNNTTYG 2 cut(s) 237, 269
AsiGI ACCGGT 1 cut(s) 715
Asp700I GAANNNNTTC 1 cut(s) 864
AspLEI GCGC 2 cut(s) 119, 323
AspS9I GGNCC 3 cut(s) 13, 183, 357
AsuC2I CCSGG 1 cut(s) 626
AsuHPI GGTGA 2 cut(s) 260, 730
AvaII GGWCC 1 cut(s) 357
BanI GGYRCC 1 cut(s) 116
BanII GRGCYC 1 cut(s) 64
BauI CACGAG 1 cut(s) 473
Bbv12I GWGCWC 1 cut(s) 64
BbvI GCAGC 2 cut(s) 696, 771
BccI CCATC 1 cut(s) 416
BceAI ACGGC 1 cut(s) 265
BciT130I CCWGG 2 cut(s) 17, 465
BclI TGATCA 1 cut(s) 766
BcnI CCSGG 1 cut(s) 626
BcoDI GTCTC 1 cut(s) 302
BfaI CTAG 3 cut(s) 314, 336, 543
BfmI CTRYAG 1 cut(s) 606
BfoI RGCGCY 1 cut(s) 120
BglII AGATCT 2 cut(s) 640, 661
BisI GCNGC 3 cut(s) 21, 710, 785
BlsI GCNGC 3 cut(s) 22, 711, 786
Bme1390I CCNGG 3 cut(s) 17, 465, 626
Bme18I GGWCC 1 cut(s) 357
BmeRI GACNNNNNGTC 1 cut(s) 220
BmgBI CACGTC 1 cut(s) 219
BmgT120I GGNCC 3 cut(s) 13, 183, 357
BmiI GGNNCC 2 cut(s) 118, 359
BmrFI CCNGG 3 cut(s) 17, 465, 626
BmsI GCATC 1 cut(s) 361
BpmI CTGGAG 1 cut(s) 782
BpuMI CCSGG 1 cut(s) 626
BsaHI GRCGYC 3 cut(s) 5, 117, 252
BsaJI CCNNGG 2 cut(s) 21, 615
BsaWI WCCGGW 1 cut(s) 715
BsaXI ACNNNNNCTCC 1 cut(s) 870
Bsc4I CCNNNNNNNGG 4 cut(s) 22, 367, 722, 817
Bse118I RCCGGY 2 cut(s) 190, 715
Bse1I ACTGG 1 cut(s) 77
BseBI CCWGG 2 cut(s) 17, 465
BseDI CCNNGG 2 cut(s) 21, 615
BseGI GGATG 3 cut(s) 376, 754, 826
BseLI CCNNNNNNNGG 4 cut(s) 22, 367, 722, 817
BseMII CTCAG 1 cut(s) 124
BseNI ACTGG 1 cut(s) 77
BseRI GAGGAG 1 cut(s) 785
BseXI GCAGC 2 cut(s) 696, 771
BseYI CCCAGC 2 cut(s) 374, 810
BsgI GTGCAG 1 cut(s) 455
Bsh1236I CGCG 2 cut(s) 23, 323
BshFI GGCC 5 cut(s) 15, 20, 184, 601, 829
BshNI GGYRCC 1 cut(s) 116
BshTI ACCGGT 1 cut(s) 715
BsiHKAI GWGCWC 1 cut(s) 64
BsiSI CCGG 3 cut(s) 191, 625, 716
BsiWI CGTACG 2 cut(s) 144, 324
BslI CCNNNNNNNGG 4 cut(s) 22, 367, 722, 817
BsmAI GTCTC 1 cut(s) 302
BsmBI CGTCTC 1 cut(s) 302
BsnI GGCC 5 cut(s) 15, 20, 184, 601, 829
Bsp1286I GDGCHC 1 cut(s) 64
Bsp143I GATC 9 cut(s) 93, 105, 265, 435, 505, 628, 640, 661, 766
BspACI CCGC 4 cut(s) 21, 23, 228, 271
BspANI GGCC 5 cut(s) 15, 20, 184, 601, 829
BspCNI CTCAG 1 cut(s) 123
BspFNI CGCG 2 cut(s) 23, 323
BspLI GGNNCC 2 cut(s) 118, 359
BspPI GGATC 2 cut(s) 100, 636
BspT107I GGYRCC 1 cut(s) 116
BsrBI CCGCTC 1 cut(s) 230
BsrFI RCCGGY 2 cut(s) 190, 715
BsrI ACTGG 1 cut(s) 77
BssAI RCCGGY 2 cut(s) 190, 715
BssECI CCNNGG 2 cut(s) 21, 615
BssMI GATC 9 cut(s) 93, 105, 265, 435, 505, 628, 640, 661, 766
BssNI GRCGYC 3 cut(s) 5, 117, 252
BssSI CACGAG 1 cut(s) 473
Bst2BI CACGAG 1 cut(s) 473
Bst2UI CCWGG 2 cut(s) 17, 465
Bst4CI ACNGT 4 cut(s) 289, 451, 610, 886
Bst6I CTCTTC 1 cut(s) 159
BstACI GRCGYC 3 cut(s) 5, 117, 252
BstAPI GCANNNNNTGC 1 cut(s) 371
BstC8I GCNNGC 3 cut(s) 60, 341, 345
BstDEI CTNAG 2 cut(s) 110, 301
BstDSI CCRYGG 2 cut(s) 21, 615
BstF5I GGATG 3 cut(s) 376, 754, 826
BstFNI CGCG 2 cut(s) 23, 323
BstH2I RGCGCY 1 cut(s) 120
BstHHI GCGC 2 cut(s) 119, 323
BstKTI GATC 9 cut(s) 96, 108, 268, 438, 508, 631, 643, 664, 769
BstMAI GTCTC 1 cut(s) 302
BstMBI GATC 9 cut(s) 93, 105, 265, 435, 505, 628, 640, 661, 766
BstMWI GCNNNNNNNGC 2 cut(s) 123, 371
BstNI CCWGG 2 cut(s) 17, 465
BstNSI RCATGY 1 cut(s) 856
BstSCI CCNGG 3 cut(s) 15, 463, 624
BstSFI CTRYAG 1 cut(s) 606
BstUI CGCG 2 cut(s) 23, 323
BstV1I GCAGC 2 cut(s) 696, 771
BstX2I RGATCY 3 cut(s) 105, 640, 661
BstYI RGATCY 3 cut(s) 105, 640, 661
BsuRI GGCC 5 cut(s) 15, 20, 184, 601, 829
BtgI CCRYGG 2 cut(s) 21, 615
BtrI CACGTC 1 cut(s) 219
BtsCI GGATG 3 cut(s) 376, 754, 826
BtsIMutI CAGTG 2 cut(s) 202, 456
Cac8I GCNNGC 3 cut(s) 60, 341, 345
CfoI GCGC 2 cut(s) 119, 323
Cfr10I RCCGGY 2 cut(s) 190, 715
Cfr13I GGNCC 3 cut(s) 13, 183, 357
Cfr42I CCGCGG 1 cut(s) 24
CseI GACGC 2 cut(s) 241, 319
Csp6I GTAC 3 cut(s) 31, 145, 325
CspAI ACCGGT 1 cut(s) 715
CviAII CATG 4 cut(s) 632, 732, 853, 875
CviQI GTAC 3 cut(s) 31, 145, 325
DdeI CTNAG 2 cut(s) 110, 301
DinI GGCGCC 1 cut(s) 118
DpnI GATC 9 cut(s) 95, 107, 267, 437, 507, 630, 642, 663, 768
DpnII GATC 9 cut(s) 93, 105, 265, 435, 505, 628, 640, 661, 766
DriI GACNNNNNGTC 1 cut(s) 220
Eam1104I CTCTTC 1 cut(s) 159
Eam1105I GACNNNNNGTC 1 cut(s) 220
EarI CTCTTC 1 cut(s) 159
Ecl136II GAGCTC 1 cut(s) 62
Eco147I AGGCCT 1 cut(s) 829
Eco24I GRGCYC 1 cut(s) 64
Eco47I GGWCC 1 cut(s) 357
Eco53kI GAGCTC 1 cut(s) 62
Eco57I CTGAAG 1 cut(s) 393
EcoICRI GAGCTC 1 cut(s) 62
EcoO109I RGGNCCY 1 cut(s) 183
EcoRII CCWGG 2 cut(s) 15, 463
EcoT22I ATGCAT 1 cut(s) 876
EcoT38I GRGCYC 1 cut(s) 64
EgeI GGCGCC 1 cut(s) 118
EheI GGCGCC 1 cut(s) 118
Esp3I CGTCTC 1 cut(s) 302
FaeI CATG 4 cut(s) 635, 735, 856, 878
FatI CATG 4 cut(s) 631, 731, 852, 874
FauNDI CATATG 1 cut(s) 760
FbaI TGATCA 1 cut(s) 766
Fnu4HI GCNGC 3 cut(s) 21, 710, 785
FokI GGATG 3 cut(s) 383, 741, 833
FriOI GRGCYC 1 cut(s) 64
Fsp4HI GCNGC 3 cut(s) 21, 710, 785
FspBI CTAG 3 cut(s) 314, 336, 543
GlaI GCGC 2 cut(s) 118, 322
GluI GCNGC 3 cut(s) 21, 710, 785
GsaI CCCAGC 2 cut(s) 378, 814
GsuI CTGGAG 1 cut(s) 782
HaeII RGCGCY 1 cut(s) 120
HaeIII GGCC 5 cut(s) 15, 20, 184, 601, 829
HapII CCGG 3 cut(s) 191, 625, 716
HgaI GACGC 2 cut(s) 241, 319
HhaI GCGC 2 cut(s) 119, 323
Hin1I GRCGYC 3 cut(s) 5, 117, 252
Hin1II CATG 4 cut(s) 635, 735, 856, 878
Hin6I GCGC 2 cut(s) 117, 321
HinP1I GCGC 2 cut(s) 117, 321
HincII GTYRAC 2 cut(s) 556, 685
HindII GTYRAC 2 cut(s) 556, 685
HindIII AAGCTT 1 cut(s) 584
HinfI GANTC 1 cut(s) 846
HpaII CCGG 3 cut(s) 191, 625, 716
HphI GGTGA 2 cut(s) 260, 730
Hpy166II GTNNAC 4 cut(s) 31, 428, 556, 685
Hpy188I TCNGA 6 cut(s) 66, 105, 113, 357, 412, 421
Hpy188III TCNNGA 5 cut(s) 91, 242, 296, 481, 530
Hpy8I GTNNAC 4 cut(s) 31, 428, 556, 685
Hpy99I CGWCG 4 cut(s) 10, 223, 257, 266
HpyAV CCTTC 3 cut(s) 284, 527, 612
HpyCH4III ACNGT 4 cut(s) 289, 451, 610, 886
HpyCH4IV ACGT 3 cut(s) 147, 218, 460
HpyCH4V TGCA 3 cut(s) 472, 712, 874
HpyF10VI GCNNNNNNNGC 2 cut(s) 123, 371
HpyF3I CTNAG 2 cut(s) 110, 301
HpySE526I ACGT 3 cut(s) 147, 218, 460
Hsp92I GRCGYC 3 cut(s) 5, 117, 252
Hsp92II CATG 4 cut(s) 635, 735, 856, 878
HspAI GCGC 2 cut(s) 117, 321
KasI GGCGCC 1 cut(s) 116
Ksp22I TGATCA 1 cut(s) 766
KspI CCGCGG 1 cut(s) 24
Kzo9I GATC 9 cut(s) 93, 105, 265, 435, 505, 628, 640, 661, 766
Lsp1109I GCAGC 2 cut(s) 696, 771
LweI GCATC 1 cut(s) 361
MaeI CTAG 3 cut(s) 314, 336, 543
MaeII ACGT 3 cut(s) 147, 218, 460
MaeIII GTNAC 4 cut(s) 256, 445, 610, 880
MalI GATC 9 cut(s) 95, 107, 267, 437, 507, 630, 642, 663, 768
MbiI CCGCTC 1 cut(s) 230
MboI GATC 9 cut(s) 93, 105, 265, 435, 505, 628, 640, 661, 766
MboII GAAGA 9 cut(s) 76, 79, 146, 156, 159, 162, 165, 399, 445
MflI RGATCY 3 cut(s) 105, 640, 661
MhlI GDGCHC 1 cut(s) 64
MluCI AATT 3 cut(s) 497, 561, 672
Mly113I GGCGCC 1 cut(s) 117
Mph1103I ATGCAT 1 cut(s) 876
MroXI GAANNNNTTC 1 cut(s) 864
MseI TTAA 1 cut(s) 582
MslI CAYNNNNRTG 1 cut(s) 759
MspA1I CMGCKG 1 cut(s) 23
MspI CCGG 3 cut(s) 191, 625, 716
MspR9I CCNGG 3 cut(s) 17, 465, 626
MvaI CCWGG 2 cut(s) 17, 465
MvnI CGCG 2 cut(s) 23, 323
MwoI GCNNNNNNNGC 2 cut(s) 123, 371
NarI GGCGCC 1 cut(s) 117
NciI CCSGG 1 cut(s) 626
NdeI CATATG 1 cut(s) 760
NdeII GATC 9 cut(s) 93, 105, 265, 435, 505, 628, 640, 661, 766
NlaIII CATG 4 cut(s) 635, 735, 856, 878
NlaIV GGNNCC 2 cut(s) 118, 359
NmuCI GTSAC 1 cut(s) 445
NsiI ATGCAT 1 cut(s) 876
NspI RCATGY 1 cut(s) 856
PceI AGGCCT 1 cut(s) 829
PcsI WCGNNNNNNNCGW 3 cut(s) 240, 249, 261
PdmI GAANNNNTTC 1 cut(s) 864
PfeI GAWTC 1 cut(s) 846
Pfl23II CGTACG 2 cut(s) 144, 324
PinAI ACCGGT 1 cut(s) 715
PkrI GCNGC 3 cut(s) 22, 711, 786
PluTI GGCGCC 1 cut(s) 120
Psp124BI GAGCTC 1 cut(s) 64
Psp6I CCWGG 2 cut(s) 15, 463
PspFI CCCAGC 2 cut(s) 374, 810
PspGI CCWGG 2 cut(s) 15, 463
PspLI CGTACG 2 cut(s) 144, 324
PspN4I GGNNCC 2 cut(s) 118, 359
PspPI GGNCC 3 cut(s) 13, 183, 357
PsuI RGATCY 3 cut(s) 105, 640, 661
RsaI GTAC 3 cut(s) 32, 146, 326
RsaNI GTAC 3 cut(s) 31, 145, 325
RseI CAYNNNNRTG 1 cut(s) 759
SacI GAGCTC 1 cut(s) 64
SacII CCGCGG 1 cut(s) 24
SaqAI TTAA 1 cut(s) 582
SatI GCNGC 3 cut(s) 21, 710, 785
Sau3AI GATC 9 cut(s) 93, 105, 265, 435, 505, 628, 640, 661, 766
Sau96I GGNCC 3 cut(s) 13, 183, 357
ScrFI CCNGG 3 cut(s) 17, 465, 626
SduI GDGCHC 1 cut(s) 64
SfaNI GCATC 1 cut(s) 361
SfcI CTRYAG 1 cut(s) 606
SfoI GGCGCC 1 cut(s) 118
Sfr303I CCGCGG 1 cut(s) 24
SgrBI CCGCGG 1 cut(s) 24
SinI GGWCC 1 cut(s) 357
SmiMI CAYNNNNRTG 1 cut(s) 759
Sse9I AATT 3 cut(s) 497, 561, 672
SseBI AGGCCT 1 cut(s) 829
SsiI CCGC 4 cut(s) 21, 23, 228, 271
SspDI GGCGCC 1 cut(s) 116
SspMI CTAG 3 cut(s) 314, 336, 543
SstI GAGCTC 1 cut(s) 64
StuI AGGCCT 1 cut(s) 829
StyD4I CCNGG 3 cut(s) 15, 463, 624
TaaI ACNGT 4 cut(s) 289, 451, 610, 886
TaiI ACGT 3 cut(s) 150, 221, 463
TaqI TCGA 3 cut(s) 243, 656, 670
TasI AATT 3 cut(s) 497, 561, 672
TauI GCSGC 1 cut(s) 23
TfiI GAWTC 1 cut(s) 846
Tru1I TTAA 1 cut(s) 582
Tru9I TTAA 1 cut(s) 582
TscAI CASTG 2 cut(s) 202, 456
TseFI GTSAC 1 cut(s) 445
TseI GCWGC 2 cut(s) 709, 784
Tsp45I GTSAC 1 cut(s) 445
TspDTI ATGAA 1 cut(s) 83
TspGWI ACGGA 3 cut(s) 383, 502, 632
TspRI CASTG 2 cut(s) 202, 456
VpaK11BI GGWCC 1 cut(s) 357
XapI RAATTY 1 cut(s) 497
XceI RCATGY 1 cut(s) 856
XcmI CCANNNNNNNNNTGG 1 cut(s) 51
XmnI GAANNNNTTC 1 cut(s) 864
XspI CTAG 3 cut(s) 314, 336, 543
Zsp2I ATGCAT 1 cut(s) 876
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.