FvH4_6g11400

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

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb6
OG0002737
Physical Location & Seq
Forward (+)
6823085 .. 6825556
2472 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_6g11400.t1

Sequence Viewer

Length: 888 bp
ATGGCGACGATGGGCCAGACGGCCGCGGAGGTTTACGAGCCGAAGCTAATCCAACTGTGGCGAGCTCTCGTAAACTGGCTCAGCTTCTTCTTCCAGATCCTCCGAGGCGCTCCCTGCCTCGCTCATTTGCTCTCCTACGTCCCCCTCCTCGCTTCTCCTCCTTCTTTCCGGCCTCTCCCCGTCGCAGAAATCCCTCTCAACGACTCGTCGTCCTCCGCCCACGTCAACCTCGAAAACGGCGTCGTATCCGACGATCACCCCCTTCCGAAGCTCACGGTAGTTCTCGACTTAGACGAGACGCTAGTGTGTGCATATGAGACATCTAGCGTGCCTGCTATTGTTAGGACGCAAGCAACAGATGCTGGTTTGAAGTGGTTCGAGATAGAATGTGTATCTTCGGACAAGGACTCTGATGGTAAACCGAAGATCAGTTATGTGACAGTGTTTGAACGTCCTGGTTTGCATGAGTTTTTGAAACGGATTGGTGAATTTGCTGATCTTGTCCTCTTCACTGCTGGTCTTGAAGGTTATGCTAGGCCCCTTGTTGACAGAATAGATGTGGAGAATCGATTCAAGTTTCGGCTTTATCGGCCTTCTACAGTTACCACGGAGAAGCGGGATCATGTGAAAGATATATCTTGTATATCGAAAGATCTCTGTCGAATTGTTATTGTTGATAACAACCCATTTAGTTTTCTGCTGCAACCGCTGAATGGAGTTCCATGCATTCCATTTTCTGCTGGACATCCGTATGATGATCAGCTCTTGGAGGTCCTGCTTCCCCTACTCAAACACCTTGGCCAGCAAAAAGATGTGAGGCCTGTGCTTTATGAGAGATTCCATATGCCTGAATGGTTTCAAATGCATGGAATTACTGTTTCCGGATAG

Protein Analysis

296

Amino Acids

33.2

Weight (kDa)

5.6

Isoelectric Point (pI)

36.14

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
NIF PF03031 91 - 273 3.1e-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)
AccII CGCG 1 cut(s) 26
AccIII TCCGGA 1 cut(s) 881
AciI CCGC 5 cut(s) 24, 26, 216, 616, 707
AclWI GGATC 2 cut(s) 91, 627
AcoI YGGCCR 2 cut(s) 21, 799
AcsI RAATTY 1 cut(s) 488
AcyI GRCGYC 1 cut(s) 240
AfiI CCNNNNNNNGG 1 cut(s) 713
AgsI TTSAA 6 cut(s) 370, 449, 475, 524, 574, 860
AhdI GACNNNNNGTC 1 cut(s) 208
AjiI CACGTC 1 cut(s) 223
AjnI CCWGG 1 cut(s) 454
AluBI AGCT 5 cut(s) 46, 65, 84, 271, 763
AluI AGCT 5 cut(s) 46, 65, 84, 271, 763
Alw21I GWGCWC 1 cut(s) 67
Alw26I GTCTC 2 cut(s) 290, 311
AlwI GGATC 2 cut(s) 91, 627
AlwNI CAGNNNCTG 1 cut(s) 362
Aor13HI TCCGGA 1 cut(s) 881
AoxI GGCC 7 cut(s) 13, 21, 170, 536, 590, 799, 818
ApeKI GCWGC 1 cut(s) 700
ApoI RAATTY 1 cut(s) 488
ArsI GACNNNNNNTTYG 2 cut(s) 225, 257
Asp700I GAANNNNTTC 3 cut(s) 374, 569, 855
AspLEI GCGC 1 cut(s) 110
AspS9I GGNCC 3 cut(s) 13, 537, 772
AsuHPI GGTGA 2 cut(s) 248, 497
AvaII GGWCC 1 cut(s) 772
BalI TGGCCA 1 cut(s) 801
BanII GRGCYC 1 cut(s) 67
Bbv12I GWGCWC 1 cut(s) 67
BbvI GCAGC 1 cut(s) 687
BccI CCATC 2 cut(s) 4, 407
BceAI ACGGC 2 cut(s) 36, 253
BciT130I CCWGG 1 cut(s) 456
BciVI GTATCC 1 cut(s) 256
BclI TGATCA 1 cut(s) 757
BcoDI GTCTC 2 cut(s) 290, 311
BfaI CTAG 3 cut(s) 302, 324, 534
BfmI CTRYAG 1 cut(s) 597
BfoI RGCGCY 1 cut(s) 111
BfuI GTATCC 1 cut(s) 256
BglII AGATCT 1 cut(s) 652
BisI GCNGC 2 cut(s) 24, 701
BlpI GCTNAGC 1 cut(s) 80
BlsI GCNGC 2 cut(s) 25, 702
Bme1390I CCNGG 1 cut(s) 456
Bme18I GGWCC 1 cut(s) 772
BmeRI GACNNNNNGTC 1 cut(s) 208
BmgBI CACGTC 1 cut(s) 223
BmgT120I GGNCC 3 cut(s) 13, 537, 772
BmiI GGNNCC 1 cut(s) 539
BmrFI CCNGG 1 cut(s) 456
BmsI GCATC 1 cut(s) 349
Bpu1102I GCTNAGC 1 cut(s) 80
Bsa29I ATCGAT 1 cut(s) 568
BsaHI GRCGYC 1 cut(s) 240
BsaJI CCNNGG 4 cut(s) 24, 103, 606, 796
BsaWI WCCGGW 1 cut(s) 881
Bsc4I CCNNNNNNNGG 1 cut(s) 713
Bse1I ACTGG 1 cut(s) 80
BseAI TCCGGA 1 cut(s) 881
BseBI CCWGG 1 cut(s) 456
BseCI ATCGAT 1 cut(s) 568
BseDI CCNNGG 4 cut(s) 24, 103, 606, 796
BseGI GGATG 1 cut(s) 745
BseLI CCNNNNNNNGG 1 cut(s) 713
BseMII CTCAG 1 cut(s) 94
BseNI ACTGG 1 cut(s) 80
BseRI GAGGAG 2 cut(s) 137, 147
BseX3I CGGCCG 1 cut(s) 21
BseXI GCAGC 1 cut(s) 687
Bsh1236I CGCG 1 cut(s) 26
Bsh1285I CGRYCG 1 cut(s) 24
BshFI GGCC 7 cut(s) 15, 23, 172, 538, 592, 801, 820
BshVI ATCGAT 1 cut(s) 568
BsiEI CGRYCG 1 cut(s) 24
BsiHKAI GWGCWC 1 cut(s) 67
BsiSI CCGG 2 cut(s) 169, 882
BslFI GGGAC 1 cut(s) 125
BslI CCNNNNNNNGG 1 cut(s) 713
BsmAI GTCTC 2 cut(s) 290, 311
BsmBI CGTCTC 1 cut(s) 290
BsmFI GGGAC 1 cut(s) 125
BsmI GAATGC 1 cut(s) 726
BsnI GGCC 7 cut(s) 15, 23, 172, 538, 592, 801, 820
Bsp1286I GDGCHC 1 cut(s) 67
Bsp13I TCCGGA 1 cut(s) 881
Bsp143I GATC 7 cut(s) 96, 253, 426, 496, 619, 652, 757
Bsp1720I GCTNAGC 1 cut(s) 80
BspACI CCGC 5 cut(s) 24, 26, 216, 616, 707
BspANI GGCC 7 cut(s) 15, 23, 172, 538, 592, 801, 820
BspCNI CTCAG 1 cut(s) 93
BspDI ATCGAT 1 cut(s) 568
BspEI TCCGGA 1 cut(s) 881
BspFNI CGCG 1 cut(s) 26
BspLI GGNNCC 1 cut(s) 539
BspPI GGATC 2 cut(s) 91, 627
BsrI ACTGG 1 cut(s) 80
BssECI CCNNGG 4 cut(s) 24, 103, 606, 796
BssMI GATC 7 cut(s) 96, 253, 426, 496, 619, 652, 757
BssNI GRCGYC 1 cut(s) 240
BssT1I CCWWGG 1 cut(s) 796
Bst2UI CCWGG 1 cut(s) 456
Bst4CI ACNGT 5 cut(s) 57, 277, 442, 601, 877
Bst6I CTCTTC 1 cut(s) 512
BstACI GRCGYC 1 cut(s) 240
BstAPI GCANNNNNTGC 1 cut(s) 359
BstC8I GCNNGC 5 cut(s) 63, 329, 333, 351, 803
BstDEI CTNAG 2 cut(s) 80, 289
BstDSI CCRYGG 2 cut(s) 24, 606
BstF5I GGATG 1 cut(s) 745
BstFNI CGCG 1 cut(s) 26
BstH2I RGCGCY 1 cut(s) 111
BstHHI GCGC 1 cut(s) 110
BstKTI GATC 7 cut(s) 99, 256, 429, 499, 622, 655, 760
BstMAI GTCTC 2 cut(s) 290, 311
BstMBI GATC 7 cut(s) 96, 253, 426, 496, 619, 652, 757
BstMCI CGRYCG 1 cut(s) 24
BstMWI GCNNNNNNNGC 4 cut(s) 114, 359, 589, 706
BstNI CCWGG 1 cut(s) 456
BstSCI CCNGG 1 cut(s) 454
BstSFI CTRYAG 1 cut(s) 597
BstUI CGCG 1 cut(s) 26
BstV1I GCAGC 1 cut(s) 687
BstX2I RGATCY 2 cut(s) 96, 652
BstYI RGATCY 2 cut(s) 96, 652
BstZI CGGCCG 1 cut(s) 21
Bsu15I ATCGAT 1 cut(s) 568
BsuI GTATCC 1 cut(s) 256
BsuRI GGCC 7 cut(s) 15, 23, 172, 538, 592, 801, 820
BsuTUI ATCGAT 1 cut(s) 568
BtgI CCRYGG 2 cut(s) 24, 606
BtrI CACGTC 1 cut(s) 223
BtsCI GGATG 1 cut(s) 745
BtsI GCAGTG 1 cut(s) 510
BtsIMutI CAGTG 2 cut(s) 447, 510
Cac8I GCNNGC 5 cut(s) 63, 329, 333, 351, 803
CaiI CAGNNNCTG 1 cut(s) 362
CfoI GCGC 1 cut(s) 110
Cfr13I GGNCC 3 cut(s) 13, 537, 772
Cfr42I CCGCGG 1 cut(s) 27
ClaI ATCGAT 1 cut(s) 568
CseI GACGC 3 cut(s) 229, 307, 355
CviAII CATG 4 cut(s) 464, 623, 723, 866
DdeI CTNAG 2 cut(s) 80, 289
DpnI GATC 7 cut(s) 98, 255, 428, 498, 621, 654, 759
DpnII GATC 7 cut(s) 96, 253, 426, 496, 619, 652, 757
DriI GACNNNNNGTC 1 cut(s) 208
EaeI YGGCCR 2 cut(s) 21, 799
EagI CGGCCG 1 cut(s) 21
Eam1104I CTCTTC 1 cut(s) 512
Eam1105I GACNNNNNGTC 1 cut(s) 208
EarI CTCTTC 1 cut(s) 512
EciI GGCGGA 1 cut(s) 205
Ecl136II GAGCTC 1 cut(s) 65
EclXI CGGCCG 1 cut(s) 21
Eco130I CCWWGG 1 cut(s) 796
Eco147I AGGCCT 1 cut(s) 820
Eco24I GRGCYC 1 cut(s) 67
Eco47I GGWCC 1 cut(s) 772
Eco52I CGGCCG 1 cut(s) 21
Eco53kI GAGCTC 1 cut(s) 65
EcoICRI GAGCTC 1 cut(s) 65
EcoO109I RGGNCCY 2 cut(s) 537, 772
EcoRII CCWGG 1 cut(s) 454
EcoT14I CCWWGG 1 cut(s) 796
EcoT22I ATGCAT 2 cut(s) 728, 867
EcoT38I GRGCYC 1 cut(s) 67
ErhI CCWWGG 1 cut(s) 796
Esp3I CGTCTC 1 cut(s) 290
FaeI CATG 4 cut(s) 467, 626, 726, 869
FaqI GGGAC 1 cut(s) 125
FatI CATG 4 cut(s) 463, 622, 722, 865
FauI CCCGC 1 cut(s) 609
FauNDI CATATG 2 cut(s) 313, 843
FbaI TGATCA 1 cut(s) 757
Fnu4HI GCNGC 2 cut(s) 24, 701
FokI GGATG 1 cut(s) 732
FriOI GRGCYC 1 cut(s) 67
Fsp4HI GCNGC 2 cut(s) 24, 701
FspBI CTAG 3 cut(s) 302, 324, 534
GlaI GCGC 1 cut(s) 109
GluI GCNGC 2 cut(s) 24, 701
HaeII RGCGCY 1 cut(s) 111
HaeIII GGCC 7 cut(s) 15, 23, 172, 538, 592, 801, 820
HapII CCGG 2 cut(s) 169, 882
HgaI GACGC 3 cut(s) 229, 307, 355
HhaI GCGC 1 cut(s) 110
Hin1I GRCGYC 1 cut(s) 240
Hin1II CATG 4 cut(s) 467, 626, 726, 869
Hin6I GCGC 1 cut(s) 108
HinP1I GCGC 1 cut(s) 108
HincII GTYRAC 2 cut(s) 226, 547
HindII GTYRAC 2 cut(s) 226, 547
HinfI GANTC 5 cut(s) 203, 407, 565, 570, 837
HpaII CCGG 2 cut(s) 169, 882
HphI GGTGA 2 cut(s) 248, 497
Hpy166II GTNNAC 5 cut(s) 34, 73, 226, 419, 547
Hpy188I TCNGA 5 cut(s) 104, 250, 267, 400, 412
Hpy188III TCNNGA 5 cut(s) 94, 284, 379, 521, 882
Hpy8I GTNNAC 5 cut(s) 34, 73, 226, 419, 547
Hpy99I CGWCG 5 cut(s) 10, 185, 211, 245, 254
HpyAV CCTTC 4 cut(s) 171, 272, 518, 603
HpyCH4III ACNGT 5 cut(s) 57, 277, 442, 601, 877
HpyCH4IV ACGT 3 cut(s) 138, 222, 451
HpyCH4V TGCA 5 cut(s) 311, 463, 703, 726, 865
HpyF10VI GCNNNNNNNGC 4 cut(s) 114, 359, 589, 706
HpyF3I CTNAG 2 cut(s) 80, 289
HpySE526I ACGT 3 cut(s) 138, 222, 451
Hsp92I GRCGYC 1 cut(s) 240
Hsp92II CATG 4 cut(s) 467, 626, 726, 869
HspAI GCGC 1 cut(s) 108
Kpn2I TCCGGA 1 cut(s) 881
Ksp22I TGATCA 1 cut(s) 757
KspI CCGCGG 1 cut(s) 27
Kzo9I GATC 7 cut(s) 96, 253, 426, 496, 619, 652, 757
LmnI GCTCC 1 cut(s) 115
Lsp1109I GCAGC 1 cut(s) 687
LweI GCATC 1 cut(s) 349
MaeI CTAG 3 cut(s) 302, 324, 534
MaeII ACGT 3 cut(s) 138, 222, 451
MaeIII GTNAC 2 cut(s) 436, 601
MalI GATC 7 cut(s) 98, 255, 428, 498, 621, 654, 759
MboI GATC 7 cut(s) 96, 253, 426, 496, 619, 652, 757
MboII GAAGA 5 cut(s) 79, 82, 387, 436, 499
MflI RGATCY 2 cut(s) 96, 652
MhlI GDGCHC 1 cut(s) 67
MlsI TGGCCA 1 cut(s) 801
MluCI AATT 3 cut(s) 488, 663, 870
MluNI TGGCCA 1 cut(s) 801
MlyI GAGTC 2 cut(s) 197, 401
MmeI TCCRAC 2 cut(s) 76, 273
Mox20I TGGCCA 1 cut(s) 801
Mph1103I ATGCAT 2 cut(s) 728, 867
MroI TCCGGA 1 cut(s) 881
MroXI GAANNNNTTC 3 cut(s) 374, 569, 855
MscI TGGCCA 1 cut(s) 801
MslI CAYNNNNRTG 1 cut(s) 750
Msp20I TGGCCA 1 cut(s) 801
MspA1I CMGCKG 2 cut(s) 26, 709
MspI CCGG 2 cut(s) 169, 882
MspR9I CCNGG 1 cut(s) 456
Mva1269I GAATGC 1 cut(s) 726
MvaI CCWGG 1 cut(s) 456
MvnI CGCG 1 cut(s) 26
MwoI GCNNNNNNNGC 4 cut(s) 114, 359, 589, 706
NdeI CATATG 2 cut(s) 313, 843
NdeII GATC 7 cut(s) 96, 253, 426, 496, 619, 652, 757
NlaIII CATG 4 cut(s) 467, 626, 726, 869
NlaIV GGNNCC 1 cut(s) 539
NmuCI GTSAC 1 cut(s) 436
NsiI ATGCAT 2 cut(s) 728, 867
PceI AGGCCT 1 cut(s) 820
PcsI WCGNNNNNNNCGW 4 cut(s) 228, 237, 249, 291
PctI GAATGC 1 cut(s) 726
PdmI GAANNNNTTC 3 cut(s) 374, 569, 855
PfeI GAWTC 3 cut(s) 565, 570, 837
PkrI GCNGC 2 cut(s) 25, 702
PleI GAGTC 2 cut(s) 197, 401
PpsI GAGTC 2 cut(s) 197, 401
PpuMI RGGWCCY 1 cut(s) 772
Psp124BI GAGCTC 1 cut(s) 67
Psp5II RGGWCCY 1 cut(s) 772
Psp6I CCWGG 1 cut(s) 454
PspGI CCWGG 1 cut(s) 454
PspN4I GGNNCC 1 cut(s) 539
PspPI GGNCC 3 cut(s) 13, 537, 772
PspPPI RGGWCCY 1 cut(s) 772
PstNI CAGNNNCTG 1 cut(s) 362
PsuI RGATCY 2 cut(s) 96, 652
RseI CAYNNNNRTG 1 cut(s) 750
SacI GAGCTC 1 cut(s) 67
SacII CCGCGG 1 cut(s) 27
SatI GCNGC 2 cut(s) 24, 701
Sau3AI GATC 7 cut(s) 96, 253, 426, 496, 619, 652, 757
Sau96I GGNCC 3 cut(s) 13, 537, 772
SchI GAGTC 2 cut(s) 197, 401
ScrFI CCNGG 1 cut(s) 456
SduI GDGCHC 1 cut(s) 67
SfaNI GCATC 1 cut(s) 349
SfcI CTRYAG 1 cut(s) 597
Sfr303I CCGCGG 1 cut(s) 27
SgrBI CCGCGG 1 cut(s) 27
SinI GGWCC 1 cut(s) 772
SmiMI CAYNNNNRTG 1 cut(s) 750
Sse9I AATT 3 cut(s) 488, 663, 870
SseBI AGGCCT 1 cut(s) 820
SsiI CCGC 5 cut(s) 24, 26, 216, 616, 707
SspMI CTAG 3 cut(s) 302, 324, 534
SstI GAGCTC 1 cut(s) 67
StuI AGGCCT 1 cut(s) 820
StyD4I CCNGG 1 cut(s) 454
StyI CCWWGG 1 cut(s) 796
TaaI ACNGT 5 cut(s) 57, 277, 442, 601, 877
TaiI ACGT 3 cut(s) 141, 225, 454
TaqI TCGA 6 cut(s) 231, 285, 378, 568, 647, 661
TasI AATT 3 cut(s) 488, 663, 870
TauI GCSGC 1 cut(s) 26
TfiI GAWTC 3 cut(s) 565, 570, 837
TscAI CASTG 2 cut(s) 447, 517
TseFI GTSAC 1 cut(s) 436
TseI GCWGC 1 cut(s) 700
Tsp45I GTSAC 1 cut(s) 436
TspGWI ACGGA 3 cut(s) 493, 623, 738
TspRI CASTG 2 cut(s) 447, 517
VpaK11BI GGWCC 1 cut(s) 772
XapI RAATTY 1 cut(s) 488
XmnI GAANNNNTTC 3 cut(s) 374, 569, 855
XspI CTAG 3 cut(s) 302, 324, 534
Zsp2I ATGCAT 2 cut(s) 728, 867
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.