AT3G42140

Ribonuclease H protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
3
OG0005646
Physical Location & Seq
Reverse (-)
14302060 .. 14303018
959 bp
Loading structure...
UTR
Exon/CDS
Intron
AT3G42140.1

Sequence Viewer

Length: 822 bp
ATGGCGGATAATCTCCAAAGACAGATGCAAGAAATTGCGCTAGGAGTACAAGAGGAAGCTATCAATCTCCTTATTGAACTATGTGATGAGGCGCTCAGGAAACCCAATTTAGCCTCATTACAAAACCGGTGCCCTAAGAACGTAGATGAAGAGGTGGTAGGCAGAATCCTGGAGATTCACAAAATCGAATTCCTTTTCCAATCTGAAGAATCCATGTTCTCAATACTCCGTCGAGGGCCATGGTCGTTTAATGATTGGATGTGCGTCATCCAAAGATGGACGAAATTGCACTCGGATGCAGAATTCAAGAGAATCCCATTCTGGATCCAAATCAGAGGAATACCCCTCCGCTTCCTCACTGCAAGGATTATTACTTCAATTGGTGAAAGAATGGGTCTGTTCCTTGAGACAAATTTGGGTCGCGATGTCAGTGTTCTGAAGTTTCAATACGAGAAACTCAAGAATTTTTGTACCACTTGTGGAATGCTGAGTCATGATGCCTCCGAATGTCCAACTTCCGGGAACCAAGGTCCTCATGCGGACGATGATGATGATGATGATGATAATGACGCAAATGAAGACCATCCCGATGTTCCTGGAGACAACCCTGACCAAGTTCATGGTCCAATGAATCAGCAACATCCGGAAGAGAGCACTGAAGATGAACACCAAAATGCGCCAAAAAGAGGAAAACTGAAGCCTCTTCTTCAACGTCTAACTATGGAAGTCCCTTGGTGTGTTGCAACATGCGCCAGGCCTATGCCACAGAAGATACTCAACACTGCGTGGCTAAAAGACAGAGAAGGGAATCATAAGTTCTAG
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
DUF4283 Exo_endo_phos_2 RNase_H RVT_1 zf-CCHC_4

Protein Analysis

273

Amino Acids

31.43

Weight (kDa)

5.1

Isoelectric Point (pI)

43.71

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
DUF4283 PF14111 33 - 95 1e-05 Domain of unknown function (DUF4283)
zf-CCHC_4 PF14392 140 - 171 3.6e-10 Zinc knuckle
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 1 cut(s) 129
AccII CGCG 1 cut(s) 423
AccIII TCCGGA 1 cut(s) 643
AciI CCGC 3 cut(s) 5, 349, 539
AclWI GGATC 2 cut(s) 319, 332
AcsI RAATTY 4 cut(s) 188, 302, 412, 463
AcuI CTGAAG 4 cut(s) 225, 458, 678, 716
AdeI CACNNNGTG 1 cut(s) 786
AfaI GTAC 2 cut(s) 48, 472
AfiI CCNNNNNNNGG 2 cut(s) 518, 686
AgeI ACCGGT 1 cut(s) 126
AgsI TTSAA 5 cut(s) 77, 307, 378, 446, 710
AjnI CCWGG 3 cut(s) 168, 595, 752
AluBI AGCT 1 cut(s) 59
AluI AGCT 1 cut(s) 59
Alw21I GWGCWC 1 cut(s) 656
Alw26I GTCTC 2 cut(s) 401, 594
AlwI GGATC 2 cut(s) 319, 332
Aor13HI TCCGGA 1 cut(s) 643
AoxI GGCC 2 cut(s) 236, 755
ApoI RAATTY 4 cut(s) 188, 302, 412, 463
AsiGI ACCGGT 1 cut(s) 126
AspLEI GCGC 4 cut(s) 40, 94, 679, 752
AspS9I GGNCC 3 cut(s) 236, 530, 623
AsuC2I CCSGG 1 cut(s) 520
AsuHPI GGTGA 1 cut(s) 395
AvaII GGWCC 2 cut(s) 530, 623
BaeGI GKGCMC 1 cut(s) 134
BamHI GGATCC 1 cut(s) 324
BanI GGYRCC 1 cut(s) 129
BarI GAAGNNNNNNTAC 2 cut(s) 431, 463
BbsI GAAGAC 1 cut(s) 585
Bbv12I GWGCWC 1 cut(s) 656
BccI CCATC 2 cut(s) 270, 591
BciT130I CCWGG 3 cut(s) 170, 597, 754
BcnI CCSGG 1 cut(s) 520
BcoDI GTCTC 2 cut(s) 401, 594
BfaI CTAG 2 cut(s) 41, 820
BfoI RGCGCY 1 cut(s) 95
Bme1390I CCNGG 4 cut(s) 170, 520, 597, 754
Bme18I GGWCC 2 cut(s) 530, 623
BmgT120I GGNCC 3 cut(s) 236, 530, 623
BmiI GGNNCC 3 cut(s) 131, 326, 524
BmrFI CCNGG 4 cut(s) 170, 520, 597, 754
BmsI GCATC 3 cut(s) 15, 286, 487
BpiI GAAGAC 1 cut(s) 585
BpmI CTGGAG 2 cut(s) 191, 618
Bpu10I CCTNAGC 1 cut(s) 95
BpuEI CTTGAG 2 cut(s) 425, 443
BpuMI CCSGG 1 cut(s) 520
BsaBI GATNNNNATC 1 cut(s) 329
BsaJI CCNNGG 3 cut(s) 239, 526, 731
BsaWI WCCGGW 2 cut(s) 126, 643
Bsc4I CCNNNNNNNGG 2 cut(s) 518, 686
Bse118I RCCGGY 1 cut(s) 126
Bse8I GATNNNNATC 1 cut(s) 329
BseAI TCCGGA 1 cut(s) 643
BseBI CCWGG 3 cut(s) 170, 597, 754
BseDI CCNNGG 3 cut(s) 239, 526, 731
BseGI GGATG 5 cut(s) 264, 267, 301, 583, 640
BseJI GATNNNNATC 1 cut(s) 329
BseLI CCNNNNNNNGG 2 cut(s) 518, 686
BseMII CTCAG 2 cut(s) 109, 479
BseSI GKGCMC 1 cut(s) 134
Bsh1236I CGCG 1 cut(s) 423
BshFI GGCC 2 cut(s) 238, 757
BshNI GGYRCC 1 cut(s) 129
BshTI ACCGGT 1 cut(s) 126
BsiHKAI GWGCWC 1 cut(s) 656
BsiSI CCGG 3 cut(s) 127, 519, 644
BslFI GGGAC 1 cut(s) 713
BslI CCNNNNNNNGG 2 cut(s) 518, 686
BsmAI GTCTC 2 cut(s) 401, 594
BsmFI GGGAC 1 cut(s) 713
BsmI GAATGC 1 cut(s) 489
BsnI GGCC 2 cut(s) 238, 757
Bsp1286I GDGCHC 2 cut(s) 134, 656
Bsp13I TCCGGA 1 cut(s) 643
Bsp143I GATC 1 cut(s) 324
Bsp19I CCATGG 1 cut(s) 239
Bsp68I TCGCGA 1 cut(s) 423
BspACI CCGC 3 cut(s) 5, 349, 539
BspANI GGCC 2 cut(s) 238, 757
BspCNI CTCAG 2 cut(s) 108, 480
BspEI TCCGGA 1 cut(s) 643
BspFNI CGCG 1 cut(s) 423
BspHI TCATGA 1 cut(s) 493
BspLI GGNNCC 3 cut(s) 131, 326, 524
BspPI GGATC 2 cut(s) 319, 332
BspT107I GGYRCC 1 cut(s) 129
BsrFI RCCGGY 1 cut(s) 126
BssAI RCCGGY 1 cut(s) 126
BssECI CCNNGG 3 cut(s) 239, 526, 731
BssMI GATC 1 cut(s) 324
BssT1I CCWWGG 3 cut(s) 239, 526, 731
Bst2UI CCWGG 3 cut(s) 170, 597, 754
Bst6I CTCTTC 3 cut(s) 144, 642, 708
BstDEI CTNAG 3 cut(s) 95, 135, 488
BstDSI CCRYGG 1 cut(s) 239
BstF5I GGATG 5 cut(s) 264, 267, 301, 583, 640
BstFNI CGCG 1 cut(s) 423
BstH2I RGCGCY 1 cut(s) 95
BstHHI GCGC 4 cut(s) 40, 94, 679, 752
BstKTI GATC 1 cut(s) 327
BstMAI GTCTC 2 cut(s) 401, 594
BstMBI GATC 1 cut(s) 324
BstMWI GCNNNNNNNGC 1 cut(s) 749
BstNI CCWGG 3 cut(s) 170, 597, 754
BstNSI RCATGY 1 cut(s) 750
BstSCI CCNGG 4 cut(s) 168, 518, 595, 752
BstSLI GKGCMC 1 cut(s) 134
BstUI CGCG 1 cut(s) 423
BstV2I GAAGAC 1 cut(s) 585
BstX2I RGATCY 1 cut(s) 324
BstXI CCANNNNNNTGG 1 cut(s) 620
BstYI RGATCY 1 cut(s) 324
BsuRI GGCC 2 cut(s) 238, 757
BtgI CCRYGG 1 cut(s) 239
BtgZI GCGATG 1 cut(s) 438
BtsCI GGATG 5 cut(s) 264, 267, 301, 583, 640
BtsI GCAGTG 2 cut(s) 357, 780
BtsIMutI CAGTG 4 cut(s) 357, 436, 654, 780
BtuMI TCGCGA 1 cut(s) 423
CciI TCATGA 1 cut(s) 493
CfoI GCGC 4 cut(s) 40, 94, 679, 752
Cfr10I RCCGGY 1 cut(s) 126
Cfr13I GGNCC 3 cut(s) 236, 530, 623
CseI GACGC 2 cut(s) 253, 578
Csp6I GTAC 2 cut(s) 47, 471
CspAI ACCGGT 1 cut(s) 126
CviAII CATG 6 cut(s) 214, 240, 494, 536, 620, 747
CviJI RGCY 6 cut(s) 59, 113, 238, 700, 757, 790
CviKI_1 RGCY 6 cut(s) 59, 113, 238, 700, 757, 790
CviQI GTAC 2 cut(s) 47, 471
DdeI CTNAG 3 cut(s) 95, 135, 488
DpnI GATC 1 cut(s) 326
DpnII GATC 1 cut(s) 324
DraIII CACNNNGTG 1 cut(s) 786
Eam1104I CTCTTC 3 cut(s) 144, 642, 708
EarI CTCTTC 3 cut(s) 144, 642, 708
EciI GGCGGA 1 cut(s) 20
Eco130I CCWWGG 3 cut(s) 239, 526, 731
Eco147I AGGCCT 1 cut(s) 757
Eco47I GGWCC 2 cut(s) 530, 623
Eco57I CTGAAG 4 cut(s) 225, 458, 678, 716
EcoO109I RGGNCCY 1 cut(s) 530
EcoRI GAATTC 2 cut(s) 188, 302
EcoRII CCWGG 3 cut(s) 168, 595, 752
EcoT14I CCWWGG 3 cut(s) 239, 526, 731
ErhI CCWWGG 3 cut(s) 239, 526, 731
FaeI CATG 6 cut(s) 217, 243, 497, 539, 623, 750
FaqI GGGAC 1 cut(s) 713
FatI CATG 6 cut(s) 213, 239, 493, 535, 619, 746
FokI GGATG 5 cut(s) 254, 271, 308, 570, 627
FspBI CTAG 2 cut(s) 41, 820
GlaI GCGC 4 cut(s) 39, 93, 678, 751
GsuI CTGGAG 2 cut(s) 191, 618
HaeII RGCGCY 1 cut(s) 95
HaeIII GGCC 2 cut(s) 238, 757
HapII CCGG 3 cut(s) 127, 519, 644
HgaI GACGC 2 cut(s) 253, 578
HhaI GCGC 4 cut(s) 40, 94, 679, 752
Hin1II CATG 6 cut(s) 217, 243, 497, 539, 623, 750
Hin6I GCGC 4 cut(s) 38, 92, 677, 750
HinP1I GCGC 4 cut(s) 38, 92, 677, 750
HinfI GANTC 7 cut(s) 165, 175, 209, 312, 490, 631, 808
HpaII CCGG 3 cut(s) 127, 519, 644
HphI GGTGA 1 cut(s) 395
Hpy188I TCNGA 5 cut(s) 205, 295, 335, 438, 505
Hpy188III TCNNGA 8 cut(s) 97, 307, 322, 422, 460, 494, 587, 644
Hpy99I CGWCG 1 cut(s) 234
HpyAV CCTTC 1 cut(s) 797
HpyCH4IV ACGT 2 cut(s) 141, 712
HpyCH4V TGCA 5 cut(s) 28, 289, 299, 362, 743
HpyF10VI GCNNNNNNNGC 1 cut(s) 749
HpyF3I CTNAG 3 cut(s) 95, 135, 488
HpySE526I ACGT 2 cut(s) 141, 712
Hsp92II CATG 6 cut(s) 217, 243, 497, 539, 623, 750
HspAI GCGC 4 cut(s) 38, 92, 677, 750
Kpn2I TCCGGA 1 cut(s) 643
Kzo9I GATC 1 cut(s) 324
LweI GCATC 3 cut(s) 15, 286, 487
MaeI CTAG 2 cut(s) 41, 820
MaeII ACGT 2 cut(s) 141, 712
MalI GATC 1 cut(s) 326
MboI GATC 1 cut(s) 324
MboII GAAGA 8 cut(s) 161, 218, 590, 659, 671, 695, 698, 781
MfeI CAATTG 1 cut(s) 378
MflI RGATCY 1 cut(s) 324
MhlI GDGCHC 2 cut(s) 134, 656
MluCI AATT 8 cut(s) 33, 106, 188, 284, 302, 378, 412, 463
MlyI GAGTC 1 cut(s) 499
MmeI TCCRAC 1 cut(s) 536
MroI TCCGGA 1 cut(s) 643
MseI TTAA 1 cut(s) 249
MslI CAYNNNNRTG 3 cut(s) 294, 588, 672
MspI CCGG 3 cut(s) 127, 519, 644
MspR9I CCNGG 4 cut(s) 170, 520, 597, 754
MunI CAATTG 1 cut(s) 378
Mva1269I GAATGC 1 cut(s) 489
MvaI CCWGG 3 cut(s) 170, 597, 754
MvnI CGCG 1 cut(s) 423
MwoI GCNNNNNNNGC 1 cut(s) 749
NciI CCSGG 1 cut(s) 520
NcoI CCATGG 1 cut(s) 239
NdeII GATC 1 cut(s) 324
NlaIII CATG 6 cut(s) 217, 243, 497, 539, 623, 750
NlaIV GGNNCC 3 cut(s) 131, 326, 524
NruI TCGCGA 1 cut(s) 423
NspI RCATGY 1 cut(s) 750
PagI TCATGA 1 cut(s) 493
PceI AGGCCT 1 cut(s) 757
PctI GAATGC 1 cut(s) 489
PfeI GAWTC 6 cut(s) 165, 175, 209, 312, 631, 808
PfoI TCCNGGA 3 cut(s) 168, 518, 595
PinAI ACCGGT 1 cut(s) 126
PleI GAGTC 1 cut(s) 498
PpsI GAGTC 1 cut(s) 498
PpuMI RGGWCCY 1 cut(s) 530
Psp5II RGGWCCY 1 cut(s) 530
Psp6I CCWGG 3 cut(s) 168, 595, 752
PspGI CCWGG 3 cut(s) 168, 595, 752
PspN4I GGNNCC 3 cut(s) 131, 326, 524
PspPI GGNCC 3 cut(s) 236, 530, 623
PspPPI RGGWCCY 1 cut(s) 530
PsuI RGATCY 1 cut(s) 324
RruI TCGCGA 1 cut(s) 423
RsaI GTAC 2 cut(s) 48, 472
RsaNI GTAC 2 cut(s) 47, 471
RseI CAYNNNNRTG 3 cut(s) 294, 588, 672
SaqAI TTAA 1 cut(s) 249
Sau3AI GATC 1 cut(s) 324
Sau96I GGNCC 3 cut(s) 236, 530, 623
SchI GAGTC 1 cut(s) 499
ScrFI CCNGG 4 cut(s) 170, 520, 597, 754
SduI GDGCHC 2 cut(s) 134, 656
SetI ASST 5 cut(s) 61, 144, 156, 532, 715
SfaNI GCATC 3 cut(s) 15, 286, 487
SinI GGWCC 2 cut(s) 530, 623
SmiMI CAYNNNNRTG 3 cut(s) 294, 588, 672
SmlI CTYRAG 2 cut(s) 404, 458
SmoI CTYRAG 2 cut(s) 404, 458
Sse9I AATT 8 cut(s) 33, 106, 188, 284, 302, 378, 412, 463
SseBI AGGCCT 1 cut(s) 757
SsiI CCGC 3 cut(s) 5, 349, 539
SspMI CTAG 2 cut(s) 41, 820
StuI AGGCCT 1 cut(s) 757
StyD4I CCNGG 4 cut(s) 168, 518, 595, 752
StyI CCWWGG 3 cut(s) 239, 526, 731
TaiI ACGT 2 cut(s) 144, 715
TaqI TCGA 2 cut(s) 186, 232
TasI AATT 8 cut(s) 33, 106, 188, 284, 302, 378, 412, 463
TatI WGTACW 1 cut(s) 46
TfiI GAWTC 6 cut(s) 165, 175, 209, 312, 631, 808
Tru1I TTAA 1 cut(s) 249
Tru9I TTAA 1 cut(s) 249
TscAI CASTG 4 cut(s) 364, 436, 661, 787
TspDTI ATGAA 5 cut(s) 162, 591, 608, 644, 678
TspGWI ACGGA 1 cut(s) 218
TspRI CASTG 4 cut(s) 364, 436, 661, 787
VpaK11BI GGWCC 2 cut(s) 530, 623
XapI RAATTY 4 cut(s) 188, 302, 412, 463
XceI RCATGY 1 cut(s) 750
XspI CTAG 2 cut(s) 41, 820
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.