RchiOBHm_Chr3g0457171

RNA polymerase II-associated protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
3
OG0005138
Physical Location & Seq
Reverse (-)
6371355 .. 6373461
2107 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ42393

Sequence Viewer

Length: 651 bp
ATGTCATATATCAAAATCAAACGGCAAGCATTCCAGGAAGCGGAGAATGACTGTACGGAGGCCTTGAATTTGGATGATCGCTATATAAAAGCATACTCACGACGTGCAACAGCTAGAAAAGAACTGGGAAAACTTAAAGCATCTATTGAGGATGCAGAGTTTGCTCTGAGGTTGGAGCCACACAACCAAGAAATCAAGAAACAGTATGCTGAGGCCAAATCTTTGTATGAGAAAAGAATTCTTCAGAAAATTTCTGAACAAGAAAAGCAGAACGTGGGAAAGTTGGATACCAAAGTGAATGGACACATCATCCAGCCTGTATCTAGTAGTACTCAAAGGAAACAAATGACTGCAGTTGAGGATCACACTAAGATTAACAAAAGTGGGAAGCAAGCATGGAAGGTATCGGTACAAGAGCTTGCTTCTAGAGCTGCTTCACGAGCCAATGTTCTAGCTGCACAAAACATCACACGACCAACTACAGCATATCAATTTGAGGCTTCTTGGAGAGGACTCTCTGGAGATCGTGCTCTTCAGGCTAAATTGTTGAAGGCTATATATCCCAGAGAACTGCCGTATATATTCAAAAATGCTTTGACTGTTCACATACTAGTTGATATCATCAAGTGTGTGACAACCTTTTTTATGTAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005829 GO:0032991 GO:0044424 GO:0044444 GO:0044464 GO:0097255
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
RPAP3_C TPR_1 TPR_8

Protein Analysis

216

Amino Acids

24.67

Weight (kDa)

9.69

Isoelectric Point (pI)

45.52

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RPAP3_C PF13877 159 - 215 5.8e-13 Potential Monad-binding region of RPAP3
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)
AciI CCGC 1 cut(s) 41
AclWI GGATC 1 cut(s) 369
AcsI RAATTY 3 cut(s) 67, 237, 249
AcuI CTGAAG 2 cut(s) 227, 518
AdeI CACNNNGTG 1 cut(s) 104
AfaI GTAC 3 cut(s) 55, 331, 411
AfiI CCNNNNNNNGG 1 cut(s) 40
AgsI TTSAA 3 cut(s) 67, 550, 586
AhlI ACTAGT 1 cut(s) 610
AjiI CACGTC 1 cut(s) 104
AjnI CCWGG 1 cut(s) 33
AluBI AGCT 4 cut(s) 113, 418, 431, 455
AluI AGCT 4 cut(s) 113, 418, 431, 455
Alw21I GWGCWC 1 cut(s) 532
AlwI GGATC 1 cut(s) 369
AoxI GGCC 2 cut(s) 60, 213
ApeKI GCWGC 2 cut(s) 431, 455
ApoI RAATTY 3 cut(s) 67, 237, 249
BaeI ACNNNNGTAYC 2 cut(s) 279, 312
BauI CACGAG 1 cut(s) 438
Bbv12I GWGCWC 1 cut(s) 532
BbvCI CCTCAGC 1 cut(s) 210
BbvI GCAGC 2 cut(s) 418, 442
BceAI ACGGC 2 cut(s) 38, 559
BciT130I CCWGG 1 cut(s) 35
BciVI GTATCC 1 cut(s) 280
BcuI ACTAGT 1 cut(s) 610
BfaI CTAG 5 cut(s) 114, 324, 426, 452, 611
BfmI CTRYAG 2 cut(s) 351, 480
BfuI GTATCC 1 cut(s) 280
BisI GCNGC 2 cut(s) 432, 456
BlsI GCNGC 2 cut(s) 433, 457
BmcAI AGTACT 1 cut(s) 331
Bme1390I CCNGG 1 cut(s) 35
BmgBI CACGTC 1 cut(s) 104
BmiI GGNNCC 1 cut(s) 177
BmrFI CCNGG 1 cut(s) 35
BmrI ACTGGG 1 cut(s) 134
BmsI GCATC 2 cut(s) 142, 149
BmuI ACTGGG 1 cut(s) 134
BpmI CTGGAG 1 cut(s) 540
Bpu10I CCTNAGC 1 cut(s) 210
Bsc4I CCNNNNNNNGG 1 cut(s) 40
Bse1I ACTGG 1 cut(s) 129
BseBI CCWGG 1 cut(s) 35
BseGI GGATG 3 cut(s) 79, 157, 309
BseLI CCNNNNNNNGG 1 cut(s) 40
BseMII CTCAG 2 cut(s) 158, 201
BseNI ACTGG 1 cut(s) 129
BseXI GCAGC 2 cut(s) 418, 442
BsgI GTGCAG 1 cut(s) 441
BshFI GGCC 2 cut(s) 62, 215
BsiHKAI GWGCWC 1 cut(s) 532
BslI CCNNNNNNNGG 1 cut(s) 40
BsmI GAATGC 1 cut(s) 29
BsnI GGCC 2 cut(s) 62, 215
Bsp1286I GDGCHC 1 cut(s) 532
Bsp143I GATC 3 cut(s) 76, 361, 523
BspACI CCGC 1 cut(s) 41
BspANI GGCC 2 cut(s) 62, 215
BspCNI CTCAG 2 cut(s) 159, 202
BspLI GGNNCC 1 cut(s) 177
BspMAI CTGCAG 1 cut(s) 355
BspPI GGATC 1 cut(s) 369
BspQI GCTCTTC 1 cut(s) 537
BsrI ACTGG 1 cut(s) 129
BssMI GATC 3 cut(s) 76, 361, 523
BssSI CACGAG 1 cut(s) 438
Bst2BI CACGAG 1 cut(s) 438
Bst2UI CCWGG 1 cut(s) 35
Bst4CI ACNGT 3 cut(s) 53, 204, 601
Bst6I CTCTTC 1 cut(s) 537
BstAPI GCANNNNNTGC 1 cut(s) 161
BstC8I GCNNGC 3 cut(s) 27, 393, 420
BstDEI CTNAG 3 cut(s) 167, 210, 369
BstF5I GGATG 3 cut(s) 79, 157, 309
BstKTI GATC 3 cut(s) 79, 364, 526
BstMBI GATC 3 cut(s) 76, 361, 523
BstMWI GCNNNNNNNGC 4 cut(s) 161, 428, 440, 536
BstNI CCWGG 1 cut(s) 35
BstSCI CCNGG 1 cut(s) 33
BstSFI CTRYAG 2 cut(s) 351, 480
BstV1I GCAGC 2 cut(s) 418, 442
BsuI GTATCC 1 cut(s) 280
BsuRI GGCC 2 cut(s) 62, 215
BtrI CACGTC 1 cut(s) 104
BtsCI GGATG 3 cut(s) 79, 157, 309
Cac8I GCNNGC 3 cut(s) 27, 393, 420
Csp6I GTAC 3 cut(s) 54, 330, 410
CviAII CATG 1 cut(s) 396
CviQI GTAC 3 cut(s) 54, 330, 410
DdeI CTNAG 3 cut(s) 167, 210, 369
DpnI GATC 3 cut(s) 78, 363, 525
DpnII GATC 3 cut(s) 76, 361, 523
DraIII CACNNNGTG 1 cut(s) 104
Eam1104I CTCTTC 1 cut(s) 537
EarI CTCTTC 1 cut(s) 537
Eco147I AGGCCT 1 cut(s) 62
Eco32I GATATC 1 cut(s) 619
Eco57I CTGAAG 2 cut(s) 227, 518
EcoRI GAATTC 1 cut(s) 237
EcoRII CCWGG 1 cut(s) 33
EcoRV GATATC 1 cut(s) 619
FaeI CATG 1 cut(s) 399
FatI CATG 1 cut(s) 395
Fnu4HI GCNGC 2 cut(s) 432, 456
FokI GGATG 3 cut(s) 86, 164, 296
Fsp4HI GCNGC 2 cut(s) 432, 456
FspBI CTAG 5 cut(s) 114, 324, 426, 452, 611
GluI GCNGC 2 cut(s) 432, 456
GsuI CTGGAG 1 cut(s) 540
HaeIII GGCC 2 cut(s) 62, 215
Hin1II CATG 1 cut(s) 399
HinfI GANTC 1 cut(s) 513
Hpy166II GTNNAC 1 cut(s) 604
Hpy188I TCNGA 3 cut(s) 168, 246, 256
Hpy188III TCNNGA 5 cut(s) 99, 196, 426, 438, 519
Hpy8I GTNNAC 1 cut(s) 604
Hpy99I CGWCG 1 cut(s) 105
HpyAV CCTTC 2 cut(s) 394, 544
HpyCH4III ACNGT 3 cut(s) 53, 204, 601
HpyCH4IV ACGT 2 cut(s) 103, 273
HpyCH4V TGCA 4 cut(s) 107, 155, 353, 458
HpyF10VI GCNNNNNNNGC 4 cut(s) 161, 428, 440, 536
HpyF3I CTNAG 3 cut(s) 167, 210, 369
HpySE526I ACGT 2 cut(s) 103, 273
Hsp92II CATG 1 cut(s) 399
Kzo9I GATC 3 cut(s) 76, 361, 523
LguI GCTCTTC 1 cut(s) 537
LmnI GCTCC 1 cut(s) 175
LpnPI CCDG 8 cut(s) 20, 47, 110, 326, 330, 504, 521, 577
Lsp1109I GCAGC 2 cut(s) 418, 442
LweI GCATC 2 cut(s) 142, 149
MaeI CTAG 5 cut(s) 114, 324, 426, 452, 611
MaeII ACGT 2 cut(s) 103, 273
MaeIII GTNAC 1 cut(s) 631
MalI GATC 3 cut(s) 78, 363, 525
MboI GATC 3 cut(s) 76, 361, 523
MboII GAAGA 2 cut(s) 233, 524
MhlI GDGCHC 1 cut(s) 532
MluCI AATT 5 cut(s) 67, 237, 249, 491, 542
MlyI GAGTC 1 cut(s) 507
MmeI TCCRAC 2 cut(s) 153, 264
MnlI CCTC 7 cut(s) 52, 142, 162, 205, 352, 490, 503
MseI TTAA 2 cut(s) 135, 375
MspR9I CCNGG 1 cut(s) 35
Mva1269I GAATGC 1 cut(s) 29
MvaI CCWGG 1 cut(s) 35
MwoI GCNNNNNNNGC 4 cut(s) 161, 428, 440, 536
NdeII GATC 3 cut(s) 76, 361, 523
NlaIII CATG 1 cut(s) 399
NlaIV GGNNCC 1 cut(s) 177
NmuCI GTSAC 1 cut(s) 631
PceI AGGCCT 1 cut(s) 62
PciSI GCTCTTC 1 cut(s) 537
PctI GAATGC 1 cut(s) 29
PfoI TCCNGGA 1 cut(s) 33
PkrI GCNGC 2 cut(s) 433, 457
PleI GAGTC 1 cut(s) 507
PpsI GAGTC 1 cut(s) 507
Psp6I CCWGG 1 cut(s) 33
PspGI CCWGG 1 cut(s) 33
PspN4I GGNNCC 1 cut(s) 177
PstI CTGCAG 1 cut(s) 355
RsaI GTAC 3 cut(s) 55, 331, 411
RsaNI GTAC 3 cut(s) 54, 330, 410
SapI GCTCTTC 1 cut(s) 537
SaqAI TTAA 2 cut(s) 135, 375
SatI GCNGC 2 cut(s) 432, 456
Sau3AI GATC 3 cut(s) 76, 361, 523
ScaI AGTACT 1 cut(s) 331
SchI GAGTC 1 cut(s) 507
ScrFI CCNGG 1 cut(s) 35
SduI GDGCHC 1 cut(s) 532
SetI ASST 9 cut(s) 106, 115, 173, 276, 405, 420, 433, 457, 641
SfaNI GCATC 2 cut(s) 142, 149
SfcI CTRYAG 2 cut(s) 351, 480
SpeI ACTAGT 1 cut(s) 610
Sse9I AATT 5 cut(s) 67, 237, 249, 491, 542
SseBI AGGCCT 1 cut(s) 62
SsiI CCGC 1 cut(s) 41
SspMI CTAG 5 cut(s) 114, 324, 426, 452, 611
StuI AGGCCT 1 cut(s) 62
StyD4I CCNGG 1 cut(s) 33
TaaI ACNGT 3 cut(s) 53, 204, 601
TaiI ACGT 2 cut(s) 106, 276
TasI AATT 5 cut(s) 67, 237, 249, 491, 542
TatI WGTACW 1 cut(s) 329
Tru1I TTAA 2 cut(s) 135, 375
Tru9I TTAA 2 cut(s) 135, 375
TseFI GTSAC 1 cut(s) 631
TseI GCWGC 2 cut(s) 431, 455
Tsp45I GTSAC 1 cut(s) 631
TspGWI ACGGA 1 cut(s) 71
XapI RAATTY 3 cut(s) 67, 237, 249
XbaI TCTAGA 1 cut(s) 425
XspI CTAG 5 cut(s) 114, 324, 426, 452, 611
ZrmI AGTACT 1 cut(s) 331
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.