Rorug02G0427300

Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs)

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_rugosa
GWHBQTZ00000002
OG0014578
Physical Location & Seq
Reverse (-)
54802954 .. 54804188
1235 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug02G0427300.1

Sequence Viewer

Length: 627 bp
ATGAACAAGAATGTGGCTGAGGAGATAGCTGAGAAGCTCTGTGAATCAGTGGCAGCTAGTCTTGAGGGAAAAAAGTTGGGTTCATTTACAAGAATATCTTCTACAGTTCAGGGAGCAATGGAAGAAGCTCTTGTTTGTATTTTAACTCCTAGGCGCTCTATTGATATACTGAGGGATGTGCATGCTGACAAGGAGCAGGGCAAGCCTTATGTTGTTGTTTTTGTTGGTGTCAATGGAGTCGGGAAATCTACTAATTTGGCCAAGGTTGCCTATTGGCTCCAGCAACATCAGGTCAGTGTTATGATGGCAGCATGTGATACATTCCGATCAGGGGCTGTTGAGCAGTTGCGTACTCATGCACGTAGACTCCAGATCCCTATTTTTGAGAAGGGATATGAGAAAGATCCTGCTGTTGTTGCAAAGGAAGCAATCCAGGAGGCCAAACTCAATGGTTCTGATGTGGTGTGGGATGCAACTGCAGCTGATCCTAAATTGCTGGCCTTTTTGAAATCGTACAGGAATTTCGTACACATTGAATCTGGTCTTTACAAGAACTTGTTCCCCTTCCTTATTTTCCTCCTCGGTGGTTCTCAAGCTGCTTCTCTGAATTTGGAAATGTCTAGCTGA
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
DUF296

Protein Analysis

208

Amino Acids

22.85

Weight (kDa)

7.71

Isoelectric Point (pI)

41.18

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
SRP54 PF00448 70 - 159 1.3e-27 SRP54-type protein, GTPase domain
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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Orthologous Genes (Group: OG0014578)

Species Orthologous Gene IDs
arabidopsis_thaliana AT2G42940
fragaria_vesca FvH4_6g38311
malus_domestica MD09G1151100.v1.1 MD17G1138700.v1.1
prunus_persica Prupe.3G173700_v2.0.a1
pyrus_communis pycom09g07090 pycom17g13180
rosa_chinensis RchiOBHm_Chr2g0151621
rosa_laevigata RLG00000020564
rosa_multiflora Rmu_sc0005287.1_g000005
rosa_roxburghii Rroxscaffold_2G00096310
rosa_rugosa Rorug02G0427300
rosa_samantha Rh2AG488200 Rh2BG500800 Rh2CG474700 Rh2DG511900
rosa_wichuraiana Rw2G040020

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccI GTMKAC 1 cut(s) 364
AclWI GGATC 3 cut(s) 367, 398, 479
AcoI YGGCCR 1 cut(s) 258
AcsI RAATTY 2 cut(s) 520, 607
AfaI GTAC 3 cut(s) 352, 515, 528
AfiI CCNNNNNNNGG 1 cut(s) 331
AgsI TTSAA 2 cut(s) 508, 536
AjnI CCWGG 1 cut(s) 432
AluBI AGCT 7 cut(s) 29, 37, 56, 128, 482, 596, 624
AluI AGCT 7 cut(s) 29, 37, 56, 128, 482, 596, 624
AlwI GGATC 3 cut(s) 367, 398, 479
AlwNI CAGNNNCTG 1 cut(s) 335
AoxI GGCC 3 cut(s) 258, 438, 498
ApeKI GCWGC 4 cut(s) 53, 308, 479, 596
ApoI RAATTY 2 cut(s) 520, 607
Asp700I GAANNNNTTC 2 cut(s) 97, 557
AspA2I CCTAGG 1 cut(s) 149
AspLEI GCGC 1 cut(s) 156
AvrII CCTAGG 1 cut(s) 149
BalI TGGCCA 1 cut(s) 260
BbvCI CCTCAGC 1 cut(s) 18
BbvI GCAGC 4 cut(s) 65, 320, 491, 583
BccI CCATC 1 cut(s) 298
BciT130I CCWGG 1 cut(s) 434
BfaI CTAG 3 cut(s) 57, 150, 621
BfmI CTRYAG 2 cut(s) 102, 477
BfoI RGCGCY 1 cut(s) 157
BisI GCNGC 4 cut(s) 54, 309, 480, 597
BlnI CCTAGG 1 cut(s) 149
BlsI GCNGC 4 cut(s) 55, 310, 481, 598
Bme1390I CCNGG 1 cut(s) 434
BmiI GGNNCC 1 cut(s) 278
BmrFI CCNGG 1 cut(s) 434
BmsI GCATC 1 cut(s) 460
BpmI CTGGAG 2 cut(s) 263, 353
Bpu10I CCTNAGC 1 cut(s) 18
BpuEI CTTGAG 2 cut(s) 83, 576
BsaAI YACGTR 1 cut(s) 362
BsaJI CCNNGG 3 cut(s) 149, 261, 580
BsaXI ACNNNNNCTCC 2 cut(s) 351, 381
Bsc4I CCNNNNNNNGG 1 cut(s) 331
Bse3DI GCAATG 1 cut(s) 123
BseBI CCWGG 1 cut(s) 434
BseDI CCNNGG 3 cut(s) 149, 261, 580
BseGI GGATG 2 cut(s) 181, 475
BseLI CCNNNNNNNGG 1 cut(s) 331
BseMI GCAATG 1 cut(s) 123
BseMII CTCAG 3 cut(s) 9, 21, 161
BseRI GAGGAG 2 cut(s) 35, 569
BseXI GCAGC 4 cut(s) 65, 320, 491, 583
BshFI GGCC 3 cut(s) 260, 440, 500
BslI CCNNNNNNNGG 1 cut(s) 331
BsnI GGCC 3 cut(s) 260, 440, 500
Bsp143I GATC 4 cut(s) 326, 372, 403, 484
BspANI GGCC 3 cut(s) 260, 440, 500
BspCNI CTCAG 3 cut(s) 10, 22, 162
BspLI GGNNCC 1 cut(s) 278
BspMAI CTGCAG 1 cut(s) 481
BspPI GGATC 3 cut(s) 367, 398, 479
BsrDI GCAATG 1 cut(s) 123
BssECI CCNNGG 3 cut(s) 149, 261, 580
BssMI GATC 4 cut(s) 326, 372, 403, 484
BssT1I CCWWGG 2 cut(s) 149, 261
Bst2UI CCWGG 1 cut(s) 434
Bst4CI ACNGT 1 cut(s) 106
BstBAI YACGTR 1 cut(s) 362
BstC8I GCNNGC 3 cut(s) 183, 203, 498
BstDEI CTNAG 3 cut(s) 18, 30, 170
BstF5I GGATG 2 cut(s) 181, 475
BstH2I RGCGCY 1 cut(s) 157
BstHHI GCGC 1 cut(s) 156
BstKTI GATC 4 cut(s) 329, 375, 406, 487
BstMBI GATC 4 cut(s) 326, 372, 403, 484
BstMWI GCNNNNNNNGC 5 cut(s) 202, 266, 416, 425, 479
BstNI CCWGG 1 cut(s) 434
BstNSI RCATGY 2 cut(s) 185, 315
BstSCI CCNGG 1 cut(s) 432
BstSFI CTRYAG 2 cut(s) 102, 477
BstV1I GCAGC 4 cut(s) 65, 320, 491, 583
BstX2I RGATCY 2 cut(s) 372, 403
BstYI RGATCY 2 cut(s) 372, 403
BsuRI GGCC 3 cut(s) 260, 440, 500
BtsCI GGATG 2 cut(s) 181, 475
BtsIMutI CAGTG 2 cut(s) 54, 301
Cac8I GCNNGC 3 cut(s) 183, 203, 498
CaiI CAGNNNCTG 1 cut(s) 335
CfoI GCGC 1 cut(s) 156
Csp6I GTAC 3 cut(s) 351, 514, 527
CviAII CATG 3 cut(s) 182, 312, 356
CviQI GTAC 3 cut(s) 351, 514, 527
DdeI CTNAG 3 cut(s) 18, 30, 170
DpnI GATC 4 cut(s) 328, 374, 405, 486
DpnII GATC 4 cut(s) 326, 372, 403, 484
EaeI YGGCCR 1 cut(s) 258
Eco130I CCWWGG 2 cut(s) 149, 261
EcoRII CCWGG 1 cut(s) 432
EcoT14I CCWWGG 2 cut(s) 149, 261
ErhI CCWWGG 2 cut(s) 149, 261
FaeI CATG 3 cut(s) 185, 315, 359
FaiI YATR 7 cut(s) 167, 183, 210, 302, 313, 357, 396
FalI AAGNNNNNCTT 4 cut(s) 82, 114, 114, 146
FatI CATG 3 cut(s) 181, 311, 355
FblI GTMKAC 1 cut(s) 364
Fnu4HI GCNGC 4 cut(s) 54, 309, 480, 597
FokI GGATG 2 cut(s) 188, 482
Fsp4HI GCNGC 4 cut(s) 54, 309, 480, 597
FspBI CTAG 3 cut(s) 57, 150, 621
GlaI GCGC 1 cut(s) 155
GluI GCNGC 4 cut(s) 54, 309, 480, 597
GsuI CTGGAG 2 cut(s) 263, 353
HaeII RGCGCY 1 cut(s) 157
HaeIII GGCC 3 cut(s) 260, 440, 500
HhaI GCGC 1 cut(s) 156
Hin1II CATG 3 cut(s) 185, 315, 359
Hin6I GCGC 1 cut(s) 154
HinP1I GCGC 1 cut(s) 154
HinfI GANTC 4 cut(s) 44, 237, 366, 536
Hpy166II GTNNAC 2 cut(s) 365, 529
Hpy188I TCNGA 3 cut(s) 326, 457, 606
Hpy188III TCNNGA 3 cut(s) 62, 241, 370
Hpy8I GTNNAC 2 cut(s) 365, 529
HpyAV CCTTC 2 cut(s) 382, 574
HpyCH4III ACNGT 1 cut(s) 106
HpyCH4IV ACGT 1 cut(s) 361
HpyCH4V TGCA 5 cut(s) 181, 359, 419, 473, 479
HpyF10VI GCNNNNNNNGC 5 cut(s) 202, 266, 416, 425, 479
HpyF3I CTNAG 3 cut(s) 18, 30, 170
HpySE526I ACGT 1 cut(s) 361
Hsp92II CATG 3 cut(s) 185, 315, 359
HspAI GCGC 1 cut(s) 154
Kzo9I GATC 4 cut(s) 326, 372, 403, 484
LmnI GCTCC 3 cut(s) 113, 193, 282
Lsp1109I GCAGC 4 cut(s) 65, 320, 491, 583
LweI GCATC 1 cut(s) 460
MaeI CTAG 3 cut(s) 57, 150, 621
MaeII ACGT 1 cut(s) 361
MalI GATC 4 cut(s) 328, 374, 405, 486
MboI GATC 4 cut(s) 326, 372, 403, 484
MboII GAAGA 2 cut(s) 90, 134
MflI RGATCY 2 cut(s) 372, 403
MlsI TGGCCA 1 cut(s) 260
MluCI AATT 4 cut(s) 253, 491, 520, 607
MluNI TGGCCA 1 cut(s) 260
MlyI GAGTC 2 cut(s) 246, 360
MnlI CCTC 6 cut(s) 13, 58, 165, 430, 587, 590
Mox20I TGGCCA 1 cut(s) 260
MroXI GAANNNNTTC 2 cut(s) 97, 557
MscI TGGCCA 1 cut(s) 260
MseI TTAA 1 cut(s) 143
Msp20I TGGCCA 1 cut(s) 260
MspA1I CMGCKG 1 cut(s) 482
MspR9I CCNGG 1 cut(s) 434
MvaI CCWGG 1 cut(s) 434
MwoI GCNNNNNNNGC 5 cut(s) 202, 266, 416, 425, 479
NdeII GATC 4 cut(s) 326, 372, 403, 484
NlaIII CATG 3 cut(s) 185, 315, 359
NlaIV GGNNCC 1 cut(s) 278
NspI RCATGY 2 cut(s) 185, 315
PaeI GCATGC 1 cut(s) 185
PdmI GAANNNNTTC 2 cut(s) 97, 557
PfeI GAWTC 2 cut(s) 44, 536
PfoI TCCNGGA 1 cut(s) 432
PkrI GCNGC 4 cut(s) 55, 310, 481, 598
PleI GAGTC 2 cut(s) 245, 360
PpsI GAGTC 2 cut(s) 245, 360
Ppu21I YACGTR 1 cut(s) 362
Psp6I CCWGG 1 cut(s) 432
PspGI CCWGG 1 cut(s) 432
PspN4I GGNNCC 1 cut(s) 278
PstI CTGCAG 1 cut(s) 481
PstNI CAGNNNCTG 1 cut(s) 335
PsuI RGATCY 2 cut(s) 372, 403
PvuII CAGCTG 1 cut(s) 482
RsaI GTAC 3 cut(s) 352, 515, 528
RsaNI GTAC 3 cut(s) 351, 514, 527
SaqAI TTAA 1 cut(s) 143
SatI GCNGC 4 cut(s) 54, 309, 480, 597
Sau3AI GATC 4 cut(s) 326, 372, 403, 484
SchI GAGTC 2 cut(s) 246, 360
ScrFI CCNGG 1 cut(s) 434
SfaNI GCATC 1 cut(s) 460
SfcI CTRYAG 2 cut(s) 102, 477
SmlI CTYRAG 2 cut(s) 62, 591
SmoI CTYRAG 2 cut(s) 62, 591
SphI GCATGC 1 cut(s) 185
Sse9I AATT 4 cut(s) 253, 491, 520, 607
SspMI CTAG 3 cut(s) 57, 150, 621
StyD4I CCNGG 1 cut(s) 432
StyI CCWWGG 2 cut(s) 149, 261
TaaI ACNGT 1 cut(s) 106
TaiI ACGT 1 cut(s) 364
TasI AATT 4 cut(s) 253, 491, 520, 607
TfiI GAWTC 2 cut(s) 44, 536
Tru1I TTAA 1 cut(s) 143
Tru9I TTAA 1 cut(s) 143
TscAI CASTG 2 cut(s) 54, 301
TseI GCWGC 4 cut(s) 53, 308, 479, 596
TspDTI ATGAA 2 cut(s) 17, 72
TspRI CASTG 2 cut(s) 54, 301
XapI RAATTY 2 cut(s) 520, 607
XceI RCATGY 2 cut(s) 185, 315
XmaJI CCTAGG 1 cut(s) 149
XmiI GTMKAC 1 cut(s) 364
XmnI GAANNNNTTC 2 cut(s) 97, 557
XspI CTAG 3 cut(s) 57, 150, 621
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.