Rh2DG169300

B3 domain-containing transcription factor VRN1-like

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr2D
OG0000156
Physical Location & Seq
Reverse (-)
14807887 .. 14810078
2192 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh2DG169300.1

Sequence Viewer

Length: 549 bp
ATGAGTGGTGTTTGGCCGACGTTTTGTTCCACAACTCCCCATTTTTTCAAGATCATTCTGGAGAATACTTCTAGAGACATCAAACTTAAAATTCCGAAGAAATTTGTGAAGAGATATGGAGAACATCTCTCAAATTCAGTATGTCTTAAGATCCCAAGTGGTTGTGAATGGGAAGTGGGAGTGACACGAAGCGGCAATAAGGTTTGGTTTGAGAAGGGCTGGCCTGCATTCTCTAAATTTTACTCCCTAGACTACGGTGCCTTCTTACTTTTTGGATATGAAGGGAATTCTAAATTCCAGAATGTACGAGCCAGTTTTGTCAAGAATTTTGCTACACAAGAGCAACAGCTTGTGAAGCTTCAGGTGGGTGATAAATCTTGGCCTGTGAAGTTGAATATCTATGATAAATATTCAACAGCTAAATTTTCTGCTGGATGGCATGCATTTTCCAACGACAATTGTTTGACTGATGGAGATGTTTGCATATTTGAGCTGATACAAATGAATGACGTTGTGCTGAAAGTTCACATTTTTAGATCCGTTGATTAG
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
B3

Protein Analysis

182

Amino Acids

20.9

Weight (kDa)

9.04

Isoelectric Point (pI)

24.78

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
B3 PF02362 15 - 100 8.3e-14 B3 DNA binding domain
B3 PF02362 105 - 180 1.1e-11 B3 DNA binding 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
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0000156)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G49475 AT3G18960 AT3G18960 AT3G18960 AT4G01580
fragaria_vesca FvH4_1g14650 FvH4_1g14650 FvH4_1g14650 FvH4_1g14650 FvH4_1g14660 FvH4_1g14660 FvH4_1g14660 FvH4_1g14660 FvH4_1g14670 FvH4_1g14680 FvH4_1g14680 FvH4_1g14680 FvH4_1g14680 FvH4_1g14680 FvH4_1g14680 FvH4_1g14690 FvH4_1g14700 FvH4_1g29250 FvH4_6g29400 FvH4_6g38681 FvH4_6g38690 FvH4_6g38700 FvH4_6g38700 FvH4_6g38700 FvH4_6g38700 FvH4_6g38700 FvH4_6g38700 FvH4_6g38700 FvH4_7g02010
malus_domestica MD00G1020600.v1.1 MD00G1022000.v1.1 MD00G1022100.v1.1 MD02G1159700.v1.1 MD02G1159800.v1.1 MD02G1159900.v1.1 MD02G1160000.v1.1 MD02G1160300.v1.1 MD15G1274100.v1.1 MD15G1274200.v1.1 MD15G1274400.v1.1 MD15G1302000.v1.1
prunus_persica Prupe.1G579400_v2.0.a1 Prupe.1G579400_v2.0.a1 Prupe.1G579400_v2.0.a1 Prupe.1G579400_v2.0.a1 Prupe.3G083400_v2.0.a1 Prupe.6G229600_v2.0.a1 Prupe.7G039600_v2.0.a1 Prupe.7G044500_v2.0.a1 Prupe.7G044800_v2.0.a1 Prupe.7G143100_v2.0.a1 Prupe.7G143500_v2.0.a1 Prupe.7G143600_v2.0.a1 Prupe.7G143700_v2.0.a1 Prupe.7G143800_v2.0.a1 Prupe.7G143900_v2.0.a1 Prupe.7G143900_v2.0.a1 Prupe.7G143900_v2.0.a1 Prupe.7G143900_v2.0.a1 Prupe.8G072800_v2.0.a1 Prupe.8G072800_v2.0.a1
pyrus_communis pycom02g12620 pycom02g12630 pycom15g23750 pycom15g26490 pycom17g21160
rosa_chinensis RchiOBHm_Chr2g0103421 RchiOBHm_Chr2g0103431 RchiOBHm_Chr2g0103441 RchiOBHm_Chr2g0103491 RchiOBHm_Chr2g0103501 RchiOBHm_Chr2g0103521 RchiOBHm_Chr2g0103541 RchiOBHm_Chr2g0103551 RchiOBHm_Chr2g0103561 RchiOBHm_Chr2g0134821 RchiOBHm_Chr2g0152161 RchiOBHm_Chr2g0152181 RchiOBHm_Chr7g0227261 RchiOBHm_Chr7g0227351 RchiOBHm_Chr7g0227431
rosa_laevigata RLG00000001649 RLG00000001653 RLG00000001659 RLG00000017235 RLG00000017236 RLG00000017240 RLG00000017241 RLG00000017242 RLG00000017243 RLG00000017244 RLG00000017349 RLG00000019424 RLG00000020614 RLG00000020615
rosa_multiflora Rmu_co8247875.1_g000001 Rmu_co8429551.1_g000001 Rmu_sc0000173.1_g000009 Rmu_sc0000718.1_g000004 Rmu_sc0001530.1_g000001 Rmu_sc0001530.1_g000002 Rmu_sc0001530.1_g000004 Rmu_sc0001530.1_g000005 Rmu_sc0001852.1_g000023 Rmu_sc0001852.1_g000024 Rmu_sc0002434.1_g000001 Rmu_sc0002434.1_g000002 Rmu_sc0003043.1_g000016 Rmu_sc0003153.1_g000005 Rmu_sc0011039.1_g000001 Rmu_sc0031822.1_g000001
rosa_roxburghii Rroxscaffold_2G00095860 Rroxscaffold_2G00095870 Rroxscaffold_2G00109720 Rroxscaffold_2G00139530 Rroxscaffold_2G00139550 Rroxscaffold_2G00139570 Rroxscaffold_2G00139580 Rroxscaffold_2G00139630 Rroxscaffold_2G00139640 Rroxscaffold_4G00328430 Rroxscaffold_4G00328440 Rroxscaffold_4G00328450
rosa_rugosa Rorug02G0114900 Rorug02G0115000 Rorug02G0115000 Rorug02G0115200 Rorug02G0115300 Rorug02G0115400 Rorug02G0115500 Rorug02G0115600 Rorug02G0115600 Rorug02G0115600 Rorug02G0115700 Rorug02G0320300 Rorug02G0431300 Rorug02G0431300 Rorug06G0028200 Rorug07G0241300
rosa_samantha Rh2AG163200 Rh2AG163300 Rh2AG163700 Rh2AG163800 Rh2AG163900 Rh2AG164000 Rh2AG373400 Rh2AG492600 Rh2BG170300 Rh2BG170400 Rh2BG170800 Rh2BG170900 Rh2BG171000 Rh2BG171100 Rh2BG171200 Rh2BG377800 Rh2BG505000 Rh2BG505100 Rh2BG505200 Rh2CG170300 Rh2CG170700 Rh2CG479000 Rh2DG169100 Rh2DG169200 Rh2DG169300 Rh2DG516400 Rh7AG391200 Rh7BG376200 Rh7CG410200 Rh7CG411500 Rh7CG412000 Rh7CG412700 Rh7DG388800
rosa_wichuraiana Rw2G012830 Rw2G012840 Rw2G012870 Rw2G012880 Rw2G012890 Rw2G012900 Rw2G030310 Rw2G040470 Rw2G040480 Rw7G032720 Rw7G032730 Rw7G032750

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 1 cut(s) 257
AciI CCGC 1 cut(s) 192
AclWI GGATC 2 cut(s) 145, 531
AcoI YGGCCR 1 cut(s) 14
AcsI RAATTY 8 cut(s) 90, 101, 133, 236, 286, 293, 325, 422
AcuI CTGAAG 1 cut(s) 344
AfaI GTAC 1 cut(s) 306
AflII CTTAAG 1 cut(s) 146
AgsI TTSAA 3 cut(s) 49, 394, 414
AluBI AGCT 4 cut(s) 349, 358, 419, 493
AluI AGCT 4 cut(s) 349, 358, 419, 493
Alw26I GTCTC 1 cut(s) 69
AlwI GGATC 2 cut(s) 145, 531
AoxI GGCC 3 cut(s) 14, 221, 380
ApoI RAATTY 8 cut(s) 90, 101, 133, 236, 286, 293, 325, 422
AsuHPI GGTGA 1 cut(s) 380
BanI GGYRCC 1 cut(s) 257
BccI CCATC 2 cut(s) 429, 464
BcoDI GTCTC 1 cut(s) 69
BfaI CTAG 2 cut(s) 72, 248
BfrI CTTAAG 1 cut(s) 146
BisI GCNGC 1 cut(s) 193
BlsI GCNGC 1 cut(s) 194
BmiI GGNNCC 1 cut(s) 259
BplI GAGNNNNNCTC 2 cut(s) 111, 143
BpmI CTGGAG 1 cut(s) 80
Bse1I ACTGG 1 cut(s) 312
BseGI GGATG 1 cut(s) 440
BseNI ACTGG 1 cut(s) 312
BshFI GGCC 3 cut(s) 16, 223, 382
BshNI GGYRCC 1 cut(s) 257
BsmAI GTCTC 1 cut(s) 69
BsmI GAATGC 1 cut(s) 227
BsnI GGCC 3 cut(s) 16, 223, 382
Bsp143I GATC 3 cut(s) 51, 150, 536
BspACI CCGC 1 cut(s) 192
BspANI GGCC 3 cut(s) 16, 223, 382
BspLI GGNNCC 1 cut(s) 259
BspPI GGATC 2 cut(s) 145, 531
BspT107I GGYRCC 1 cut(s) 257
BspTI CTTAAG 1 cut(s) 146
BsrI ACTGG 1 cut(s) 312
BssMI GATC 3 cut(s) 51, 150, 536
Bst4CI ACNGT 1 cut(s) 257
Bst6I CTCTTC 1 cut(s) 104
BstAFI CTTAAG 1 cut(s) 146
BstC8I GCNNGC 3 cut(s) 221, 225, 441
BstF5I GGATG 1 cut(s) 440
BstKTI GATC 3 cut(s) 54, 153, 539
BstMAI GTCTC 1 cut(s) 69
BstMBI GATC 3 cut(s) 51, 150, 536
BstMWI GCNNNNNNNGC 1 cut(s) 355
BstNSI RCATGY 1 cut(s) 443
BstX2I RGATCY 2 cut(s) 150, 536
BstYI RGATCY 2 cut(s) 150, 536
BsuRI GGCC 3 cut(s) 16, 223, 382
BtsCI GGATG 1 cut(s) 440
Cac8I GCNNGC 3 cut(s) 221, 225, 441
Csp6I GTAC 1 cut(s) 305
CviAII CATG 1 cut(s) 440
CviJI RGCY 9 cut(s) 16, 219, 223, 311, 349, 358, 382, 419, 493
CviKI_1 RGCY 9 cut(s) 16, 219, 223, 311, 349, 358, 382, 419, 493
CviQI GTAC 1 cut(s) 305
DpnI GATC 3 cut(s) 53, 152, 538
DpnII GATC 3 cut(s) 51, 150, 536
EaeI YGGCCR 1 cut(s) 14
Eam1104I CTCTTC 1 cut(s) 104
EarI CTCTTC 1 cut(s) 104
Eco57I CTGAAG 1 cut(s) 344
EcoRI GAATTC 1 cut(s) 286
EcoT22I ATGCAT 1 cut(s) 445
FaeI CATG 1 cut(s) 443
FaiI YATR 6 cut(s) 117, 142, 279, 402, 441, 485
FatI CATG 1 cut(s) 439
Fnu4HI GCNGC 1 cut(s) 193
FokI GGATG 1 cut(s) 447
Fsp4HI GCNGC 1 cut(s) 193
FspBI CTAG 2 cut(s) 72, 248
GluI GCNGC 1 cut(s) 193
GsuI CTGGAG 1 cut(s) 80
HaeIII GGCC 3 cut(s) 16, 223, 382
Hin1II CATG 1 cut(s) 443
HindIII AAGCTT 1 cut(s) 356
HphI GGTGA 1 cut(s) 380
Hpy166II GTNNAC 1 cut(s) 526
Hpy188I TCNGA 1 cut(s) 96
Hpy188III TCNNGA 5 cut(s) 49, 59, 72, 298, 322
Hpy8I GTNNAC 1 cut(s) 526
Hpy99I CGWCG 1 cut(s) 22
HpyAV CCTTC 3 cut(s) 208, 271, 275
HpyCH4III ACNGT 1 cut(s) 257
HpyCH4IV ACGT 2 cut(s) 20, 510
HpyCH4V TGCA 3 cut(s) 227, 443, 483
HpyF10VI GCNNNNNNNGC 1 cut(s) 355
HpySE526I ACGT 2 cut(s) 20, 510
Hsp92II CATG 1 cut(s) 443
Kzo9I GATC 3 cut(s) 51, 150, 536
LpnPI CCDG 8 cut(s) 44, 205, 237, 311, 325, 347, 396, 417
MaeI CTAG 2 cut(s) 72, 248
MaeII ACGT 2 cut(s) 20, 510
MaeIII GTNAC 1 cut(s) 181
MalI GATC 3 cut(s) 53, 152, 538
MboI GATC 3 cut(s) 51, 150, 536
MboII GAAGA 2 cut(s) 109, 121
MfeI CAATTG 1 cut(s) 457
MflI RGATCY 2 cut(s) 150, 536
MluCI AATT 9 cut(s) 90, 101, 133, 236, 286, 293, 325, 422, 457
MmeI TCCRAC 1 cut(s) 474
Mph1103I ATGCAT 1 cut(s) 445
MseI TTAA 2 cut(s) 87, 147
MspCI CTTAAG 1 cut(s) 146
MunI CAATTG 1 cut(s) 457
Mva1269I GAATGC 1 cut(s) 227
MwoI GCNNNNNNNGC 1 cut(s) 355
NdeII GATC 3 cut(s) 51, 150, 536
NlaIII CATG 1 cut(s) 443
NlaIV GGNNCC 1 cut(s) 259
NmuCI GTSAC 1 cut(s) 181
NsiI ATGCAT 1 cut(s) 445
NspI RCATGY 1 cut(s) 443
PaeI GCATGC 1 cut(s) 443
PctI GAATGC 1 cut(s) 227
PkrI GCNGC 1 cut(s) 194
PspN4I GGNNCC 1 cut(s) 259
PsuI RGATCY 2 cut(s) 150, 536
RsaI GTAC 1 cut(s) 306
RsaNI GTAC 1 cut(s) 305
SaqAI TTAA 2 cut(s) 87, 147
SatI GCNGC 1 cut(s) 193
Sau3AI GATC 3 cut(s) 51, 150, 536
SetI ASST 8 cut(s) 23, 204, 351, 360, 366, 421, 495, 513
SmlI CTYRAG 1 cut(s) 146
SmoI CTYRAG 1 cut(s) 146
SphI GCATGC 1 cut(s) 443
Sse9I AATT 9 cut(s) 90, 101, 133, 236, 286, 293, 325, 422, 457
SsiI CCGC 1 cut(s) 192
SspI AATATT 1 cut(s) 410
SspMI CTAG 2 cut(s) 72, 248
TaaI ACNGT 1 cut(s) 257
TaiI ACGT 2 cut(s) 23, 513
TasI AATT 9 cut(s) 90, 101, 133, 236, 286, 293, 325, 422, 457
TauI GCSGC 1 cut(s) 195
Tru1I TTAA 2 cut(s) 87, 147
Tru9I TTAA 2 cut(s) 87, 147
TseFI GTSAC 1 cut(s) 181
Tsp45I GTSAC 1 cut(s) 181
TspDTI ATGAA 2 cut(s) 294, 518
TspGWI ACGGA 1 cut(s) 529
Vha464I CTTAAG 1 cut(s) 146
XapI RAATTY 8 cut(s) 90, 101, 133, 236, 286, 293, 325, 422
XbaI TCTAGA 1 cut(s) 71
XceI RCATGY 1 cut(s) 443
XspI CTAG 2 cut(s) 72, 248
Zsp2I ATGCAT 1 cut(s) 445
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.