RLG00000019424

B3 domain-containing transcription factor VRN1-like

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_laevigata
Chr4
OG0000156
Physical Location & Seq
Forward (+)
51908104 .. 51909672
1569 bp
Loading structure...
UTR
Exon/CDS
Intron
RLM00000019424

Sequence Viewer

Length: 1164 bp
ATGAAATATGGAGAAGATGTATCAAATTCAGCTTTTCTTAAGCTTCCAAGCGGTTCTGAGTGGGAAGTGGAATTGACAAGGTGCAACGGTAAGGTTTGGTTTGAGAAGGGCTGGCCAGAGTTCTCTAAGTTCTGCTCTTTAGACTACGGTGACTTCCTAGTTTTTCGATATGAAGGGAATTCTATATTCCAAGTCTGCATATTTGATAGAACTGCCACAGAAATTGATTATCCCATAACAATGCCCGATATGGAAAAGACGGATCATGAAGATGAAGAAGATGATAATATATCTATTGAAATCTCGGAGGATTCTCCACCCCACCCGAAAACAAGGGAGAAATCTCCATTACCATGCCCTCCGTCATTCAAAAAAATGAGAACAAGTTGGAGTGGTAAAGCAGCCGACACGATGTTCGGAAATGATGGCGGAGGCTCGTCTAGTGCACGAAGATACCAGAAGGGAACAGTTGAGACTACTGGGGAGATGCATTCACTGAATAAAAGTGAAAAAGCTCAAGCTCTATGGAGAGCTGATGCTTTTATATCTGAAAACCCTCTCTTCAAGGTTGTGTTGCAGCCTTCATATGTGCAACAAAGTTATTTGCGTTTTCCAGTGAAGTTTTTCAAGAGAAATGTAATTAAGGAAGCTGGTAATGTCACCCTTCGGGTTTCAAATGGAAAAACTTGGTCTGTCAAGTTCAAATATGAAAAATCAAGCGCCAGACTCAAGCATGGTTGGCTTGCATTTGTAAAGGACAATTGTTTGAAAGTGGGTGATGTGTGTGTCTTTGTCTTGATTAAGGACATTAAGCTTTTATTTCAAGTCGAATTTTTTCGAGCTACAAGTTTCCCCTTGCTACCAGTGGCAGGGCATGGTAGAGGTGCAATTGAACAAGATGAACATAGTAGAAGCTCAATAATTAAAGTGGAATCGGATTACAGCATGAATTGTGGTATGACCTCTATTAGTCCTTCTCCTCATGAAATTGGCAAGAACAAAAGGTCAAAAACTAGTGGGAAGGTTGCTGAAAGGCGTTGCTCCTCTTTGAGGGTTCCAAGGGTTAATCTTGAAGCTGCCAACAAGTTCATTCCAAACAATCCCTTCTTCAAAGTCTCTCTTGGGGCTTTTCATATGGAGAAGTCAAATGTGTGTACCAACTAG
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

388

Amino Acids

43.81

Weight (kDa)

8.79

Isoelectric Point (pI)

42.74

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
B3 PF02362 10 - 70 1.3e-10 B3 DNA binding domain
B3 PF02362 188 - 281 1.8e-18 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
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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)
AciI CCGC 2 cut(s) 51, 429
AclWI GGATC 1 cut(s) 270
AcoI YGGCCR 1 cut(s) 113
AcsI RAATTY 3 cut(s) 25, 178, 830
AfaI GTAC 1 cut(s) 1156
AfiI CCNNNNNNNGG 2 cut(s) 869, 1050
AflII CTTAAG 1 cut(s) 38
AhlI ACTAGT 1 cut(s) 1013
Alw21I GWGCWC 1 cut(s) 448
Alw26I GTCTC 2 cut(s) 467, 1120
Alw44I GTGCAC 1 cut(s) 444
AlwI GGATC 1 cut(s) 270
AoxI GGCC 1 cut(s) 113
ApaLI GTGCAC 1 cut(s) 444
ApeKI GCWGC 3 cut(s) 401, 577, 1076
ApoI RAATTY 3 cut(s) 25, 178, 830
ArsI GACNNNNNNTTYG 2 cut(s) 398, 430
Asp700I GAANNNNTTC 2 cut(s) 623, 834
AspLEI GCGC 1 cut(s) 722
AsuHPI GGTGA 3 cut(s) 161, 652, 788
BaeGI GKGCMC 1 cut(s) 448
BalI TGGCCA 1 cut(s) 115
Bbv12I GWGCWC 1 cut(s) 448
BbvI GCAGC 3 cut(s) 413, 589, 1063
BccI CCATC 1 cut(s) 419
BcoDI GTCTC 2 cut(s) 467, 1120
BcuI ACTAGT 1 cut(s) 1013
BfaI CTAG 4 cut(s) 158, 441, 1014, 1162
BfoI RGCGCY 1 cut(s) 723
BfrI CTTAAG 1 cut(s) 38
BisI GCNGC 3 cut(s) 402, 578, 1077
BlsI GCNGC 3 cut(s) 403, 579, 1078
BmiI GGNNCC 1 cut(s) 1056
BmrI ACTGGG 1 cut(s) 489
BmsI GCATC 2 cut(s) 477, 526
BmuI ACTGGG 1 cut(s) 489
BpuEI CTTGAG 2 cut(s) 501, 713
BsaJI CCNNGG 1 cut(s) 1058
BsaXI ACNNNNNCTCC 1 cut(s) 33
Bsc4I CCNNNNNNNGG 2 cut(s) 869, 1050
Bse1I ACTGG 3 cut(s) 484, 614, 863
BseDI CCNNGG 1 cut(s) 1058
BseLI CCNNNNNNNGG 2 cut(s) 869, 1050
BseMII CTCAG 1 cut(s) 48
BseNI ACTGG 3 cut(s) 484, 614, 863
BseRI GAGGAG 2 cut(s) 969, 1033
BseSI GKGCMC 1 cut(s) 448
BseXI GCAGC 3 cut(s) 413, 589, 1063
BshFI GGCC 1 cut(s) 115
BsiHKAI GWGCWC 1 cut(s) 448
BslI CCNNNNNNNGG 2 cut(s) 869, 1050
BsmAI GTCTC 2 cut(s) 467, 1120
BsmI GAATGC 1 cut(s) 490
BsnI GGCC 1 cut(s) 115
Bsp1286I GDGCHC 1 cut(s) 448
Bsp143I GATC 1 cut(s) 262
BspACI CCGC 2 cut(s) 51, 429
BspANI GGCC 1 cut(s) 115
BspCNI CTCAG 1 cut(s) 49
BspHI TCATGA 2 cut(s) 265, 982
BspLI GGNNCC 1 cut(s) 1056
BspPI GGATC 1 cut(s) 270
BspTI CTTAAG 1 cut(s) 38
BsrI ACTGG 3 cut(s) 484, 614, 863
BssECI CCNNGG 1 cut(s) 1058
BssMI GATC 1 cut(s) 262
BssT1I CCWWGG 1 cut(s) 1058
Bst4CI ACNGT 3 cut(s) 89, 149, 469
Bst6I CTCTTC 1 cut(s) 566
BstAFI CTTAAG 1 cut(s) 38
BstC8I GCNNGC 2 cut(s) 113, 744
BstDEI CTNAG 2 cut(s) 57, 126
BstENI CCTNNNNNAGG 1 cut(s) 1048
BstH2I RGCGCY 1 cut(s) 723
BstHHI GCGC 1 cut(s) 722
BstKTI GATC 1 cut(s) 265
BstMAI GTCTC 2 cut(s) 467, 1120
BstMBI GATC 1 cut(s) 262
BstMWI GCNNNNNNNGC 1 cut(s) 739
BstSLI GKGCMC 1 cut(s) 448
BstV1I GCAGC 3 cut(s) 413, 589, 1063
BsuRI GGCC 1 cut(s) 115
BtsIMutI CAGTG 3 cut(s) 494, 621, 870
Cac8I GCNNGC 2 cut(s) 113, 744
CciI TCATGA 2 cut(s) 265, 982
CfoI GCGC 1 cut(s) 722
Csp6I GTAC 1 cut(s) 1155
CspCI CAANNNNNGTGG 2 cut(s) 205, 240
CviAII CATG 6 cut(s) 266, 354, 734, 875, 946, 983
CviQI GTAC 1 cut(s) 1155
DdeI CTNAG 2 cut(s) 57, 126
DpnI GATC 1 cut(s) 264
DpnII GATC 1 cut(s) 262
EaeI YGGCCR 1 cut(s) 113
Eam1104I CTCTTC 1 cut(s) 566
EarI CTCTTC 1 cut(s) 566
EciI GGCGGA 1 cut(s) 444
Eco130I CCWWGG 1 cut(s) 1058
EcoNI CCTNNNNNAGG 1 cut(s) 1048
EcoRI GAATTC 1 cut(s) 178
EcoT14I CCWWGG 1 cut(s) 1058
EcoT22I ATGCAT 1 cut(s) 492
ErhI CCWWGG 1 cut(s) 1058
FaeI CATG 6 cut(s) 269, 357, 737, 878, 949, 986
FalI AAGNNNNNCTT 2 cut(s) 1104, 1136
FatI CATG 6 cut(s) 265, 353, 733, 874, 945, 982
FauNDI CATATG 2 cut(s) 586, 1134
Fnu4HI GCNGC 3 cut(s) 402, 578, 1077
Fsp4HI GCNGC 3 cut(s) 402, 578, 1077
FspBI CTAG 4 cut(s) 158, 441, 1014, 1162
GlaI GCGC 1 cut(s) 721
GluI GCNGC 3 cut(s) 402, 578, 1077
HaeII RGCGCY 1 cut(s) 723
HaeIII GGCC 1 cut(s) 115
HhaI GCGC 1 cut(s) 722
Hin1II CATG 6 cut(s) 269, 357, 737, 878, 949, 986
Hin6I GCGC 1 cut(s) 720
HinP1I GCGC 1 cut(s) 720
HindIII AAGCTT 2 cut(s) 41, 812
HinfI GANTC 3 cut(s) 311, 726, 932
HphI GGTGA 3 cut(s) 161, 652, 788
Hpy166II GTNNAC 2 cut(s) 446, 1155
Hpy188I TCNGA 5 cut(s) 58, 307, 419, 550, 937
Hpy188III TCNNGA 5 cut(s) 266, 628, 796, 983, 1070
Hpy8I GTNNAC 2 cut(s) 446, 1155
HpyAV CCTTC 8 cut(s) 100, 167, 454, 591, 674, 984, 1015, 1114
HpyCH4III ACNGT 3 cut(s) 89, 149, 469
HpyCH4V TGCA 8 cut(s) 84, 198, 446, 490, 577, 592, 746, 887
HpyF10VI GCNNNNNNNGC 1 cut(s) 739
HpyF3I CTNAG 2 cut(s) 57, 126
Hsp92II CATG 6 cut(s) 269, 357, 737, 878, 949, 986
HspAI GCGC 1 cut(s) 720
Kzo9I GATC 1 cut(s) 262
LmnI GCTCC 1 cut(s) 1046
LpnPI CCDG 9 cut(s) 97, 129, 465, 470, 627, 636, 736, 855, 876
Lsp1109I GCAGC 3 cut(s) 413, 589, 1063
LweI GCATC 2 cut(s) 477, 526
MaeI CTAG 4 cut(s) 158, 441, 1014, 1162
MaeIII GTNAC 2 cut(s) 149, 658
MalI GATC 1 cut(s) 264
MboI GATC 1 cut(s) 262
MboII GAAGA 7 cut(s) 26, 281, 287, 290, 462, 553, 1099
MfeI CAATTG 2 cut(s) 760, 888
MhlI GDGCHC 1 cut(s) 448
MlsI TGGCCA 1 cut(s) 115
MluNI TGGCCA 1 cut(s) 115
MlyI GAGTC 1 cut(s) 720
MmeI TCCRAC 1 cut(s) 368
MnlI CCTC 9 cut(s) 301, 369, 425, 567, 875, 973, 990, 1044, 1054
Mox20I TGGCCA 1 cut(s) 115
Mph1103I ATGCAT 1 cut(s) 492
MroXI GAANNNNTTC 2 cut(s) 623, 834
MscI TGGCCA 1 cut(s) 115
MseI TTAA 6 cut(s) 39, 642, 801, 810, 924, 1065
MslI CAYNNNNRTG 3 cut(s) 239, 270, 352
Msp20I TGGCCA 1 cut(s) 115
MspCI CTTAAG 1 cut(s) 38
MunI CAATTG 2 cut(s) 760, 888
Mva1269I GAATGC 1 cut(s) 490
MwoI GCNNNNNNNGC 1 cut(s) 739
NdeI CATATG 2 cut(s) 586, 1134
NdeII GATC 1 cut(s) 262
NlaIII CATG 6 cut(s) 269, 357, 737, 878, 949, 986
NlaIV GGNNCC 1 cut(s) 1056
NmuCI GTSAC 2 cut(s) 149, 658
NsiI ATGCAT 1 cut(s) 492
PagI TCATGA 2 cut(s) 265, 982
PctI GAATGC 1 cut(s) 490
PdmI GAANNNNTTC 2 cut(s) 623, 834
PfeI GAWTC 2 cut(s) 311, 932
PkrI GCNGC 3 cut(s) 403, 579, 1078
PleI GAGTC 1 cut(s) 720
PpsI GAGTC 1 cut(s) 720
PspN4I GGNNCC 1 cut(s) 1056
RsaI GTAC 1 cut(s) 1156
RsaNI GTAC 1 cut(s) 1155
RseI CAYNNNNRTG 3 cut(s) 239, 270, 352
SaqAI TTAA 6 cut(s) 39, 642, 801, 810, 924, 1065
SatI GCNGC 3 cut(s) 402, 578, 1077
Sau3AI GATC 1 cut(s) 262
SchI GAGTC 1 cut(s) 720
SduI GDGCHC 1 cut(s) 448
SfaNI GCATC 2 cut(s) 477, 526
SmiMI CAYNNNNRTG 3 cut(s) 239, 270, 352
SmlI CTYRAG 3 cut(s) 38, 516, 728
SmoI CTYRAG 3 cut(s) 38, 516, 728
SpeI ACTAGT 1 cut(s) 1013
SsiI CCGC 2 cut(s) 51, 429
SspMI CTAG 4 cut(s) 158, 441, 1014, 1162
StyI CCWWGG 1 cut(s) 1058
TaaI ACNGT 3 cut(s) 89, 149, 469
TaqI TCGA 3 cut(s) 166, 828, 838
TfiI GAWTC 2 cut(s) 311, 932
Tru1I TTAA 6 cut(s) 39, 642, 801, 810, 924, 1065
Tru9I TTAA 6 cut(s) 39, 642, 801, 810, 924, 1065
TscAI CASTG 3 cut(s) 501, 621, 870
TseFI GTSAC 2 cut(s) 149, 658
TseI GCWGC 3 cut(s) 401, 577, 1076
Tsp45I GTSAC 2 cut(s) 149, 658
TspGWI ACGGA 2 cut(s) 275, 351
TspRI CASTG 3 cut(s) 501, 621, 870
Vha464I CTTAAG 1 cut(s) 38
VneI GTGCAC 1 cut(s) 444
XagI CCTNNNNNAGG 1 cut(s) 1048
XapI RAATTY 3 cut(s) 25, 178, 830
XmnI GAANNNNTTC 2 cut(s) 623, 834
XspI CTAG 4 cut(s) 158, 441, 1014, 1162
Zsp2I ATGCAT 1 cut(s) 492
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.