Rh3BG080500

Homeobox protein knotted-1-like

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr3B
OG0013693
Physical Location & Seq
Reverse (-)
6245880 .. 6249339
3460 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh3BG080500.1

Sequence Viewer

Length: 900 bp
ATGGATGATTTTTACAGGCTAAACCCTATGAATATAATATCAAGCTCATCGGAGAATGTGAATCAGGTTGAAAATGATACTAGGGCTACTGCTACTTGTTTTGGTGCTGGTTATCATGGTGGTCCGTTAATACTAAGTGACGGTAACCTCAACCTCAACATGCTTCAATTTGAAACGGATCAGAGTATGAACCAGCTGATTAAGACCCAGATAGCCAATCACCCTCGTTACCCAGATTTGGTTTCTGCTTACATAGATTGCCAAAAGGTTGGAGCTCCACCAGAGATGAAAAGCCTACTTGAAGAAATGGGGCGGCTAAGCCTCCCCATAAGCACTTGCAGGAGTGAGATAGGAGCTGATCCAGAACTAGATGAGTTCATGGACTCATACTGTGGGATTCTTCATACATACAAGGAAGAGCTTTCTAAACCGGTTGTTGAAGCCACCGCATTCTTGAGCAACATTGAATTGCAGCTTAGCAACCTCTGCAAAGGCACATTTCAGAAACCCAAATCGGACTATCATTCAACTGATGAAGCAGTTGGAAGTTCAGAAGAGGACTTAAGTTATGGGGAGGTGGAAGCAGCCGAGGGCCAAGAAATCTCAGCGTTTCGTGCTTGTGATAGGGAGCTTAAAGATATGCTGCTGCATAAGTACAGTGGCTACCTCAGCAAGCTGAAGAAGGACTTCTTAAAGACAAGAAAGAAAGGAAAGCTTCCGAAGGATGCTAGGTCTGCACTATTGGACTGGTGGAACACTCACTATAGATGGCCATATCCTACGGTAATGGATTCAATATATGCCAATTATATAATGGAAGTTAAATATCTAAACTTTCAAATGCAGGTAATTTATAATGGATCAATTAGTTTCCCTTTACTATTATTTATGTATGAATAG
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
ELK Homeobox_KN KNOX1 KNOX2

Protein Analysis

299

Amino Acids

34.04

Weight (kDa)

4.98

Isoelectric Point (pI)

35.93

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
KNOX1 PF03790 67 - 105 8.2e-19 KNOX1 domain
KNOX2 PF03791 116 - 163 8.8e-22 KNOX2 domain
ELK PF03789 210 - 231 3.4e-07 ELK 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: OG0013693)

Species Orthologous Gene IDs
fragaria_vesca FvH4_6g07460 FvH4_6g07460 FvH4_6g07460
malus_domestica MD04G1215500.v1.1 MD12G1205700.v1.1
prunus_persica Prupe.6G312900_v2.0.a1
pyrus_communis pycom04g17070 pycom12g19370
rosa_chinensis RchiOBHm_Chr3g0457121
rosa_laevigata RLG00000025247
rosa_multiflora Rmu_sc0000488.1_g000009
rosa_roxburghii Rroxscaffold_6G00422170
rosa_rugosa Rorug03G0018800
rosa_samantha Rh3AG078700 Rh3BG080500 Rh3CG080500 Rh3DG082300
rosa_wichuraiana Rw3G006760

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 855
Acc36I ACCTGC 1 cut(s) 835
AciI CCGC 2 cut(s) 313, 447
AclWI GGATC 3 cut(s) 186, 353, 868
AcoI YGGCCR 1 cut(s) 770
AcuI CTGAAG 1 cut(s) 698
AfaI GTAC 1 cut(s) 656
AfiI CCNNNNNNNGG 1 cut(s) 238
AflII CTTAAG 1 cut(s) 562
AgeI ACCGGT 1 cut(s) 430
AgsI TTSAA 9 cut(s) 71, 167, 173, 302, 440, 467, 528, 795, 839
AluBI AGCT 9 cut(s) 45, 196, 275, 356, 421, 475, 631, 676, 715
AluI AGCT 9 cut(s) 45, 196, 275, 356, 421, 475, 631, 676, 715
Alw21I GWGCWC 1 cut(s) 277
AlwI GGATC 3 cut(s) 186, 353, 868
AoxI GGCC 2 cut(s) 592, 770
ApeKI GCWGC 4 cut(s) 472, 584, 643, 646
AsiGI ACCGGT 1 cut(s) 430
Asp700I GAANNNNTTC 1 cut(s) 686
AspS9I GGNCC 2 cut(s) 122, 592
AsuHPI GGTGA 1 cut(s) 212
AvaII GGWCC 1 cut(s) 122
BalI TGGCCA 1 cut(s) 772
BanII GRGCYC 1 cut(s) 277
Bbv12I GWGCWC 1 cut(s) 277
BbvCI CCTCAGC 1 cut(s) 668
BbvI GCAGC 4 cut(s) 484, 596, 630, 633
BccI CCATC 1 cut(s) 762
BfaI CTAG 3 cut(s) 81, 368, 729
BfmI CTRYAG 1 cut(s) 763
BfrI CTTAAG 1 cut(s) 562
BfuAI ACCTGC 1 cut(s) 835
BisI GCNGC 5 cut(s) 314, 473, 585, 644, 647
BlpI GCTNAGC 2 cut(s) 317, 476
BlsI GCNGC 5 cut(s) 315, 474, 586, 645, 648
Bme18I GGWCC 1 cut(s) 122
BmgT120I GGNCC 2 cut(s) 122, 592
BmsI GCATC 1 cut(s) 715
Bpu10I CCTNAGC 1 cut(s) 668
Bpu1102I GCTNAGC 2 cut(s) 317, 476
BpuEI CTTGAG 1 cut(s) 475
BsaJI CCNNGG 1 cut(s) 588
BsaWI WCCGGW 1 cut(s) 430
Bsc4I CCNNNNNNNGG 1 cut(s) 238
Bse118I RCCGGY 1 cut(s) 430
Bse1I ACTGG 1 cut(s) 752
BseDI CCNNGG 1 cut(s) 588
BseGI GGATG 2 cut(s) 10, 730
BseLI CCNNNNNNNGG 1 cut(s) 238
BseMII CTCAG 2 cut(s) 618, 682
BseNI ACTGG 1 cut(s) 752
BseXI GCAGC 4 cut(s) 484, 596, 630, 633
BsgI GTGCAG 1 cut(s) 720
BshFI GGCC 2 cut(s) 594, 772
BshTI ACCGGT 1 cut(s) 430
BsiHKAI GWGCWC 1 cut(s) 277
BsiSI CCGG 1 cut(s) 431
BslI CCNNNNNNNGG 1 cut(s) 238
BsmI GAATGC 1 cut(s) 449
BsnI GGCC 2 cut(s) 594, 772
Bsp1286I GDGCHC 1 cut(s) 277
Bsp143I GATC 3 cut(s) 178, 358, 860
Bsp1720I GCTNAGC 2 cut(s) 317, 476
BspACI CCGC 2 cut(s) 313, 447
BspANI GGCC 2 cut(s) 594, 772
BspCNI CTCAG 2 cut(s) 617, 681
BspMI ACCTGC 1 cut(s) 835
BspPI GGATC 3 cut(s) 186, 353, 868
BspQI GCTCTTC 1 cut(s) 411
BspTI CTTAAG 1 cut(s) 562
BsrFI RCCGGY 1 cut(s) 430
BsrI ACTGG 1 cut(s) 752
BssAI RCCGGY 1 cut(s) 430
BssECI CCNNGG 1 cut(s) 588
BssMI GATC 3 cut(s) 178, 358, 860
Bst4CI ACNGT 4 cut(s) 143, 392, 659, 784
Bst6I CTCTTC 2 cut(s) 411, 549
BstAFI CTTAAG 1 cut(s) 562
BstAPI GCANNNNNTGC 1 cut(s) 486
BstC8I GCNNGC 1 cut(s) 674
BstDEI CTNAG 5 cut(s) 134, 317, 476, 604, 668
BstEII GGTNACC 1 cut(s) 143
BstF5I GGATG 2 cut(s) 10, 730
BstKTI GATC 3 cut(s) 181, 361, 863
BstMBI GATC 3 cut(s) 178, 358, 860
BstMWI GCNNNNNNNGC 4 cut(s) 486, 614, 669, 734
BstNSI RCATGY 1 cut(s) 163
BstPI GGTNACC 1 cut(s) 143
BstSFI CTRYAG 1 cut(s) 763
BstV1I GCAGC 4 cut(s) 484, 596, 630, 633
BstXI CCANNNNNNTGG 1 cut(s) 269
BsuRI GGCC 2 cut(s) 594, 772
BtsCI GGATG 2 cut(s) 10, 730
BtsIMutI CAGTG 1 cut(s) 664
BveI ACCTGC 1 cut(s) 835
Cac8I GCNNGC 1 cut(s) 674
Cfr10I RCCGGY 1 cut(s) 430
Cfr13I GGNCC 2 cut(s) 122, 592
Csp6I GTAC 1 cut(s) 655
CspAI ACCGGT 1 cut(s) 430
CviAII CATG 3 cut(s) 116, 160, 379
CviQI GTAC 1 cut(s) 655
DdeI CTNAG 5 cut(s) 134, 317, 476, 604, 668
DpnI GATC 3 cut(s) 180, 360, 862
DpnII GATC 3 cut(s) 178, 358, 860
EaeI YGGCCR 1 cut(s) 770
Eam1104I CTCTTC 2 cut(s) 411, 549
EarI CTCTTC 2 cut(s) 411, 549
Ecl136II GAGCTC 1 cut(s) 275
Eco24I GRGCYC 1 cut(s) 277
Eco47I GGWCC 1 cut(s) 122
Eco53kI GAGCTC 1 cut(s) 275
Eco57I CTGAAG 1 cut(s) 698
Eco91I GGTNACC 1 cut(s) 143
EcoICRI GAGCTC 1 cut(s) 275
EcoO65I GGTNACC 1 cut(s) 143
EcoT38I GRGCYC 1 cut(s) 277
FaeI CATG 3 cut(s) 119, 163, 382
FalI AAGNNNNNCTT 6 cut(s) 671, 703, 674, 706, 699, 731
FatI CATG 3 cut(s) 115, 159, 378
Fnu4HI GCNGC 5 cut(s) 314, 473, 585, 644, 647
FokI GGATG 2 cut(s) 17, 737
FriOI GRGCYC 1 cut(s) 277
Fsp4HI GCNGC 5 cut(s) 314, 473, 585, 644, 647
FspBI CTAG 3 cut(s) 81, 368, 729
GluI GCNGC 5 cut(s) 314, 473, 585, 644, 647
HaeIII GGCC 2 cut(s) 594, 772
HapII CCGG 1 cut(s) 431
Hin1II CATG 3 cut(s) 119, 163, 382
HindIII AAGCTT 1 cut(s) 713
HinfI GANTC 4 cut(s) 61, 383, 397, 791
HpaII CCGG 1 cut(s) 431
HphI GGTGA 1 cut(s) 212
Hpy188I TCNGA 6 cut(s) 52, 183, 504, 517, 553, 720
Hpy188III TCNNGA 2 cut(s) 362, 454
HpyAV CCTTC 2 cut(s) 676, 715
HpyCH4III ACNGT 4 cut(s) 143, 392, 659, 784
HpyCH4V TGCA 6 cut(s) 339, 472, 489, 649, 737, 844
HpyF10VI GCNNNNNNNGC 4 cut(s) 486, 614, 669, 734
HpyF3I CTNAG 5 cut(s) 134, 317, 476, 604, 668
Hsp92II CATG 3 cut(s) 119, 163, 382
Kzo9I GATC 3 cut(s) 178, 358, 860
LguI GCTCTTC 1 cut(s) 411
LmnI GCTCC 4 cut(s) 272, 280, 353, 628
Lsp1109I GCAGC 4 cut(s) 484, 596, 630, 633
LweI GCATC 1 cut(s) 715
MaeI CTAG 3 cut(s) 81, 368, 729
MaeIII GTNAC 3 cut(s) 137, 143, 227
MalI GATC 3 cut(s) 180, 360, 862
MboI GATC 3 cut(s) 178, 358, 860
MboII GAAGA 5 cut(s) 314, 392, 428, 566, 691
MhlI GDGCHC 1 cut(s) 277
MlsI TGGCCA 1 cut(s) 772
MluCI AATT 5 cut(s) 167, 467, 805, 849, 864
MluNI TGGCCA 1 cut(s) 772
MlyI GAGTC 1 cut(s) 377
MmeI TCCRAC 2 cut(s) 250, 523
MnlI CCTC 9 cut(s) 158, 164, 234, 332, 494, 550, 568, 583, 677
Mox20I TGGCCA 1 cut(s) 772
MroXI GAANNNNTTC 1 cut(s) 686
MscI TGGCCA 1 cut(s) 772
MseI TTAA 6 cut(s) 128, 201, 563, 633, 692, 822
Msp20I TGGCCA 1 cut(s) 772
MspA1I CMGCKG 1 cut(s) 196
MspCI CTTAAG 1 cut(s) 562
MspI CCGG 1 cut(s) 431
Mva1269I GAATGC 1 cut(s) 449
MwoI GCNNNNNNNGC 4 cut(s) 486, 614, 669, 734
NdeII GATC 3 cut(s) 178, 358, 860
NlaIII CATG 3 cut(s) 119, 163, 382
NmeAIII GCCGAG 1 cut(s) 613
NmuCI GTSAC 1 cut(s) 137
NspI RCATGY 1 cut(s) 163
PciSI GCTCTTC 1 cut(s) 411
PctI GAATGC 1 cut(s) 449
PdmI GAANNNNTTC 1 cut(s) 686
PfeI GAWTC 3 cut(s) 61, 397, 791
PinAI ACCGGT 1 cut(s) 430
PkrI GCNGC 5 cut(s) 315, 474, 586, 645, 648
PleI GAGTC 1 cut(s) 377
PpsI GAGTC 1 cut(s) 377
PsiI TTATAA 1 cut(s) 855
Psp124BI GAGCTC 1 cut(s) 277
PspEI GGTNACC 1 cut(s) 143
PspPI GGNCC 2 cut(s) 122, 592
PvuII CAGCTG 1 cut(s) 196
RsaI GTAC 1 cut(s) 656
RsaNI GTAC 1 cut(s) 655
SacI GAGCTC 1 cut(s) 277
SapI GCTCTTC 1 cut(s) 411
SaqAI TTAA 6 cut(s) 128, 201, 563, 633, 692, 822
SatI GCNGC 5 cut(s) 314, 473, 585, 644, 647
Sau3AI GATC 3 cut(s) 178, 358, 860
Sau96I GGNCC 2 cut(s) 122, 592
SchI GAGTC 1 cut(s) 377
SduI GDGCHC 1 cut(s) 277
SfaNI GCATC 1 cut(s) 715
SfcI CTRYAG 1 cut(s) 763
SinI GGWCC 1 cut(s) 122
SmlI CTYRAG 2 cut(s) 454, 562
SmoI CTYRAG 2 cut(s) 454, 562
Sse9I AATT 5 cut(s) 167, 467, 805, 849, 864
SsiI CCGC 2 cut(s) 313, 447
SspMI CTAG 3 cut(s) 81, 368, 729
SstI GAGCTC 1 cut(s) 277
TaaI ACNGT 4 cut(s) 143, 392, 659, 784
TasI AATT 5 cut(s) 167, 467, 805, 849, 864
TatI WGTACW 1 cut(s) 654
TauI GCSGC 1 cut(s) 316
TfiI GAWTC 3 cut(s) 61, 397, 791
Tru1I TTAA 6 cut(s) 128, 201, 563, 633, 692, 822
Tru9I TTAA 6 cut(s) 128, 201, 563, 633, 692, 822
TscAI CASTG 1 cut(s) 664
TseFI GTSAC 1 cut(s) 137
TseI GCWGC 4 cut(s) 472, 584, 643, 646
Tsp45I GTSAC 1 cut(s) 137
TspDTI ATGAA 6 cut(s) 44, 203, 302, 367, 392, 549
TspGWI ACGGA 2 cut(s) 114, 191
TspRI CASTG 1 cut(s) 664
Vha464I CTTAAG 1 cut(s) 562
VpaK11BI GGWCC 1 cut(s) 122
XceI RCATGY 1 cut(s) 163
XcmI CCANNNNNNNNNTGG 1 cut(s) 811
XmnI GAANNNNTTC 1 cut(s) 686
XspI CTAG 3 cut(s) 81, 368, 729
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.