Rw4G010420

HD domain-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr4
OG0011001
Physical Location & Seq
Forward (+)
24230906 .. 24233670
2765 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw4G010420.1

Sequence Viewer

Length: 750 bp
ATGAGTCGAGCGTTCCTCTGTAGATCGCTCCTCCTAACACCTTCTCTCTACTCCGCTCCCCTCACATCCTTGAAGCCCACACTCACCTCTGCTTCTCCTTCTTCTAGGGTTCGCCGTATGGCCACCGAAGCTTCGTCGTCACCGTCATCCCACACCGGCGGTGACGCCATCCGCGCCGACCCAACCTCTTCCTCTCCTCCCGCCTCCTCTGCCATTGATTTTCTCTCCCTCTGCCACCGCCTTAAGACGACGAAAAGAGCTGGATGGGTTAAGAGAGATGTGAAGGATCCAGAGTCTGTAGCTGACCATATGTACCGCATGGGTTTAATGGCTCTCATTGCTTCGGATATTCCTGGTGTCAATCGAGACAAGTGCATAAAGATCGCCATTGTTCATGACATTGCTGAAGCTATTGTTGGGGATATAACCCCCACAGATGGGGTACCGAAGGCAGAGAAGAACCGAAGAGAACAAGAGGCAATAGACCACATGTGCAAATTACTTGGTGGAGGCTCAATAGCTAAGGAAATAGGTGAATTGTGGATGGAGTATGAGGCGAATTCCTCCCCAGAAGCTAAAATTGTCAAGGACTTTGACAAGGTGGAGATGATACTTCAAGCCTTGGAATATGAGAATGGTCAAGGAAAGGACTTGGATGAGTTTTTCCAGTCAACTGCTGGGAAGTTCCAGACTGATGTAGGCAAAGCTTGGGCAGCAGAGATAGTATCCAGAAGAAAAAAACAAGGCTAA
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
HD_3

Protein Analysis

249

Amino Acids

27.12

Weight (kDa)

7.67

Isoelectric Point (pI)

50.49

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
YfbR-like PF12917 74 - 217 1.4e-06 5'-deoxynucleotidase YfbR-like
HD_3 PF13023 79 - 236 1.8e-49 HD domain
HD PF01966 100 - 203 8.9e-12 HD 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: OG0011001)

Species Orthologous Gene IDs
arabidopsis_thaliana AT2G23820 AT2G23820
fragaria_vesca FvH4_4g08640 FvH4_4g08640
malus_domestica MD13G1274800.v1.1
prunus_persica Prupe.1G099200_v2.0.a1 Prupe.1G099200_v2.0.a1
pyrus_communis pycom13g28700
rosa_chinensis RchiOBHm_Chr4g0405131
rosa_laevigata RLG00000008870
rosa_multiflora Rmu_sc0002480.1_g000031 Rmu_ssc0000255.1_g000040
rosa_roxburghii Rroxscaffold_5G00349360
rosa_rugosa Rorug04G0053800 Rorug04G0053900
rosa_samantha Rh4AG129100 Rh4BG122400 Rh4CG136200 Rh4DG122600
rosa_wichuraiana Rw4G010420

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc65I GGTACC 1 cut(s) 442
AccB1I GGYRCC 1 cut(s) 442
AccBSI CCGCTC 1 cut(s) 56
AccII CGCG 1 cut(s) 174
AciI CCGC 6 cut(s) 54, 159, 172, 201, 238, 316
AclWI GGATC 2 cut(s) 281, 294
AcoI YGGCCR 1 cut(s) 120
AcsI RAATTY 1 cut(s) 559
AcuI CTGAAG 1 cut(s) 426
AcyI GRCGYC 1 cut(s) 165
AfaI GTAC 2 cut(s) 314, 444
AfiI CCNNNNNNNGG 2 cut(s) 437, 438
AflII CTTAAG 1 cut(s) 242
AflIII ACRYGT 1 cut(s) 489
AgsI TTSAA 2 cut(s) 73, 617
AjnI CCWGG 1 cut(s) 352
AjuI GAANNNNNNNTTGG 2 cut(s) 399, 431
AluBI AGCT 7 cut(s) 131, 260, 302, 410, 521, 575, 707
AluI AGCT 7 cut(s) 131, 260, 302, 410, 521, 575, 707
Alw26I GTCTC 1 cut(s) 360
AlwI GGATC 2 cut(s) 281, 294
AlwNI CAGNNNCTG 1 cut(s) 296
AoxI GGCC 1 cut(s) 120
ApeKI GCWGC 1 cut(s) 713
ApoI RAATTY 1 cut(s) 559
Asp718I GGTACC 1 cut(s) 442
AspLEI GCGC 1 cut(s) 176
AsuHPI GGTGA 4 cut(s) 76, 132, 173, 545
BalI TGGCCA 1 cut(s) 122
BamHI GGATCC 1 cut(s) 286
BanI GGYRCC 1 cut(s) 442
BbvI GCAGC 1 cut(s) 725
BccI CCATC 4 cut(s) 176, 258, 431, 538
BceAI ACGGC 1 cut(s) 99
BcgI CGANNNNNNTGC 4 cut(s) 354, 364, 388, 398
BciT130I CCWGG 1 cut(s) 354
BciVI GTATCC 1 cut(s) 736
BcoDI GTCTC 1 cut(s) 360
BfaI CTAG 1 cut(s) 105
BfmI CTRYAG 2 cut(s) 19, 297
BfrI CTTAAG 1 cut(s) 242
BfuI GTATCC 1 cut(s) 736
BisI GCNGC 1 cut(s) 714
BlsI GCNGC 1 cut(s) 715
Bme1390I CCNGG 1 cut(s) 354
BmiI GGNNCC 2 cut(s) 288, 444
BmrFI CCNGG 1 cut(s) 354
BplI GAGNNNNNCTC 1 cut(s) 32
Bpu10I CCTNAGC 1 cut(s) 522
BsaHI GRCGYC 1 cut(s) 165
BsaJI CCNNGG 1 cut(s) 621
Bsc4I CCNNNNNNNGG 2 cut(s) 437, 438
Bse118I RCCGGY 1 cut(s) 155
Bse1I ACTGG 1 cut(s) 667
Bse3DI GCAATG 2 cut(s) 336, 399
BseBI CCWGG 1 cut(s) 354
BseDI CCNNGG 1 cut(s) 621
BseGI GGATG 6 cut(s) 65, 146, 168, 269, 549, 661
BseLI CCNNNNNNNGG 2 cut(s) 437, 438
BseMI GCAATG 2 cut(s) 336, 399
BseNI ACTGG 1 cut(s) 667
BseRI GAGGAG 3 cut(s) 20, 186, 196
BseXI GCAGC 1 cut(s) 725
BseYI CCCAGC 1 cut(s) 677
Bsh1236I CGCG 1 cut(s) 174
BshFI GGCC 1 cut(s) 122
BshNI GGYRCC 1 cut(s) 442
BsiSI CCGG 1 cut(s) 156
BslI CCNNNNNNNGG 2 cut(s) 437, 438
BsmAI GTCTC 1 cut(s) 360
BsnI GGCC 1 cut(s) 122
Bsp143I GATC 3 cut(s) 23, 286, 381
BspACI CCGC 6 cut(s) 54, 159, 172, 201, 238, 316
BspANI GGCC 1 cut(s) 122
BspFNI CGCG 1 cut(s) 174
BspHI TCATGA 1 cut(s) 394
BspLI GGNNCC 2 cut(s) 288, 444
BspPI GGATC 2 cut(s) 281, 294
BspT107I GGYRCC 1 cut(s) 442
BspTI CTTAAG 1 cut(s) 242
BsrBI CCGCTC 1 cut(s) 56
BsrDI GCAATG 2 cut(s) 336, 399
BsrFI RCCGGY 1 cut(s) 155
BsrI ACTGG 1 cut(s) 667
BssAI RCCGGY 1 cut(s) 155
BssECI CCNNGG 1 cut(s) 621
BssMI GATC 3 cut(s) 23, 286, 381
BssNI GRCGYC 1 cut(s) 165
BssT1I CCWWGG 1 cut(s) 621
Bst2UI CCWGG 1 cut(s) 354
Bst4CI ACNGT 1 cut(s) 144
Bst6I CTCTTC 2 cut(s) 193, 460
BstACI GRCGYC 1 cut(s) 165
BstAFI CTTAAG 1 cut(s) 242
BstDEI CTNAG 1 cut(s) 522
BstF5I GGATG 6 cut(s) 65, 146, 168, 269, 549, 661
BstFNI CGCG 1 cut(s) 174
BstHHI GCGC 1 cut(s) 176
BstKTI GATC 3 cut(s) 26, 289, 384
BstMAI GTCTC 1 cut(s) 360
BstMBI GATC 3 cut(s) 23, 286, 381
BstMWI GCNNNNNNNGC 5 cut(s) 128, 173, 209, 338, 713
BstNI CCWGG 1 cut(s) 354
BstNSI RCATGY 1 cut(s) 493
BstSCI CCNGG 1 cut(s) 352
BstSFI CTRYAG 2 cut(s) 19, 297
BstUI CGCG 1 cut(s) 174
BstV1I GCAGC 1 cut(s) 725
BstX2I RGATCY 1 cut(s) 286
BstYI RGATCY 1 cut(s) 286
BsuI GTATCC 1 cut(s) 736
BsuRI GGCC 1 cut(s) 122
BtsCI GGATG 6 cut(s) 65, 146, 168, 269, 549, 661
CaiI CAGNNNCTG 1 cut(s) 296
CciI TCATGA 1 cut(s) 394
CfoI GCGC 1 cut(s) 176
Cfr10I RCCGGY 1 cut(s) 155
CseI GACGC 1 cut(s) 173
Csp6I GTAC 2 cut(s) 313, 443
CviAII CATG 3 cut(s) 319, 395, 490
CviQI GTAC 2 cut(s) 313, 443
DdeI CTNAG 1 cut(s) 522
DpnI GATC 3 cut(s) 25, 288, 383
DpnII GATC 3 cut(s) 23, 286, 381
EaeI YGGCCR 1 cut(s) 120
Eam1104I CTCTTC 2 cut(s) 193, 460
EarI CTCTTC 2 cut(s) 193, 460
Eco130I CCWWGG 1 cut(s) 621
Eco57I CTGAAG 1 cut(s) 426
EcoRI GAATTC 1 cut(s) 559
EcoRII CCWGG 1 cut(s) 352
EcoT14I CCWWGG 1 cut(s) 621
ErhI CCWWGG 1 cut(s) 621
FaeI CATG 3 cut(s) 322, 398, 493
FatI CATG 3 cut(s) 318, 394, 489
FauI CCCGC 1 cut(s) 208
FauNDI CATATG 1 cut(s) 309
Fnu4HI GCNGC 1 cut(s) 714
FokI GGATG 6 cut(s) 52, 133, 155, 276, 556, 668
Fsp4HI GCNGC 1 cut(s) 714
FspBI CTAG 1 cut(s) 105
GlaI GCGC 1 cut(s) 175
GluI GCNGC 1 cut(s) 714
GsaI CCCAGC 1 cut(s) 681
HaeIII GGCC 1 cut(s) 122
HapII CCGG 1 cut(s) 156
HgaI GACGC 1 cut(s) 173
HhaI GCGC 1 cut(s) 176
Hin1I GRCGYC 1 cut(s) 165
Hin1II CATG 3 cut(s) 322, 398, 493
Hin6I GCGC 1 cut(s) 174
HinP1I GCGC 1 cut(s) 174
HincII GTYRAC 1 cut(s) 672
HindII GTYRAC 1 cut(s) 672
HindIII AAGCTT 2 cut(s) 129, 705
HinfI GANTC 2 cut(s) 4, 293
HpaII CCGG 1 cut(s) 156
HphI GGTGA 4 cut(s) 76, 132, 173, 545
Hpy166II GTNNAC 1 cut(s) 672
Hpy188I TCNGA 1 cut(s) 346
Hpy188III TCNNGA 5 cut(s) 290, 365, 395, 688, 729
Hpy8I GTNNAC 1 cut(s) 672
Hpy99I CGWCG 2 cut(s) 139, 253
HpyAV CCTTC 4 cut(s) 51, 108, 277, 442
HpyCH4III ACNGT 1 cut(s) 144
HpyCH4V TGCA 2 cut(s) 375, 495
HpyF10VI GCNNNNNNNGC 5 cut(s) 128, 173, 209, 338, 713
HpyF3I CTNAG 1 cut(s) 522
Hsp92I GRCGYC 1 cut(s) 165
Hsp92II CATG 3 cut(s) 322, 398, 493
HspAI GCGC 1 cut(s) 174
KpnI GGTACC 1 cut(s) 446
Kzo9I GATC 3 cut(s) 23, 286, 381
LmnI GCTCC 2 cut(s) 33, 61
Lsp1109I GCAGC 1 cut(s) 725
MaeI CTAG 1 cut(s) 105
MaeIII GTNAC 2 cut(s) 138, 161
MalI GATC 3 cut(s) 25, 288, 383
MbiI CCGCTC 1 cut(s) 56
MboI GATC 3 cut(s) 23, 286, 381
MboII GAAGA 5 cut(s) 93, 180, 469, 477, 744
MflI RGATCY 1 cut(s) 286
MlsI TGGCCA 1 cut(s) 122
MluCI AATT 4 cut(s) 497, 536, 559, 579
MluNI TGGCCA 1 cut(s) 122
MlyI GAGTC 2 cut(s) 13, 302
Mox20I TGGCCA 1 cut(s) 122
MscI TGGCCA 1 cut(s) 122
MseI TTAA 3 cut(s) 243, 270, 326
Msp20I TGGCCA 1 cut(s) 122
MspCI CTTAAG 1 cut(s) 242
MspI CCGG 1 cut(s) 156
MspR9I CCNGG 1 cut(s) 354
MvaI CCWGG 1 cut(s) 354
MvnI CGCG 1 cut(s) 174
MwoI GCNNNNNNNGC 5 cut(s) 128, 173, 209, 338, 713
NdeI CATATG 1 cut(s) 309
NdeII GATC 3 cut(s) 23, 286, 381
NlaIII CATG 3 cut(s) 322, 398, 493
NlaIV GGNNCC 2 cut(s) 288, 444
NmuCI GTSAC 2 cut(s) 138, 161
NspI RCATGY 1 cut(s) 493
PagI TCATGA 1 cut(s) 394
PciI ACATGT 1 cut(s) 489
PcsI WCGNNNNNNNCGW 1 cut(s) 140
PkrI GCNGC 1 cut(s) 715
PleI GAGTC 2 cut(s) 12, 301
PpsI GAGTC 2 cut(s) 12, 301
PscI ACATGT 1 cut(s) 489
Psp6I CCWGG 1 cut(s) 352
PspFI CCCAGC 1 cut(s) 677
PspGI CCWGG 1 cut(s) 352
PspN4I GGNNCC 2 cut(s) 288, 444
PstNI CAGNNNCTG 1 cut(s) 296
PsuI RGATCY 1 cut(s) 286
RsaI GTAC 2 cut(s) 314, 444
RsaNI GTAC 2 cut(s) 313, 443
SaqAI TTAA 3 cut(s) 243, 270, 326
SatI GCNGC 1 cut(s) 714
Sau3AI GATC 3 cut(s) 23, 286, 381
SchI GAGTC 2 cut(s) 13, 302
ScrFI CCNGG 1 cut(s) 354
SfcI CTRYAG 2 cut(s) 19, 297
SgrAI CRCCGGYG 1 cut(s) 155
SmlI CTYRAG 1 cut(s) 242
SmoI CTYRAG 1 cut(s) 242
Sse9I AATT 4 cut(s) 497, 536, 559, 579
SsiI CCGC 6 cut(s) 54, 159, 172, 201, 238, 316
SspMI CTAG 1 cut(s) 105
StyD4I CCNGG 1 cut(s) 352
StyI CCWWGG 1 cut(s) 621
TaaI ACNGT 1 cut(s) 144
TaqI TCGA 2 cut(s) 7, 364
TasI AATT 4 cut(s) 497, 536, 559, 579
Tru1I TTAA 3 cut(s) 243, 270, 326
Tru9I TTAA 3 cut(s) 243, 270, 326
TseFI GTSAC 2 cut(s) 138, 161
TseI GCWGC 1 cut(s) 713
Tsp45I GTSAC 2 cut(s) 138, 161
TspDTI ATGAA 1 cut(s) 383
Vha464I CTTAAG 1 cut(s) 242
XapI RAATTY 1 cut(s) 559
XceI RCATGY 1 cut(s) 493
XcmI CCANNNNNNNNNTGG 1 cut(s) 674
XspI CTAG 1 cut(s) 105
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.