Rroxscaffold_5G00349360

HD domain-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000005
OG0011001
Physical Location & Seq
Forward (+)
22267396 .. 22269724
2329 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_5G00349360.1

Sequence Viewer

Length: 723 bp
ATGAGCCGAGTGTTCCTCTGTAAATCGCTCCTCCTAACACCTTCCCTCTACTCCGCTCCCCTCACCTCCTTGAAGCCCACACTCACCTCTGCTTCTTCTTCTAGGGTTCACCGTATGGCCACCGAAGCTTCGTCGTCACACCGTCATCCCCACACCGGCGGTGACGCCATCAACCCCAACCCAACCCAATCTACGACGAAAAGAGCTGGATGGGTTAAGAGAGATGTGAGGGATCCAGAGTCTGTAGCTGACCATATGTACCGCATGGGTTTAATGGCTCTCATTGCTTCGGATATTCCTGGTGTCAATCGAGACAAGTGCATAAAGATCGCCATTGTTCATGACATTGCTGAAGGTGAAACAGCATTCAAGTCTCTGATTTCTATTGTTGGGGATATAACCCCCACAGATGGGGTACCGAAGGCAGAGAAGAACCGAAGAGAACAAGAGGCAATAGACCACATGTGCAAATTACTGGGTGGAGGCTCAATAGCTAAGGAAATAGGTGAATTGTGGATGGAGTATGAGGGGAATTCCTCCCCAGAAGCTCAAATTGTCAAGGACTTTGACAAGGTGGAGATGATACTTCAAGCCTTGGAATATGAGAATGGTCAAGGAAAGGACTTGGAAGAGTTTTTCCAGTCAACTGCTGGGAAGTTCCAGACTGATGTAGGCAAAGCTTGGGCAGCAGAGATAGTATCCAGAAGAAAAAAACAAGGCTAA
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

240

Amino Acids

26.36

Weight (kDa)

6.67

Isoelectric Point (pI)

38.84

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
HD_3 PF13023 65 - 227 1.3e-40 HD domain
HD PF01966 82 - 194 6.9e-10 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) 415
AccB1I GGYRCC 1 cut(s) 415
AccBSI CCGCTC 1 cut(s) 56
AciI CCGC 3 cut(s) 54, 159, 262
AclWI GGATC 2 cut(s) 227, 240
AcoI YGGCCR 1 cut(s) 117
AcsI RAATTY 1 cut(s) 532
AcuI CTGAAG 1 cut(s) 372
AcyI GRCGYC 1 cut(s) 165
AfaI GTAC 2 cut(s) 260, 417
AfiI CCNNNNNNNGG 3 cut(s) 155, 410, 411
AflIII ACRYGT 1 cut(s) 462
AgsI TTSAA 3 cut(s) 73, 370, 590
AjnI CCWGG 1 cut(s) 298
AluBI AGCT 6 cut(s) 128, 206, 248, 494, 548, 680
AluI AGCT 6 cut(s) 128, 206, 248, 494, 548, 680
Alw26I GTCTC 2 cut(s) 306, 378
AlwI GGATC 2 cut(s) 227, 240
AlwNI CAGNNNCTG 1 cut(s) 242
AoxI GGCC 1 cut(s) 117
ApeKI GCWGC 1 cut(s) 686
ApoI RAATTY 1 cut(s) 532
Asp718I GGTACC 1 cut(s) 415
AsuHPI GGTGA 6 cut(s) 55, 76, 101, 173, 368, 518
BalI TGGCCA 1 cut(s) 119
BamHI GGATCC 1 cut(s) 232
BanI GGYRCC 1 cut(s) 415
BbvI GCAGC 1 cut(s) 698
BccI CCATC 4 cut(s) 176, 204, 404, 511
BcgI CGANNNNNNTGC 4 cut(s) 300, 310, 334, 344
BciT130I CCWGG 1 cut(s) 300
BciVI GTATCC 1 cut(s) 709
BcoDI GTCTC 2 cut(s) 306, 378
BfaI CTAG 1 cut(s) 102
BfmI CTRYAG 1 cut(s) 243
BfuI GTATCC 1 cut(s) 709
BisI GCNGC 1 cut(s) 687
BlsI GCNGC 1 cut(s) 688
Bme1390I CCNGG 1 cut(s) 300
BmiI GGNNCC 2 cut(s) 234, 417
BmrFI CCNGG 1 cut(s) 300
BmrI ACTGGG 1 cut(s) 485
BmuI ACTGGG 1 cut(s) 485
BplI GAGNNNNNCTC 1 cut(s) 32
Bpu10I CCTNAGC 1 cut(s) 495
BsaHI GRCGYC 1 cut(s) 165
BsaJI CCNNGG 1 cut(s) 594
Bsc4I CCNNNNNNNGG 3 cut(s) 155, 410, 411
Bse118I RCCGGY 1 cut(s) 155
Bse1I ACTGG 2 cut(s) 480, 640
Bse3DI GCAATG 2 cut(s) 282, 345
BseBI CCWGG 1 cut(s) 300
BseDI CCNNGG 1 cut(s) 594
BseGI GGATG 3 cut(s) 145, 215, 522
BseLI CCNNNNNNNGG 3 cut(s) 155, 410, 411
BseMI GCAATG 2 cut(s) 282, 345
BseNI ACTGG 2 cut(s) 480, 640
BseRI GAGGAG 1 cut(s) 20
BseXI GCAGC 1 cut(s) 698
BseYI CCCAGC 1 cut(s) 650
BshFI GGCC 1 cut(s) 119
BshNI GGYRCC 1 cut(s) 415
BsiSI CCGG 1 cut(s) 156
BslI CCNNNNNNNGG 3 cut(s) 155, 410, 411
BsmAI GTCTC 2 cut(s) 306, 378
BsmI GAATGC 1 cut(s) 365
BsnI GGCC 1 cut(s) 119
Bsp143I GATC 2 cut(s) 232, 327
BspACI CCGC 3 cut(s) 54, 159, 262
BspANI GGCC 1 cut(s) 119
BspHI TCATGA 1 cut(s) 340
BspLI GGNNCC 2 cut(s) 234, 417
BspPI GGATC 2 cut(s) 227, 240
BspT107I GGYRCC 1 cut(s) 415
BsrBI CCGCTC 1 cut(s) 56
BsrDI GCAATG 2 cut(s) 282, 345
BsrFI RCCGGY 1 cut(s) 155
BsrI ACTGG 2 cut(s) 480, 640
BssAI RCCGGY 1 cut(s) 155
BssECI CCNNGG 1 cut(s) 594
BssMI GATC 2 cut(s) 232, 327
BssNI GRCGYC 1 cut(s) 165
BssT1I CCWWGG 1 cut(s) 594
Bst2UI CCWGG 1 cut(s) 300
Bst4CI ACNGT 2 cut(s) 113, 143
Bst6I CTCTTC 2 cut(s) 433, 624
BstACI GRCGYC 1 cut(s) 165
BstDEI CTNAG 1 cut(s) 495
BstF5I GGATG 3 cut(s) 145, 215, 522
BstKTI GATC 2 cut(s) 235, 330
BstMAI GTCTC 2 cut(s) 306, 378
BstMBI GATC 2 cut(s) 232, 327
BstMWI GCNNNNNNNGC 3 cut(s) 125, 284, 686
BstNI CCWGG 1 cut(s) 300
BstNSI RCATGY 1 cut(s) 466
BstSCI CCNGG 1 cut(s) 298
BstSFI CTRYAG 1 cut(s) 243
BstV1I GCAGC 1 cut(s) 698
BstX2I RGATCY 1 cut(s) 232
BstYI RGATCY 1 cut(s) 232
BsuI GTATCC 1 cut(s) 709
BsuRI GGCC 1 cut(s) 119
BtsCI GGATG 3 cut(s) 145, 215, 522
CaiI CAGNNNCTG 1 cut(s) 242
CciI TCATGA 1 cut(s) 340
Cfr10I RCCGGY 1 cut(s) 155
CseI GACGC 1 cut(s) 173
Csp6I GTAC 2 cut(s) 259, 416
CviAII CATG 3 cut(s) 265, 341, 463
CviQI GTAC 2 cut(s) 259, 416
DdeI CTNAG 1 cut(s) 495
DpnI GATC 2 cut(s) 234, 329
DpnII GATC 2 cut(s) 232, 327
EaeI YGGCCR 1 cut(s) 117
Eam1104I CTCTTC 2 cut(s) 433, 624
EarI CTCTTC 2 cut(s) 433, 624
Eco130I CCWWGG 1 cut(s) 594
Eco57I CTGAAG 1 cut(s) 372
EcoRI GAATTC 1 cut(s) 532
EcoRII CCWGG 1 cut(s) 298
EcoT14I CCWWGG 1 cut(s) 594
ErhI CCWWGG 1 cut(s) 594
FaeI CATG 3 cut(s) 268, 344, 466
FatI CATG 3 cut(s) 264, 340, 462
FauNDI CATATG 1 cut(s) 255
Fnu4HI GCNGC 1 cut(s) 687
FokI GGATG 3 cut(s) 132, 222, 529
Fsp4HI GCNGC 1 cut(s) 687
FspBI CTAG 1 cut(s) 102
GluI GCNGC 1 cut(s) 687
GsaI CCCAGC 1 cut(s) 654
HaeIII GGCC 1 cut(s) 119
HapII CCGG 1 cut(s) 156
HgaI GACGC 1 cut(s) 173
Hin1I GRCGYC 1 cut(s) 165
Hin1II CATG 3 cut(s) 268, 344, 466
HincII GTYRAC 1 cut(s) 645
HindII GTYRAC 1 cut(s) 645
HindIII AAGCTT 2 cut(s) 126, 678
HinfI GANTC 1 cut(s) 239
HpaII CCGG 1 cut(s) 156
HphI GGTGA 6 cut(s) 55, 76, 101, 173, 368, 518
Hpy166II GTNNAC 2 cut(s) 109, 645
Hpy188I TCNGA 2 cut(s) 292, 378
Hpy188III TCNNGA 5 cut(s) 236, 311, 341, 661, 702
Hpy8I GTNNAC 2 cut(s) 109, 645
Hpy99I CGWCG 2 cut(s) 136, 199
HpyAV CCTTC 3 cut(s) 51, 347, 415
HpyCH4III ACNGT 2 cut(s) 113, 143
HpyCH4V TGCA 2 cut(s) 321, 468
HpyF10VI GCNNNNNNNGC 3 cut(s) 125, 284, 686
HpyF3I CTNAG 1 cut(s) 495
Hsp92I GRCGYC 1 cut(s) 165
Hsp92II CATG 3 cut(s) 268, 344, 466
KpnI GGTACC 1 cut(s) 419
Kzo9I GATC 2 cut(s) 232, 327
LmnI GCTCC 2 cut(s) 33, 61
Lsp1109I GCAGC 1 cut(s) 698
MaeI CTAG 1 cut(s) 102
MaeIII GTNAC 2 cut(s) 135, 161
MalI GATC 2 cut(s) 234, 329
MbiI CCGCTC 1 cut(s) 56
MboI GATC 2 cut(s) 232, 327
MboII GAAGA 6 cut(s) 87, 90, 442, 450, 641, 717
MflI RGATCY 1 cut(s) 232
MlsI TGGCCA 1 cut(s) 119
MluCI AATT 4 cut(s) 470, 509, 532, 552
MluNI TGGCCA 1 cut(s) 119
MlyI GAGTC 1 cut(s) 248
Mox20I TGGCCA 1 cut(s) 119
MscI TGGCCA 1 cut(s) 119
MseI TTAA 2 cut(s) 216, 272
Msp20I TGGCCA 1 cut(s) 119
MspI CCGG 1 cut(s) 156
MspR9I CCNGG 1 cut(s) 300
Mva1269I GAATGC 1 cut(s) 365
MvaI CCWGG 1 cut(s) 300
MwoI GCNNNNNNNGC 3 cut(s) 125, 284, 686
NdeI CATATG 1 cut(s) 255
NdeII GATC 2 cut(s) 232, 327
NlaIII CATG 3 cut(s) 268, 344, 466
NlaIV GGNNCC 2 cut(s) 234, 417
NmeAIII GCCGAG 1 cut(s) 32
NmuCI GTSAC 2 cut(s) 135, 161
NspI RCATGY 1 cut(s) 466
PagI TCATGA 1 cut(s) 340
PciI ACATGT 1 cut(s) 462
PctI GAATGC 1 cut(s) 365
PkrI GCNGC 1 cut(s) 688
PleI GAGTC 1 cut(s) 247
PpsI GAGTC 1 cut(s) 247
PscI ACATGT 1 cut(s) 462
Psp6I CCWGG 1 cut(s) 298
PspFI CCCAGC 1 cut(s) 650
PspGI CCWGG 1 cut(s) 298
PspN4I GGNNCC 2 cut(s) 234, 417
PstNI CAGNNNCTG 1 cut(s) 242
PsuI RGATCY 1 cut(s) 232
RsaI GTAC 2 cut(s) 260, 417
RsaNI GTAC 2 cut(s) 259, 416
SaqAI TTAA 2 cut(s) 216, 272
SatI GCNGC 1 cut(s) 687
Sau3AI GATC 2 cut(s) 232, 327
SchI GAGTC 1 cut(s) 248
ScrFI CCNGG 1 cut(s) 300
SfcI CTRYAG 1 cut(s) 243
SgrAI CRCCGGYG 1 cut(s) 155
Sse9I AATT 4 cut(s) 470, 509, 532, 552
SsiI CCGC 3 cut(s) 54, 159, 262
SspMI CTAG 1 cut(s) 102
StyD4I CCNGG 1 cut(s) 298
StyI CCWWGG 1 cut(s) 594
TaaI ACNGT 2 cut(s) 113, 143
TaqI TCGA 1 cut(s) 310
TasI AATT 4 cut(s) 470, 509, 532, 552
Tru1I TTAA 2 cut(s) 216, 272
Tru9I TTAA 2 cut(s) 216, 272
TseFI GTSAC 2 cut(s) 135, 161
TseI GCWGC 1 cut(s) 686
Tsp45I GTSAC 2 cut(s) 135, 161
TspDTI ATGAA 1 cut(s) 329
XapI RAATTY 1 cut(s) 532
XceI RCATGY 1 cut(s) 466
XcmI CCANNNNNNNNNTGG 1 cut(s) 647
XspI CTAG 1 cut(s) 102
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.