Rh4DG122600

HD domain-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr4D
OG0011001
Physical Location & Seq
Forward (+)
19726243 .. 19728672
2430 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh4DG122600.1

Sequence Viewer

Length: 825 bp
ATGGACCCAACAAAATTTGACCAAAAATTAAAGGAAAGCAAAAAGGAAGGAAATCGAAAAAAGAAAGGAAAAAAAATGAGTCGAGCGTTCCTCTGTAGATCGCTCCTCCTAACACCTTCTCTCTACTCCGCTCCCCTCACATCCTTGAAGCCCACACTCACCTCTGCTTCTCCTTCTTCTAGGGTTCGCCGTATGGCCACCGAAGCTTCGTCGTCACCGTCATCCCACACCGGCGGTGACGCCATCCGCGCCGACCCAACCTCTTCCTCTCCTCCCGCCTCCTCTGCCATTGATTTTCTCTCCCTCTGCCACCGCCTTAAGACGACGAAAAGAGCTGGATGGGTTAAGAGAGATGTGAAGGATCCAGAGTCTGTAGCTGACCATATGTACCGCATGGGTTTAATGGCTCTCATTGCTTCGGATATTCCTGGTGTCAATCGAGACAAGTGCATAAAGATCGCCATTGTTCATGACATTGCTGAAGCTATTGTTGGGGATATAACCCCCACAGATGGGGTACCGAAGGCAGAGAAGAACCGAAGAGAACAAGAGGCAATAGACCACATGTGCAAATTACTTGGTGGAGGCTCAATAGCTAAGGAAATAGGTGAATTGTGGATGGAGTATGAGGCGAATTCCTCCCCAGAAGCTAAAATTGTCAAGGACTTTGACAAGGTGGAGATGATACTTCAAGCCTTGGAATATGAGAATGGTCAAGGAAAGGACTTGGATGAGTTTTTCCAGTCAACTGCTGGGAAGTTCCAGACTGATGTAGGCAAAGCTTGGGCAGCAGAGATAGTATCCAGAAGAAAAAAACAAGGCTAA
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

274

Amino Acids

30.08

Weight (kDa)

9.2

Isoelectric Point (pI)

47.59

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
YfbR-like PF12917 99 - 242 1.9e-06 5'-deoxynucleotidase YfbR-like
HD_3 PF13023 104 - 261 2.4e-49 HD domain
HD PF01966 125 - 228 1.1e-11 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) 517
AccB1I GGYRCC 1 cut(s) 517
AccBSI CCGCTC 1 cut(s) 131
AccII CGCG 1 cut(s) 249
AciI CCGC 6 cut(s) 129, 234, 247, 276, 313, 391
AclWI GGATC 2 cut(s) 356, 369
AcoI YGGCCR 1 cut(s) 195
AcsI RAATTY 2 cut(s) 14, 634
AcuI CTGAAG 1 cut(s) 501
AcyI GRCGYC 1 cut(s) 240
AfaI GTAC 2 cut(s) 389, 519
AfiI CCNNNNNNNGG 2 cut(s) 512, 513
AflII CTTAAG 1 cut(s) 317
AflIII ACRYGT 1 cut(s) 564
AgsI TTSAA 2 cut(s) 148, 692
AjnI CCWGG 1 cut(s) 427
AjuI GAANNNNNNNTTGG 2 cut(s) 474, 506
AluBI AGCT 7 cut(s) 206, 335, 377, 485, 596, 650, 782
AluI AGCT 7 cut(s) 206, 335, 377, 485, 596, 650, 782
Alw26I GTCTC 1 cut(s) 435
AlwI GGATC 2 cut(s) 356, 369
AlwNI CAGNNNCTG 1 cut(s) 371
AoxI GGCC 1 cut(s) 195
ApeKI GCWGC 1 cut(s) 788
ApoI RAATTY 2 cut(s) 14, 634
Asp718I GGTACC 1 cut(s) 517
AspLEI GCGC 1 cut(s) 251
AspS9I GGNCC 1 cut(s) 4
AsuHPI GGTGA 4 cut(s) 151, 207, 248, 620
AvaII GGWCC 1 cut(s) 4
BalI TGGCCA 1 cut(s) 197
BamHI GGATCC 1 cut(s) 361
BanI GGYRCC 1 cut(s) 517
BbvI GCAGC 1 cut(s) 800
BccI CCATC 4 cut(s) 251, 333, 506, 613
BceAI ACGGC 1 cut(s) 174
BcgI CGANNNNNNTGC 4 cut(s) 429, 439, 463, 473
BciT130I CCWGG 1 cut(s) 429
BciVI GTATCC 1 cut(s) 811
BcoDI GTCTC 1 cut(s) 435
BfaI CTAG 1 cut(s) 180
BfmI CTRYAG 2 cut(s) 94, 372
BfrI CTTAAG 1 cut(s) 317
BfuI GTATCC 1 cut(s) 811
BisI GCNGC 1 cut(s) 789
BlsI GCNGC 1 cut(s) 790
Bme1390I CCNGG 1 cut(s) 429
Bme18I GGWCC 1 cut(s) 4
BmgT120I GGNCC 1 cut(s) 4
BmiI GGNNCC 3 cut(s) 6, 363, 519
BmrFI CCNGG 1 cut(s) 429
BplI GAGNNNNNCTC 2 cut(s) 75, 107
Bpu10I CCTNAGC 1 cut(s) 597
BsaHI GRCGYC 1 cut(s) 240
BsaJI CCNNGG 1 cut(s) 696
Bsc4I CCNNNNNNNGG 2 cut(s) 512, 513
Bse118I RCCGGY 1 cut(s) 230
Bse1I ACTGG 1 cut(s) 742
Bse3DI GCAATG 2 cut(s) 411, 474
BseBI CCWGG 1 cut(s) 429
BseDI CCNNGG 1 cut(s) 696
BseGI GGATG 6 cut(s) 140, 221, 243, 344, 624, 736
BseLI CCNNNNNNNGG 2 cut(s) 512, 513
BseMI GCAATG 2 cut(s) 411, 474
BseNI ACTGG 1 cut(s) 742
BseRI GAGGAG 3 cut(s) 95, 261, 271
BseXI GCAGC 1 cut(s) 800
BseYI CCCAGC 1 cut(s) 752
Bsh1236I CGCG 1 cut(s) 249
BshFI GGCC 1 cut(s) 197
BshNI GGYRCC 1 cut(s) 517
BsiSI CCGG 1 cut(s) 231
BslI CCNNNNNNNGG 2 cut(s) 512, 513
BsmAI GTCTC 1 cut(s) 435
BsnI GGCC 1 cut(s) 197
Bsp143I GATC 3 cut(s) 98, 361, 456
BspACI CCGC 6 cut(s) 129, 234, 247, 276, 313, 391
BspANI GGCC 1 cut(s) 197
BspFNI CGCG 1 cut(s) 249
BspHI TCATGA 1 cut(s) 469
BspLI GGNNCC 3 cut(s) 6, 363, 519
BspPI GGATC 2 cut(s) 356, 369
BspT107I GGYRCC 1 cut(s) 517
BspTI CTTAAG 1 cut(s) 317
BsrBI CCGCTC 1 cut(s) 131
BsrDI GCAATG 2 cut(s) 411, 474
BsrFI RCCGGY 1 cut(s) 230
BsrI ACTGG 1 cut(s) 742
BssAI RCCGGY 1 cut(s) 230
BssECI CCNNGG 1 cut(s) 696
BssMI GATC 3 cut(s) 98, 361, 456
BssNI GRCGYC 1 cut(s) 240
BssT1I CCWWGG 1 cut(s) 696
Bst2UI CCWGG 1 cut(s) 429
Bst4CI ACNGT 1 cut(s) 219
Bst6I CTCTTC 2 cut(s) 268, 535
BstACI GRCGYC 1 cut(s) 240
BstAFI CTTAAG 1 cut(s) 317
BstDEI CTNAG 1 cut(s) 597
BstF5I GGATG 6 cut(s) 140, 221, 243, 344, 624, 736
BstFNI CGCG 1 cut(s) 249
BstHHI GCGC 1 cut(s) 251
BstKTI GATC 3 cut(s) 101, 364, 459
BstMAI GTCTC 1 cut(s) 435
BstMBI GATC 3 cut(s) 98, 361, 456
BstMWI GCNNNNNNNGC 5 cut(s) 203, 248, 284, 413, 788
BstNI CCWGG 1 cut(s) 429
BstNSI RCATGY 1 cut(s) 568
BstSCI CCNGG 1 cut(s) 427
BstSFI CTRYAG 2 cut(s) 94, 372
BstUI CGCG 1 cut(s) 249
BstV1I GCAGC 1 cut(s) 800
BstX2I RGATCY 1 cut(s) 361
BstYI RGATCY 1 cut(s) 361
BsuI GTATCC 1 cut(s) 811
BsuRI GGCC 1 cut(s) 197
BtsCI GGATG 6 cut(s) 140, 221, 243, 344, 624, 736
CaiI CAGNNNCTG 1 cut(s) 371
CciI TCATGA 1 cut(s) 469
CfoI GCGC 1 cut(s) 251
Cfr10I RCCGGY 1 cut(s) 230
Cfr13I GGNCC 1 cut(s) 4
CseI GACGC 1 cut(s) 248
Csp6I GTAC 2 cut(s) 388, 518
CviAII CATG 3 cut(s) 394, 470, 565
CviQI GTAC 2 cut(s) 388, 518
DdeI CTNAG 1 cut(s) 597
DpnI GATC 3 cut(s) 100, 363, 458
DpnII GATC 3 cut(s) 98, 361, 456
EaeI YGGCCR 1 cut(s) 195
Eam1104I CTCTTC 2 cut(s) 268, 535
EarI CTCTTC 2 cut(s) 268, 535
Eco130I CCWWGG 1 cut(s) 696
Eco47I GGWCC 1 cut(s) 4
Eco57I CTGAAG 1 cut(s) 501
EcoRI GAATTC 1 cut(s) 634
EcoRII CCWGG 1 cut(s) 427
EcoT14I CCWWGG 1 cut(s) 696
ErhI CCWWGG 1 cut(s) 696
FaeI CATG 3 cut(s) 397, 473, 568
FatI CATG 3 cut(s) 393, 469, 564
FauI CCCGC 1 cut(s) 283
FauNDI CATATG 1 cut(s) 384
Fnu4HI GCNGC 1 cut(s) 789
FokI GGATG 6 cut(s) 127, 208, 230, 351, 631, 743
Fsp4HI GCNGC 1 cut(s) 789
FspBI CTAG 1 cut(s) 180
GlaI GCGC 1 cut(s) 250
GluI GCNGC 1 cut(s) 789
GsaI CCCAGC 1 cut(s) 756
HaeIII GGCC 1 cut(s) 197
HapII CCGG 1 cut(s) 231
HgaI GACGC 1 cut(s) 248
HhaI GCGC 1 cut(s) 251
Hin1I GRCGYC 1 cut(s) 240
Hin1II CATG 3 cut(s) 397, 473, 568
Hin6I GCGC 1 cut(s) 249
HinP1I GCGC 1 cut(s) 249
HincII GTYRAC 1 cut(s) 747
HindII GTYRAC 1 cut(s) 747
HindIII AAGCTT 2 cut(s) 204, 780
HinfI GANTC 2 cut(s) 79, 368
HpaII CCGG 1 cut(s) 231
HphI GGTGA 4 cut(s) 151, 207, 248, 620
Hpy166II GTNNAC 1 cut(s) 747
Hpy188I TCNGA 1 cut(s) 421
Hpy188III TCNNGA 5 cut(s) 365, 440, 470, 763, 804
Hpy8I GTNNAC 1 cut(s) 747
Hpy99I CGWCG 2 cut(s) 214, 328
HpyAV CCTTC 5 cut(s) 41, 126, 183, 352, 517
HpyCH4III ACNGT 1 cut(s) 219
HpyCH4V TGCA 2 cut(s) 450, 570
HpyF10VI GCNNNNNNNGC 5 cut(s) 203, 248, 284, 413, 788
HpyF3I CTNAG 1 cut(s) 597
Hsp92I GRCGYC 1 cut(s) 240
Hsp92II CATG 3 cut(s) 397, 473, 568
HspAI GCGC 1 cut(s) 249
KpnI GGTACC 1 cut(s) 521
Kzo9I GATC 3 cut(s) 98, 361, 456
LmnI GCTCC 2 cut(s) 108, 136
Lsp1109I GCAGC 1 cut(s) 800
MaeI CTAG 1 cut(s) 180
MaeIII GTNAC 2 cut(s) 213, 236
MalI GATC 3 cut(s) 100, 363, 458
MbiI CCGCTC 1 cut(s) 131
MboI GATC 3 cut(s) 98, 361, 456
MboII GAAGA 5 cut(s) 168, 255, 544, 552, 819
MflI RGATCY 1 cut(s) 361
MlsI TGGCCA 1 cut(s) 197
MluCI AATT 6 cut(s) 14, 26, 572, 611, 634, 654
MluNI TGGCCA 1 cut(s) 197
MlyI GAGTC 2 cut(s) 88, 377
Mox20I TGGCCA 1 cut(s) 197
MscI TGGCCA 1 cut(s) 197
MseI TTAA 4 cut(s) 29, 318, 345, 401
Msp20I TGGCCA 1 cut(s) 197
MspCI CTTAAG 1 cut(s) 317
MspI CCGG 1 cut(s) 231
MspR9I CCNGG 1 cut(s) 429
MvaI CCWGG 1 cut(s) 429
MvnI CGCG 1 cut(s) 249
MwoI GCNNNNNNNGC 5 cut(s) 203, 248, 284, 413, 788
NdeI CATATG 1 cut(s) 384
NdeII GATC 3 cut(s) 98, 361, 456
NlaIII CATG 3 cut(s) 397, 473, 568
NlaIV GGNNCC 3 cut(s) 6, 363, 519
NmuCI GTSAC 2 cut(s) 213, 236
NspI RCATGY 1 cut(s) 568
PagI TCATGA 1 cut(s) 469
PciI ACATGT 1 cut(s) 564
PcsI WCGNNNNNNNCGW 1 cut(s) 215
PkrI GCNGC 1 cut(s) 790
PleI GAGTC 2 cut(s) 87, 376
PpsI GAGTC 2 cut(s) 87, 376
PscI ACATGT 1 cut(s) 564
Psp6I CCWGG 1 cut(s) 427
PspFI CCCAGC 1 cut(s) 752
PspGI CCWGG 1 cut(s) 427
PspN4I GGNNCC 3 cut(s) 6, 363, 519
PspPI GGNCC 1 cut(s) 4
PstNI CAGNNNCTG 1 cut(s) 371
PsuI RGATCY 1 cut(s) 361
RsaI GTAC 2 cut(s) 389, 519
RsaNI GTAC 2 cut(s) 388, 518
SaqAI TTAA 4 cut(s) 29, 318, 345, 401
SatI GCNGC 1 cut(s) 789
Sau3AI GATC 3 cut(s) 98, 361, 456
Sau96I GGNCC 1 cut(s) 4
SchI GAGTC 2 cut(s) 88, 377
ScrFI CCNGG 1 cut(s) 429
SfcI CTRYAG 2 cut(s) 94, 372
SgrAI CRCCGGYG 1 cut(s) 230
SinI GGWCC 1 cut(s) 4
SmlI CTYRAG 1 cut(s) 317
SmoI CTYRAG 1 cut(s) 317
Sse9I AATT 6 cut(s) 14, 26, 572, 611, 634, 654
SsiI CCGC 6 cut(s) 129, 234, 247, 276, 313, 391
SspMI CTAG 1 cut(s) 180
StyD4I CCNGG 1 cut(s) 427
StyI CCWWGG 1 cut(s) 696
TaaI ACNGT 1 cut(s) 219
TaqI TCGA 3 cut(s) 55, 82, 439
TasI AATT 6 cut(s) 14, 26, 572, 611, 634, 654
Tru1I TTAA 4 cut(s) 29, 318, 345, 401
Tru9I TTAA 4 cut(s) 29, 318, 345, 401
TseFI GTSAC 2 cut(s) 213, 236
TseI GCWGC 1 cut(s) 788
Tsp45I GTSAC 2 cut(s) 213, 236
TspDTI ATGAA 1 cut(s) 458
Vha464I CTTAAG 1 cut(s) 317
VpaK11BI GGWCC 1 cut(s) 4
XapI RAATTY 2 cut(s) 14, 634
XceI RCATGY 1 cut(s) 568
XcmI CCANNNNNNNNNTGG 1 cut(s) 749
XspI CTAG 1 cut(s) 180
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.