Rh4CG136200

HD domain-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr4C
OG0011001
Physical Location & Seq
Forward (+)
26965907 .. 26968832
2926 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh4CG136200.1

Sequence Viewer

Length: 792 bp
ATGAGTCGAGTGTTCCTCTGTAAATCGCTCCTCCTAACACCCTCTCTCTACTCCGCTCCCCTCACATCCTTGAAGCCCACACTCACCTCTGCTTCTCCTTCTTCTAGGGTTCGCCGTATGGCCACCGAAGCTTCGTCGTCACCGTCATCCCACACCGGCGGTGACGCCATCCATCCCGACCCAACCTCTTCCTCTCCTCCCGCCTCCTCTGCCATTGATTTTCTCTCCCTCTGCCACAGCCTTAAGACGACGAAAAGAGCTGGATGGGTTAAGAGAGATGTGAAGGATCCAGAGTCTGTAGCTGACCATATGTACCGCATGGGTTTAATGGCTCTCATTGCTTCGGATATTCCTGGTGTCAATCGAGACAAGTGCATAAAGATCGCCATTGTTCATGACATTGCTGAAGCTATTGTTGGGGATATAACCCCCACAGATGGGGTACCGAAGGCAGAGAAGAACCGAAGAGAACAAGAGGCAATAGACCACATGTGCAAATTACTTGGTGGAGGCTCAATAGCTAAGGAAATAGGTGAATTGTGGATGGAGTATGAGGGGAATTCCTCCCCAGAAGCTCAAATTGTCAAGGACTTTGACAAGGTGGAGATGATACTTCAAGCCTTGGAATATGAGAATGGTGAGGCTGTTCTTATCATTTTGGTATTACAGTATCAAACATGCTGTTACTTTTTCAAACACAATATTAACTATAATTACATATCCTTTTTGGCAATTATTTATAATAACACTTTCAAAGAATATAAAGTTTGCACCTATAGCGTGCGCTTATGA
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

263

Amino Acids

29.1

Weight (kDa)

6.39

Isoelectric Point (pI)

46.92

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
HD_3 PF13023 79 - 214 3.4e-46 HD domain
HD PF01966 100 - 203 1.6e-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)
AanI TTATAA 1 cut(s) 741
Acc65I GGTACC 1 cut(s) 442
AccB1I GGYRCC 1 cut(s) 442
AccBSI CCGCTC 1 cut(s) 56
AciI CCGC 4 cut(s) 54, 159, 201, 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 4 cut(s) 73, 617, 694, 754
AjnI CCWGG 1 cut(s) 352
AjuI GAANNNNNNNTTGG 2 cut(s) 399, 431
AluBI AGCT 6 cut(s) 131, 260, 302, 410, 521, 575
AluI AGCT 6 cut(s) 131, 260, 302, 410, 521, 575
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
ApoI RAATTY 1 cut(s) 559
Asp718I GGTACC 1 cut(s) 442
AspLEI GCGC 1 cut(s) 786
AsuHPI GGTGA 5 cut(s) 76, 132, 173, 545, 650
BalI TGGCCA 1 cut(s) 122
BamHI GGATCC 1 cut(s) 286
BanI GGYRCC 1 cut(s) 442
BccI CCATC 5 cut(s) 176, 180, 258, 431, 538
BceAI ACGGC 1 cut(s) 99
BcgI CGANNNNNNTGC 4 cut(s) 354, 364, 388, 398
BciT130I CCWGG 1 cut(s) 354
BcoDI GTCTC 1 cut(s) 360
BfaI CTAG 1 cut(s) 105
BfmI CTRYAG 2 cut(s) 297, 775
BfrI CTTAAG 1 cut(s) 242
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
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, 172, 269, 549
BseLI CCNNNNNNNGG 2 cut(s) 437, 438
BseMI GCAATG 2 cut(s) 336, 399
BseRI GAGGAG 3 cut(s) 20, 186, 196
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 2 cut(s) 286, 381
BspACI CCGC 4 cut(s) 54, 159, 201, 316
BspANI GGCC 1 cut(s) 122
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
BssAI RCCGGY 1 cut(s) 155
BssECI CCNNGG 1 cut(s) 621
BssMI GATC 2 cut(s) 286, 381
BssNI GRCGYC 1 cut(s) 165
BssT1I CCWWGG 1 cut(s) 621
Bst2UI CCWGG 1 cut(s) 354
Bst4CI ACNGT 2 cut(s) 144, 669
Bst6I CTCTTC 2 cut(s) 193, 460
BstACI GRCGYC 1 cut(s) 165
BstAFI CTTAAG 1 cut(s) 242
BstC8I GCNNGC 1 cut(s) 782
BstDEI CTNAG 1 cut(s) 522
BstF5I GGATG 6 cut(s) 65, 146, 168, 172, 269, 549
BstHHI GCGC 1 cut(s) 786
BstKTI GATC 2 cut(s) 289, 384
BstMAI GTCTC 1 cut(s) 360
BstMBI GATC 2 cut(s) 286, 381
BstMWI GCNNNNNNNGC 4 cut(s) 128, 209, 338, 777
BstNI CCWGG 1 cut(s) 354
BstNSI RCATGY 2 cut(s) 493, 681
BstSCI CCNGG 1 cut(s) 352
BstSFI CTRYAG 2 cut(s) 297, 775
BstX2I RGATCY 1 cut(s) 286
BstYI RGATCY 1 cut(s) 286
BsuRI GGCC 1 cut(s) 122
BtsCI GGATG 6 cut(s) 65, 146, 168, 172, 269, 549
Cac8I GCNNGC 1 cut(s) 782
CaiI CAGNNNCTG 1 cut(s) 296
CciI TCATGA 1 cut(s) 394
CfoI GCGC 1 cut(s) 786
Cfr10I RCCGGY 1 cut(s) 155
CseI GACGC 1 cut(s) 173
Csp6I GTAC 2 cut(s) 313, 443
CviAII CATG 4 cut(s) 319, 395, 490, 678
CviQI GTAC 2 cut(s) 313, 443
DdeI CTNAG 1 cut(s) 522
DpnI GATC 2 cut(s) 288, 383
DpnII GATC 2 cut(s) 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 4 cut(s) 322, 398, 493, 681
FatI CATG 4 cut(s) 318, 394, 489, 677
FauI CCCGC 1 cut(s) 208
FauNDI CATATG 1 cut(s) 309
FokI GGATG 6 cut(s) 52, 133, 155, 159, 276, 556
FspBI CTAG 1 cut(s) 105
GlaI GCGC 1 cut(s) 785
HaeIII GGCC 1 cut(s) 122
HapII CCGG 1 cut(s) 156
HgaI GACGC 1 cut(s) 173
HhaI GCGC 1 cut(s) 786
Hin1I GRCGYC 1 cut(s) 165
Hin1II CATG 4 cut(s) 322, 398, 493, 681
Hin6I GCGC 1 cut(s) 784
HinP1I GCGC 1 cut(s) 784
HindIII AAGCTT 1 cut(s) 129
HinfI GANTC 2 cut(s) 4, 293
HpaII CCGG 1 cut(s) 156
HphI GGTGA 5 cut(s) 76, 132, 173, 545, 650
Hpy188I TCNGA 1 cut(s) 346
Hpy188III TCNNGA 4 cut(s) 176, 290, 365, 395
Hpy99I CGWCG 2 cut(s) 139, 253
HpyAV CCTTC 3 cut(s) 108, 277, 442
HpyCH4III ACNGT 2 cut(s) 144, 669
HpyCH4V TGCA 3 cut(s) 375, 495, 771
HpyF10VI GCNNNNNNNGC 4 cut(s) 128, 209, 338, 777
HpyF3I CTNAG 1 cut(s) 522
Hsp92I GRCGYC 1 cut(s) 165
Hsp92II CATG 4 cut(s) 322, 398, 493, 681
HspAI GCGC 1 cut(s) 784
KpnI GGTACC 1 cut(s) 446
Kzo9I GATC 2 cut(s) 286, 381
LmnI GCTCC 2 cut(s) 33, 61
LpnPI CCDG 6 cut(s) 169, 246, 303, 339, 366, 582
MaeI CTAG 1 cut(s) 105
MaeIII GTNAC 3 cut(s) 138, 161, 683
MalI GATC 2 cut(s) 288, 383
MbiI CCGCTC 1 cut(s) 56
MboI GATC 2 cut(s) 286, 381
MboII GAAGA 4 cut(s) 93, 180, 469, 477
MflI RGATCY 1 cut(s) 286
MlsI TGGCCA 1 cut(s) 122
MluCI AATT 6 cut(s) 497, 536, 559, 579, 712, 732
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 4 cut(s) 243, 270, 326, 705
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
MwoI GCNNNNNNNGC 4 cut(s) 128, 209, 338, 777
NdeI CATATG 1 cut(s) 309
NdeII GATC 2 cut(s) 286, 381
NlaIII CATG 4 cut(s) 322, 398, 493, 681
NlaIV GGNNCC 2 cut(s) 288, 444
NmuCI GTSAC 2 cut(s) 138, 161
NspI RCATGY 2 cut(s) 493, 681
PagI TCATGA 1 cut(s) 394
PciI ACATGT 1 cut(s) 489
PcsI WCGNNNNNNNCGW 1 cut(s) 140
PleI GAGTC 2 cut(s) 12, 301
PpsI GAGTC 2 cut(s) 12, 301
PscI ACATGT 1 cut(s) 489
PsiI TTATAA 1 cut(s) 741
Psp6I CCWGG 1 cut(s) 352
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 4 cut(s) 243, 270, 326, 705
Sau3AI GATC 2 cut(s) 286, 381
SchI GAGTC 2 cut(s) 13, 302
ScrFI CCNGG 1 cut(s) 354
SfcI CTRYAG 2 cut(s) 297, 775
SgrAI CRCCGGYG 1 cut(s) 155
SmlI CTYRAG 1 cut(s) 242
SmoI CTYRAG 1 cut(s) 242
Sse9I AATT 6 cut(s) 497, 536, 559, 579, 712, 732
SsiI CCGC 4 cut(s) 54, 159, 201, 316
SspI AATATT 1 cut(s) 703
SspMI CTAG 1 cut(s) 105
StyD4I CCNGG 1 cut(s) 352
StyI CCWWGG 1 cut(s) 621
TaaI ACNGT 2 cut(s) 144, 669
TaqI TCGA 2 cut(s) 7, 364
TasI AATT 6 cut(s) 497, 536, 559, 579, 712, 732
Tru1I TTAA 4 cut(s) 243, 270, 326, 705
Tru9I TTAA 4 cut(s) 243, 270, 326, 705
TseFI GTSAC 2 cut(s) 138, 161
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 2 cut(s) 493, 681
XspI CTAG 1 cut(s) 105
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.