RLG00000008870

HD domain-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_laevigata
Chr2
OG0011001
Physical Location & Seq
Reverse (-)
41491415 .. 41493755
2341 bp
Loading structure...
UTR
Exon/CDS
Intron
RLM00000008870

Sequence Viewer

Length: 756 bp
ATGAGTCGAGTGTTCCTCTGTAAATCGCTCCTCCTGACACCTTCGCTCTACTCCGCTCCCCTCACCTCCTTCAAGCCCACACTCACCTCGGCTTCTTCTTCTTCTTCTTCTAGGGTTCACCGTATGGCCACCGAAGCTTCGTCGTCACCGTCATCCCACACCGGCGGTGACGCCATCAACCCCGACCCAACCTCTTCCTCTCCTCCCGCCTCCTCTGCCATTGATTTTCTCTCCCTCTGTCACCGCCTCAAGACGACGAAAAGAGCTGGATGGGTTAAGAGAGATGTGAAGGATCCAGAGTCTGTAGCTGACCATATGTACCTCATGGGTTTAATGGCTCTCATTGCTTCGGATATTCCTGGTGTCAATCGAGACAAGTGCATAAAGATCGCCATTGTTCACGACATTGCTGAAGCTATTGTTGGGGATATAACCCCCACAGATGGGGTACCGAAGGCAGAGAAGAACCGAAGAGAACAAGAGGCAATAGATCACATGTGCAAATTACTTGGTGGAGGCTCAATTGCTGAGGAAATAGGTGAATTGTGGATGGAGTATGAGGGGAATTCCTCCCCAGAAGCTAAAATTGTCAAGGACTTTGACAAGGTGGAGATGATACTTCAAGCCTTGGAATATGAGAATGGTCAAGGAAAGGACTTGGATGAGTTTTTCCAGTCAACTGCTGGGAAGTTCCAGACTGATGTAGGCAAAGCTTGGGCAGCAGAGATAGTATCCAGAAGAAAAAAACAAGGCTAA
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

252

Amino Acids

27.23

Weight (kDa)

5.9

Isoelectric Point (pI)

47.98

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
YfbR-like PF12917 76 - 219 6.6e-06 5'-deoxynucleotidase YfbR-like
HD_3 PF13023 81 - 238 2.5e-48 HD domain
HD PF01966 102 - 205 1.4e-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) 448
AccB1I GGYRCC 1 cut(s) 448
AccBSI CCGCTC 1 cut(s) 56
AciI CCGC 4 cut(s) 54, 165, 207, 244
AclWI GGATC 2 cut(s) 287, 300
AcoI YGGCCR 1 cut(s) 126
AcsI RAATTY 1 cut(s) 565
AcuI CTGAAG 1 cut(s) 432
AcyI GRCGYC 1 cut(s) 171
AfaI GTAC 2 cut(s) 320, 450
AfiI CCNNNNNNNGG 2 cut(s) 443, 444
AflIII ACRYGT 1 cut(s) 495
AgsI TTSAA 2 cut(s) 73, 623
AjnI CCWGG 1 cut(s) 358
AjuI GAANNNNNNNTTGG 2 cut(s) 405, 437
AluBI AGCT 6 cut(s) 137, 266, 308, 416, 581, 713
AluI AGCT 6 cut(s) 137, 266, 308, 416, 581, 713
Alw26I GTCTC 1 cut(s) 366
AlwI GGATC 2 cut(s) 287, 300
AlwNI CAGNNNCTG 1 cut(s) 302
AoxI GGCC 1 cut(s) 126
ApeKI GCWGC 1 cut(s) 719
ApoI RAATTY 1 cut(s) 565
Asp718I GGTACC 1 cut(s) 448
AsuHPI GGTGA 7 cut(s) 55, 76, 110, 138, 179, 233, 551
BalI TGGCCA 1 cut(s) 128
BamHI GGATCC 1 cut(s) 292
BanI GGYRCC 1 cut(s) 448
BbvCI CCTCAGC 1 cut(s) 528
BbvI GCAGC 1 cut(s) 731
BccI CCATC 4 cut(s) 182, 264, 437, 544
BcgI CGANNNNNNTGC 4 cut(s) 360, 370, 394, 404
BciT130I CCWGG 1 cut(s) 360
BciVI GTATCC 1 cut(s) 742
BcoDI GTCTC 1 cut(s) 366
BfaI CTAG 1 cut(s) 111
BfmI CTRYAG 1 cut(s) 303
BfuI GTATCC 1 cut(s) 742
BisI GCNGC 1 cut(s) 720
BlsI GCNGC 1 cut(s) 721
Bme1390I CCNGG 1 cut(s) 360
BmiI GGNNCC 2 cut(s) 294, 450
BmrFI CCNGG 1 cut(s) 360
BplI GAGNNNNNCTC 1 cut(s) 32
Bpu10I CCTNAGC 1 cut(s) 528
BpuEI CTTGAG 1 cut(s) 233
BsaHI GRCGYC 1 cut(s) 171
BsaJI CCNNGG 2 cut(s) 87, 627
Bsc4I CCNNNNNNNGG 2 cut(s) 443, 444
Bse118I RCCGGY 1 cut(s) 161
Bse1I ACTGG 1 cut(s) 673
Bse3DI GCAATG 2 cut(s) 342, 405
BseBI CCWGG 1 cut(s) 360
BseDI CCNNGG 2 cut(s) 87, 627
BseGI GGATG 4 cut(s) 152, 275, 555, 667
BseLI CCNNNNNNNGG 2 cut(s) 443, 444
BseMI GCAATG 2 cut(s) 342, 405
BseMII CTCAG 1 cut(s) 519
BseNI ACTGG 1 cut(s) 673
BseRI GAGGAG 3 cut(s) 20, 192, 202
BseXI GCAGC 1 cut(s) 731
BseYI CCCAGC 1 cut(s) 683
BshFI GGCC 1 cut(s) 128
BshNI GGYRCC 1 cut(s) 448
BsiSI CCGG 1 cut(s) 162
BslI CCNNNNNNNGG 2 cut(s) 443, 444
BsmAI GTCTC 1 cut(s) 366
BsnI GGCC 1 cut(s) 128
Bsp143I GATC 3 cut(s) 292, 387, 490
BspACI CCGC 4 cut(s) 54, 165, 207, 244
BspANI GGCC 1 cut(s) 128
BspCNI CTCAG 1 cut(s) 520
BspLI GGNNCC 2 cut(s) 294, 450
BspPI GGATC 2 cut(s) 287, 300
BspT107I GGYRCC 1 cut(s) 448
BsrBI CCGCTC 1 cut(s) 56
BsrDI GCAATG 2 cut(s) 342, 405
BsrFI RCCGGY 1 cut(s) 161
BsrI ACTGG 1 cut(s) 673
BssAI RCCGGY 1 cut(s) 161
BssECI CCNNGG 2 cut(s) 87, 627
BssMI GATC 3 cut(s) 292, 387, 490
BssNI GRCGYC 1 cut(s) 171
BssT1I CCWWGG 1 cut(s) 627
Bst2UI CCWGG 1 cut(s) 360
Bst4CI ACNGT 2 cut(s) 122, 150
Bst6I CTCTTC 2 cut(s) 199, 466
BstACI GRCGYC 1 cut(s) 171
BstDEI CTNAG 1 cut(s) 528
BstF5I GGATG 4 cut(s) 152, 275, 555, 667
BstKTI GATC 3 cut(s) 295, 390, 493
BstMAI GTCTC 1 cut(s) 366
BstMBI GATC 3 cut(s) 292, 387, 490
BstMWI GCNNNNNNNGC 4 cut(s) 134, 215, 344, 719
BstNI CCWGG 1 cut(s) 360
BstNSI RCATGY 1 cut(s) 499
BstSCI CCNGG 1 cut(s) 358
BstSFI CTRYAG 1 cut(s) 303
BstV1I GCAGC 1 cut(s) 731
BstX2I RGATCY 1 cut(s) 292
BstYI RGATCY 1 cut(s) 292
BsuI GTATCC 1 cut(s) 742
BsuRI GGCC 1 cut(s) 128
BtsCI GGATG 4 cut(s) 152, 275, 555, 667
CaiI CAGNNNCTG 1 cut(s) 302
Cfr10I RCCGGY 1 cut(s) 161
CseI GACGC 1 cut(s) 179
Csp6I GTAC 2 cut(s) 319, 449
CviAII CATG 2 cut(s) 325, 496
CviQI GTAC 2 cut(s) 319, 449
DdeI CTNAG 1 cut(s) 528
DpnI GATC 3 cut(s) 294, 389, 492
DpnII GATC 3 cut(s) 292, 387, 490
EaeI YGGCCR 1 cut(s) 126
Eam1104I CTCTTC 2 cut(s) 199, 466
EarI CTCTTC 2 cut(s) 199, 466
Eco130I CCWWGG 1 cut(s) 627
Eco57I CTGAAG 1 cut(s) 432
EcoRI GAATTC 1 cut(s) 565
EcoRII CCWGG 1 cut(s) 358
EcoT14I CCWWGG 1 cut(s) 627
ErhI CCWWGG 1 cut(s) 627
FaeI CATG 2 cut(s) 328, 499
FaiI YATR 9 cut(s) 125, 315, 317, 326, 383, 431, 497, 558, 636
FatI CATG 2 cut(s) 324, 495
FauI CCCGC 1 cut(s) 214
FauNDI CATATG 1 cut(s) 315
Fnu4HI GCNGC 1 cut(s) 720
FokI GGATG 4 cut(s) 139, 282, 562, 674
Fsp4HI GCNGC 1 cut(s) 720
FspBI CTAG 1 cut(s) 111
GluI GCNGC 1 cut(s) 720
GsaI CCCAGC 1 cut(s) 687
HaeIII GGCC 1 cut(s) 128
HapII CCGG 1 cut(s) 162
HgaI GACGC 1 cut(s) 179
Hin1I GRCGYC 1 cut(s) 171
Hin1II CATG 2 cut(s) 328, 499
HincII GTYRAC 1 cut(s) 678
HindII GTYRAC 1 cut(s) 678
HindIII AAGCTT 2 cut(s) 135, 711
HinfI GANTC 2 cut(s) 4, 299
HpaII CCGG 1 cut(s) 162
HphI GGTGA 7 cut(s) 55, 76, 110, 138, 179, 233, 551
Hpy166II GTNNAC 3 cut(s) 118, 400, 678
Hpy188I TCNGA 1 cut(s) 352
Hpy188III TCNNGA 7 cut(s) 34, 250, 296, 371, 401, 694, 735
Hpy8I GTNNAC 3 cut(s) 118, 400, 678
Hpy99I CGWCG 2 cut(s) 145, 259
HpyAV CCTTC 4 cut(s) 51, 79, 283, 448
HpyCH4III ACNGT 2 cut(s) 122, 150
HpyCH4V TGCA 2 cut(s) 381, 501
HpyF10VI GCNNNNNNNGC 4 cut(s) 134, 215, 344, 719
HpyF3I CTNAG 1 cut(s) 528
Hsp92I GRCGYC 1 cut(s) 171
Hsp92II CATG 2 cut(s) 328, 499
KpnI GGTACC 1 cut(s) 452
Kzo9I GATC 3 cut(s) 292, 387, 490
LmnI GCTCC 2 cut(s) 33, 61
Lsp1109I GCAGC 1 cut(s) 731
MaeI CTAG 1 cut(s) 111
MaeIII GTNAC 3 cut(s) 144, 167, 239
MalI GATC 3 cut(s) 294, 389, 492
MbiI CCGCTC 1 cut(s) 56
MboI GATC 3 cut(s) 292, 387, 490
MboII GAAGA 9 cut(s) 87, 90, 93, 96, 99, 186, 475, 483, 750
MfeI CAATTG 1 cut(s) 522
MflI RGATCY 1 cut(s) 292
MlsI TGGCCA 1 cut(s) 128
MluCI AATT 5 cut(s) 503, 522, 542, 565, 585
MluNI TGGCCA 1 cut(s) 128
MlyI GAGTC 2 cut(s) 13, 308
Mox20I TGGCCA 1 cut(s) 128
MscI TGGCCA 1 cut(s) 128
MseI TTAA 2 cut(s) 276, 332
Msp20I TGGCCA 1 cut(s) 128
MspI CCGG 1 cut(s) 162
MspR9I CCNGG 1 cut(s) 360
MunI CAATTG 1 cut(s) 522
MvaI CCWGG 1 cut(s) 360
MwoI GCNNNNNNNGC 4 cut(s) 134, 215, 344, 719
NdeI CATATG 1 cut(s) 315
NdeII GATC 3 cut(s) 292, 387, 490
NlaIII CATG 2 cut(s) 328, 499
NlaIV GGNNCC 2 cut(s) 294, 450
NmeAIII GCCGAG 1 cut(s) 68
NmuCI GTSAC 3 cut(s) 144, 167, 239
NspI RCATGY 1 cut(s) 499
PciI ACATGT 1 cut(s) 495
PcsI WCGNNNNNNNCGW 1 cut(s) 146
PkrI GCNGC 1 cut(s) 721
PleI GAGTC 2 cut(s) 12, 307
PpsI GAGTC 2 cut(s) 12, 307
PscI ACATGT 1 cut(s) 495
Psp6I CCWGG 1 cut(s) 358
PspFI CCCAGC 1 cut(s) 683
PspGI CCWGG 1 cut(s) 358
PspN4I GGNNCC 2 cut(s) 294, 450
PstNI CAGNNNCTG 1 cut(s) 302
PsuI RGATCY 1 cut(s) 292
RsaI GTAC 2 cut(s) 320, 450
RsaNI GTAC 2 cut(s) 319, 449
SaqAI TTAA 2 cut(s) 276, 332
SatI GCNGC 1 cut(s) 720
Sau3AI GATC 3 cut(s) 292, 387, 490
SchI GAGTC 2 cut(s) 13, 308
ScrFI CCNGG 1 cut(s) 360
SfcI CTRYAG 1 cut(s) 303
SgrAI CRCCGGYG 1 cut(s) 161
SmlI CTYRAG 1 cut(s) 248
SmoI CTYRAG 1 cut(s) 248
Sse9I AATT 5 cut(s) 503, 522, 542, 565, 585
SsiI CCGC 4 cut(s) 54, 165, 207, 244
SspMI CTAG 1 cut(s) 111
StyD4I CCNGG 1 cut(s) 358
StyI CCWWGG 1 cut(s) 627
TaaI ACNGT 2 cut(s) 122, 150
TaqI TCGA 2 cut(s) 7, 370
TasI AATT 5 cut(s) 503, 522, 542, 565, 585
Tru1I TTAA 2 cut(s) 276, 332
Tru9I TTAA 2 cut(s) 276, 332
TseFI GTSAC 3 cut(s) 144, 167, 239
TseI GCWGC 1 cut(s) 719
Tsp45I GTSAC 3 cut(s) 144, 167, 239
XapI RAATTY 1 cut(s) 565
XceI RCATGY 1 cut(s) 499
XcmI CCANNNNNNNNNTGG 1 cut(s) 680
XspI CTAG 1 cut(s) 111
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.