FvH4_2g01580

Cold shock protein domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb2
OG0017069
Physical Location & Seq
Reverse (-)
1432959 .. 1433570
612 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_2g01580.t1

Sequence Viewer

Length: 612 bp
ATGAGTGACCGGTTGACCGGAACGGTGAAGTGGTTCAATGACCAGAAGGGGTTCGGCTTCATCACCCCGGAGAACGGCGGCGAAGATCTCTTCGTCCACCAGTCCTCGATCCGAACCGAAGGCTTCCGCACTCTCGGCGACGGCGAGTCCGTCGAGTTCCAGATCGAGACCGACAACGACGGCCGCACCAAGGCCGTTGATGTCACCGGTCCCGAGGAGGGCCCCGTCCAGGGGAGAGGATCCGGAGGCGGAGGAGGTCGCGGCGGCGGTGGAGGACGTGGCGGTGGAAGAGGCGGCCGCGGAGGCGGGAGCTATGGAGGCGGTGGTGGATATGGAGGTGGCGGCGGCTATGGAGGCGGCAGCGGTGGTTATGGTGGTGGCAGTGGAGGCGGTGGGAACTGCTTCAAGTGTGGTGAGGCTGGACACATTGCGAGGGACTGCTCTGAGGGAGGTGGGAGCTATGGAGGCGGCGGCCGTGGCGGAGGTGGCTATGGAGGCAGTGGAGGCGGTGGGAGGTACTCTGGTGGAGGAGGCGGCGGCGGTGCTTCTGGCGGCTGCTATCAGTGTGGTGAATCTGGTCATTTCGCAAGGGAGTGCCCCAACAGAGGTTGA
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
CSD zf-CCHC

Protein Analysis

204

Amino Acids

19.18

Weight (kDa)

5.93

Isoelectric Point (pI)

45.81

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
CSD PF00313 6 - 70 1.5e-26 'Cold-shock' DNA-binding domain
zf-CCHC PF00098 133 - 148 4.7e-07 Zinc knuckle
zf-CCHC PF00098 185 - 201 6.1e-07 Zinc knuckle
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: OG0017069)

Species Orthologous Gene IDs
arabidopsis_thaliana AT2G21060 AT4G38680
fragaria_vesca FvH4_2g01580
malus_domestica MD10G1121500.v1.1
prunus_persica Prupe.8G163000_v2.0.a1
pyrus_communis pycom05g11220
rosa_chinensis RchiOBHm_Chr6g0244251
rosa_laevigata RLG00000015370
rosa_rugosa Rorug05G0507900
rosa_samantha Rh6BG018600 Rh6CG015700 Rh6DG016900
rosa_wichuraiana Rw6G001890

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccII CGCG 2 cut(s) 261, 300
AccIII TCCGGA 1 cut(s) 242
AclWI GGATC 3 cut(s) 103, 234, 247
AcoI YGGCCR 3 cut(s) 181, 295, 472
AfaI GTAC 1 cut(s) 518
AfiI CCNNNNNNNGG 7 cut(s) 74, 190, 218, 229, 230, 231, 605
AgeI ACCGGT 2 cut(s) 9, 206
AgsI TTSAA 2 cut(s) 37, 406
AhdI GACNNNNNGTC 1 cut(s) 145
AjiI CACGTC 1 cut(s) 278
AjnI CCWGG 1 cut(s) 228
AluBI AGCT 2 cut(s) 312, 459
AluI AGCT 2 cut(s) 312, 459
Alw26I GTCTC 1 cut(s) 161
AlwI GGATC 3 cut(s) 103, 234, 247
Ama87I CYCGRG 1 cut(s) 212
Aor13HI TCCGGA 1 cut(s) 242
AoxI GGCC 5 cut(s) 181, 192, 220, 295, 472
ApaI GGGCCC 1 cut(s) 224
ApeKI GCWGC 2 cut(s) 360, 555
AsiGI ACCGGT 2 cut(s) 9, 206
Asp700I GAANNNNTTC 3 cut(s) 32, 50, 401
AspS9I GGNCC 3 cut(s) 209, 220, 221
AsuC2I CCSGG 1 cut(s) 68
AsuHPI GGTGA 5 cut(s) 37, 55, 196, 425, 581
AvaI CYCGRG 1 cut(s) 212
AvaII GGWCC 1 cut(s) 209
BaeGI GKGCMC 2 cut(s) 224, 599
BaeI ACNNNNGTAYC 2 cut(s) 508, 541
BamHI GGATCC 1 cut(s) 239
BanII GRGCYC 1 cut(s) 224
BbvI GCAGC 2 cut(s) 372, 542
BceAI ACGGC 5 cut(s) 91, 157, 179, 196, 459
BciT130I CCWGG 1 cut(s) 230
BcnI CCSGG 1 cut(s) 68
BcoDI GTCTC 1 cut(s) 161
BglI GCCNNNNNGGC 1 cut(s) 303
BglII AGATCT 1 cut(s) 85
Bme1390I CCNGG 2 cut(s) 68, 230
Bme18I GGWCC 1 cut(s) 209
BmeRI GACNNNNNGTC 1 cut(s) 145
BmeT110I CYCGRG 1 cut(s) 212
BmgBI CACGTC 1 cut(s) 278
BmgT120I GGNCC 3 cut(s) 209, 220, 221
BmiI GGNNCC 4 cut(s) 211, 222, 223, 241
BmrFI CCNGG 2 cut(s) 68, 230
BpuMI CCSGG 1 cut(s) 68
BsaI GGTCTC 1 cut(s) 161
BsaJI CCNNGG 6 cut(s) 66, 189, 213, 229, 298, 475
BsaWI WCCGGW 4 cut(s) 9, 17, 206, 242
Bsc4I CCNNNNNNNGG 7 cut(s) 74, 190, 218, 229, 230, 231, 605
Bse118I RCCGGY 2 cut(s) 9, 206
Bse1I ACTGG 1 cut(s) 100
Bse3DI GCAATG 1 cut(s) 426
BseAI TCCGGA 1 cut(s) 242
BseBI CCWGG 1 cut(s) 230
BseDI CCNNGG 6 cut(s) 66, 189, 213, 229, 298, 475
BseLI CCNNNNNNNGG 7 cut(s) 74, 190, 218, 229, 230, 231, 605
BseMI GCAATG 1 cut(s) 426
BseMII CTCAG 1 cut(s) 435
BseNI ACTGG 1 cut(s) 100
BseRI GAGGAG 3 cut(s) 230, 267, 543
BseSI GKGCMC 2 cut(s) 224, 599
BseX3I CGGCCG 3 cut(s) 181, 295, 472
BseXI GCAGC 2 cut(s) 372, 542
Bsh1236I CGCG 2 cut(s) 261, 300
Bsh1285I CGRYCG 3 cut(s) 184, 298, 475
BshFI GGCC 5 cut(s) 183, 194, 222, 297, 474
BshTI ACCGGT 2 cut(s) 9, 206
BsiEI CGRYCG 3 cut(s) 184, 298, 475
BsiHKCI CYCGRG 1 cut(s) 212
BsiSI CCGG 5 cut(s) 10, 18, 68, 207, 243
BslFI GGGAC 2 cut(s) 195, 449
BslI CCNNNNNNNGG 7 cut(s) 74, 190, 218, 229, 230, 231, 605
BsmAI GTCTC 1 cut(s) 161
BsmFI GGGAC 2 cut(s) 195, 449
BsnI GGCC 5 cut(s) 183, 194, 222, 297, 474
Bso31I GGTCTC 1 cut(s) 161
BsoBI CYCGRG 1 cut(s) 212
Bsp120I GGGCCC 1 cut(s) 220
Bsp1286I GDGCHC 2 cut(s) 224, 599
Bsp13I TCCGGA 1 cut(s) 242
Bsp143I GATC 4 cut(s) 85, 108, 162, 239
BspANI GGCC 5 cut(s) 183, 194, 222, 297, 474
BspCNI CTCAG 1 cut(s) 436
BspEI TCCGGA 1 cut(s) 242
BspFNI CGCG 2 cut(s) 261, 300
BspLI GGNNCC 4 cut(s) 211, 222, 223, 241
BspPI GGATC 3 cut(s) 103, 234, 247
BspTNI GGTCTC 1 cut(s) 161
BsrDI GCAATG 1 cut(s) 426
BsrFI RCCGGY 2 cut(s) 9, 206
BsrI ACTGG 1 cut(s) 100
BssAI RCCGGY 2 cut(s) 9, 206
BssECI CCNNGG 6 cut(s) 66, 189, 213, 229, 298, 475
BssMI GATC 4 cut(s) 85, 108, 162, 239
BssT1I CCWWGG 1 cut(s) 189
Bst2UI CCWGG 1 cut(s) 230
Bst4CI ACNGT 1 cut(s) 25
Bst6I CTCTTC 2 cut(s) 95, 283
BstDEI CTNAG 1 cut(s) 444
BstDSI CCRYGG 2 cut(s) 298, 475
BstFNI CGCG 2 cut(s) 261, 300
BstKTI GATC 4 cut(s) 88, 111, 165, 242
BstMAI GTCTC 1 cut(s) 161
BstMBI GATC 4 cut(s) 85, 108, 162, 239
BstMCI CGRYCG 3 cut(s) 184, 298, 475
BstNI CCWGG 1 cut(s) 230
BstSCI CCNGG 2 cut(s) 66, 228
BstSLI GKGCMC 2 cut(s) 224, 599
BstUI CGCG 2 cut(s) 261, 300
BstV1I GCAGC 2 cut(s) 372, 542
BstX2I RGATCY 2 cut(s) 85, 239
BstYI RGATCY 2 cut(s) 85, 239
BstZI CGGCCG 3 cut(s) 181, 295, 472
BsuRI GGCC 5 cut(s) 183, 194, 222, 297, 474
BtgI CCRYGG 2 cut(s) 298, 475
BtrI CACGTC 1 cut(s) 278
BtsI GCAGTG 2 cut(s) 388, 505
BtsIMutI CAGTG 3 cut(s) 388, 505, 569
CciNI GCGGCCGC 1 cut(s) 295
Cfr10I RCCGGY 2 cut(s) 9, 206
Cfr13I GGNCC 3 cut(s) 209, 220, 221
Cfr42I CCGCGG 1 cut(s) 301
Csp6I GTAC 1 cut(s) 517
CspAI ACCGGT 2 cut(s) 9, 206
CviQI GTAC 1 cut(s) 517
DdeI CTNAG 1 cut(s) 444
DpnI GATC 4 cut(s) 87, 110, 164, 241
DpnII GATC 4 cut(s) 85, 108, 162, 239
DriI GACNNNNNGTC 1 cut(s) 145
EaeI YGGCCR 3 cut(s) 181, 295, 472
EagI CGGCCG 3 cut(s) 181, 295, 472
Eam1104I CTCTTC 2 cut(s) 95, 283
Eam1105I GACNNNNNGTC 1 cut(s) 145
EarI CTCTTC 2 cut(s) 95, 283
EciI GGCGGA 2 cut(s) 264, 495
EclXI CGGCCG 3 cut(s) 181, 295, 472
Eco130I CCWWGG 1 cut(s) 189
Eco24I GRGCYC 1 cut(s) 224
Eco31I GGTCTC 1 cut(s) 161
Eco47I GGWCC 1 cut(s) 209
Eco52I CGGCCG 3 cut(s) 181, 295, 472
Eco88I CYCGRG 1 cut(s) 212
EcoO109I RGGNCCY 2 cut(s) 220, 221
EcoRII CCWGG 1 cut(s) 228
EcoT14I CCWWGG 1 cut(s) 189
EcoT38I GRGCYC 1 cut(s) 224
ErhI CCWWGG 1 cut(s) 189
FaiI YATR 6 cut(s) 315, 333, 351, 372, 462, 492
FaqI GGGAC 2 cut(s) 195, 449
FauI CCCGC 1 cut(s) 299
FriOI GRGCYC 1 cut(s) 224
HaeIII GGCC 5 cut(s) 183, 194, 222, 297, 474
HapII CCGG 5 cut(s) 10, 18, 68, 207, 243
HincII GTYRAC 1 cut(s) 15
HindII GTYRAC 1 cut(s) 15
HinfI GANTC 2 cut(s) 146, 572
HpaII CCGG 5 cut(s) 10, 18, 68, 207, 243
HphI GGTGA 5 cut(s) 37, 55, 196, 425, 581
Hpy166II GTNNAC 2 cut(s) 15, 97
Hpy188I TCNGA 2 cut(s) 113, 445
Hpy188III TCNNGA 4 cut(s) 160, 166, 212, 243
Hpy8I GTNNAC 2 cut(s) 15, 97
Hpy99I CGWCG 3 cut(s) 143, 155, 182
HpyAV CCTTC 2 cut(s) 40, 113
HpyCH4III ACNGT 1 cut(s) 25
HpyCH4IV ACGT 1 cut(s) 277
HpyF3I CTNAG 1 cut(s) 444
HpySE526I ACGT 1 cut(s) 277
Kpn2I TCCGGA 1 cut(s) 242
KspI CCGCGG 1 cut(s) 301
Kzo9I GATC 4 cut(s) 85, 108, 162, 239
LmnI GCTCC 2 cut(s) 309, 456
Lsp1109I GCAGC 2 cut(s) 372, 542
MaeII ACGT 1 cut(s) 277
MaeIII GTNAC 2 cut(s) 5, 202
MalI GATC 4 cut(s) 87, 110, 164, 241
MboI GATC 4 cut(s) 85, 108, 162, 239
MboII GAAGA 3 cut(s) 82, 95, 300
MflI RGATCY 2 cut(s) 85, 239
MhlI GDGCHC 2 cut(s) 224, 599
MlyI GAGTC 1 cut(s) 155
MroI TCCGGA 1 cut(s) 242
MroXI GAANNNNTTC 3 cut(s) 32, 50, 401
MspA1I CMGCKG 2 cut(s) 300, 363
MspI CCGG 5 cut(s) 10, 18, 68, 207, 243
MspR9I CCNGG 2 cut(s) 68, 230
MvaI CCWGG 1 cut(s) 230
MvnI CGCG 2 cut(s) 261, 300
NciI CCSGG 1 cut(s) 68
NdeII GATC 4 cut(s) 85, 108, 162, 239
NlaIV GGNNCC 4 cut(s) 211, 222, 223, 241
NmeAIII GCCGAG 1 cut(s) 114
NmuCI GTSAC 2 cut(s) 5, 202
NotI GCGGCCGC 1 cut(s) 295
PcsI WCGNNNNNNNCGW 2 cut(s) 141, 147
PdmI GAANNNNTTC 3 cut(s) 32, 50, 401
PfeI GAWTC 1 cut(s) 572
PinAI ACCGGT 2 cut(s) 9, 206
PleI GAGTC 1 cut(s) 154
PpsI GAGTC 1 cut(s) 154
Psp6I CCWGG 1 cut(s) 228
PspGI CCWGG 1 cut(s) 228
PspN4I GGNNCC 4 cut(s) 211, 222, 223, 241
PspOMI GGGCCC 1 cut(s) 220
PspPI GGNCC 3 cut(s) 209, 220, 221
PsuI RGATCY 2 cut(s) 85, 239
RsaI GTAC 1 cut(s) 518
RsaNI GTAC 1 cut(s) 517
SacII CCGCGG 1 cut(s) 301
Sau3AI GATC 4 cut(s) 85, 108, 162, 239
Sau96I GGNCC 3 cut(s) 209, 220, 221
SchI GAGTC 1 cut(s) 155
ScrFI CCNGG 2 cut(s) 68, 230
SduI GDGCHC 2 cut(s) 224, 599
SetI ASST 9 cut(s) 259, 280, 314, 340, 454, 461, 487, 518, 610
Sfr303I CCGCGG 1 cut(s) 301
SgrBI CCGCGG 1 cut(s) 301
SinI GGWCC 1 cut(s) 209
StyD4I CCNGG 2 cut(s) 66, 228
StyI CCWWGG 1 cut(s) 189
TaaI ACNGT 1 cut(s) 25
TaiI ACGT 1 cut(s) 280
TaqI TCGA 3 cut(s) 107, 153, 165
TaqII GACCGA 1 cut(s) 185
TfiI GAWTC 1 cut(s) 572
TscAI CASTG 3 cut(s) 388, 505, 569
TseFI GTSAC 2 cut(s) 5, 202
TseI GCWGC 2 cut(s) 360, 555
Tsp45I GTSAC 2 cut(s) 5, 202
TspDTI ATGAA 1 cut(s) 49
TspGWI ACGGA 1 cut(s) 139
TspRI CASTG 3 cut(s) 388, 505, 569
VpaK11BI GGWCC 1 cut(s) 209
XmnI GAANNNNTTC 3 cut(s) 32, 50, 401
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.