Rh6DG016900

Cold shock protein domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr6D
OG0017069
Physical Location & Seq
Reverse (-)
1585532 .. 1586116
585 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh6DG016900.1

Sequence Viewer

Length: 585 bp
ATGAGTGAGAGGCTGACCGGAACGGTGAAGTGGTTCAATGACCAGAAGGGGTTCGGCTTCATCACCCCGGCGGACGGCGGCGAGGATCTCTTCGTCCACCAGTCCTCGATCCGAACCGAAGGCTTCCGGACTCTCGGCGACGGTGAGTCCGTCGAGTTCCAGATCGAGTCCGACAACGACGGCCGCACCAAGGCCGTTGATGTGACCGGACCTGAGGAGGGTCCCGTTCAGGGGAGAGGATCCGGAGGCGGCGGCCGTGGCGGTGGAGGCCGTGGTGGCGGGAGAGGTGGCCGTGGAGGCGGGAGCTATGGCGGTGGTGGAGGCTATGGCGGCGGTGGAGGTGGATATGGAGGCGGTGGAGGTGGTGGTAACTGCTTCAAGTGCGGTGAGGCTGGACACATGGCGAGGGACTGCTCTGAGGGAGGGGGTAGCTATGGAGGCGGCGGCCGAGGTGGAGGCGGTTACGGCGGCGGAGGCGGTGGGAGGTACTCGGGAGGTGGAGGAGGCGGCGGCGGTGCTTCCGGGGGCTGCTATCAGTGTGGTGAAACTGGTCATTTCGCAAGGGAGTGCCCTAACAGAGGCTGA
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

194

Amino Acids

18.45

Weight (kDa)

5.93

Isoelectric Point (pI)

47.46

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
CSD PF00313 6 - 70 8.9e-27 'Cold-shock' DNA-binding domain
zf-CCHC PF00098 124 - 139 4e-07 Zinc knuckle
zf-CCHC PF00098 176 - 192 2.2e-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)
AccIII TCCGGA 2 cut(s) 126, 242
AclWI GGATC 4 cut(s) 93, 103, 234, 247
AcoI YGGCCR 4 cut(s) 181, 253, 289, 445
AfaI GTAC 1 cut(s) 488
AfiI CCNNNNNNNGG 6 cut(s) 74, 190, 218, 230, 231, 578
AgsI TTSAA 2 cut(s) 37, 379
AhdI GACNNNNNGTC 1 cut(s) 145
AluBI AGCT 2 cut(s) 306, 432
AluI AGCT 2 cut(s) 306, 432
AlwI GGATC 4 cut(s) 93, 103, 234, 247
AlwNI CAGNNNCTG 1 cut(s) 582
Ama87I CYCGRG 1 cut(s) 490
Aor13HI TCCGGA 2 cut(s) 126, 242
AoxI GGCC 6 cut(s) 181, 192, 253, 268, 289, 445
ApeKI GCWGC 1 cut(s) 528
Asp700I GAANNNNTTC 2 cut(s) 32, 50
AspS9I GGNCC 2 cut(s) 209, 221
AsuC2I CCSGG 2 cut(s) 68, 523
AsuHPI GGTGA 5 cut(s) 37, 55, 155, 398, 554
AvaI CYCGRG 1 cut(s) 490
AvaII GGWCC 2 cut(s) 209, 221
AxyI CCTNAGG 1 cut(s) 213
BaeGI GKGCMC 1 cut(s) 572
BamHI GGATCC 1 cut(s) 239
BbvI GCAGC 1 cut(s) 515
BceAI ACGGC 7 cut(s) 91, 179, 196, 240, 255, 276, 481
BcnI CCSGG 2 cut(s) 68, 523
BglI GCCNNNNNGGC 2 cut(s) 276, 297
Bme1390I CCNGG 2 cut(s) 68, 523
Bme18I GGWCC 2 cut(s) 209, 221
BmeRI GACNNNNNGTC 1 cut(s) 145
BmeT110I CYCGRG 1 cut(s) 490
BmgT120I GGNCC 2 cut(s) 209, 221
BmiI GGNNCC 3 cut(s) 222, 223, 241
BmrFI CCNGG 2 cut(s) 68, 523
BpuMI CCSGG 2 cut(s) 68, 523
BsaJI CCNNGG 7 cut(s) 66, 189, 256, 271, 292, 448, 522
BsaWI WCCGGW 4 cut(s) 17, 126, 206, 242
Bsc4I CCNNNNNNNGG 6 cut(s) 74, 190, 218, 230, 231, 578
Bse1I ACTGG 2 cut(s) 100, 553
Bse21I CCTNAGG 1 cut(s) 213
BseAI TCCGGA 2 cut(s) 126, 242
BseDI CCNNGG 7 cut(s) 66, 189, 256, 271, 292, 448, 522
BseLI CCNNNNNNNGG 6 cut(s) 74, 190, 218, 230, 231, 578
BseMII CTCAG 2 cut(s) 204, 408
BseNI ACTGG 2 cut(s) 100, 553
BseRI GAGGAG 2 cut(s) 230, 516
BseSI GKGCMC 1 cut(s) 572
BseX3I CGGCCG 3 cut(s) 181, 253, 445
BseXI GCAGC 1 cut(s) 515
Bsh1285I CGRYCG 3 cut(s) 184, 256, 448
BshFI GGCC 6 cut(s) 183, 194, 255, 270, 291, 447
BsiEI CGRYCG 3 cut(s) 184, 256, 448
BsiHKCI CYCGRG 1 cut(s) 490
BsiSI CCGG 6 cut(s) 18, 68, 127, 207, 243, 522
BslFI GGGAC 2 cut(s) 207, 422
BslI CCNNNNNNNGG 6 cut(s) 74, 190, 218, 230, 231, 578
BsmFI GGGAC 2 cut(s) 207, 422
BsnI GGCC 6 cut(s) 183, 194, 255, 270, 291, 447
BsoBI CYCGRG 1 cut(s) 490
Bsp1286I GDGCHC 1 cut(s) 572
Bsp13I TCCGGA 2 cut(s) 126, 242
Bsp143I GATC 4 cut(s) 85, 108, 162, 239
BspANI GGCC 6 cut(s) 183, 194, 255, 270, 291, 447
BspCNI CTCAG 2 cut(s) 205, 409
BspEI TCCGGA 2 cut(s) 126, 242
BspLI GGNNCC 3 cut(s) 222, 223, 241
BspPI GGATC 4 cut(s) 93, 103, 234, 247
BsrI ACTGG 2 cut(s) 100, 553
BssECI CCNNGG 7 cut(s) 66, 189, 256, 271, 292, 448, 522
BssMI GATC 4 cut(s) 85, 108, 162, 239
BssT1I CCWWGG 1 cut(s) 189
Bst4CI ACNGT 2 cut(s) 25, 143
Bst6I CTCTTC 1 cut(s) 95
BstDEI CTNAG 2 cut(s) 213, 417
BstDSI CCRYGG 3 cut(s) 256, 271, 292
BstENI CCTNNNNNAGG 1 cut(s) 576
BstKTI GATC 4 cut(s) 88, 111, 165, 242
BstMBI GATC 4 cut(s) 85, 108, 162, 239
BstMCI CGRYCG 3 cut(s) 184, 256, 448
BstMWI GCNNNNNNNGC 9 cut(s) 258, 267, 276, 297, 330, 381, 438, 465, 474
BstSCI CCNGG 2 cut(s) 66, 521
BstSLI GKGCMC 1 cut(s) 572
BstV1I GCAGC 1 cut(s) 515
BstX2I RGATCY 2 cut(s) 85, 239
BstYI RGATCY 2 cut(s) 85, 239
BstZI CGGCCG 3 cut(s) 181, 253, 445
Bsu36I CCTNAGG 1 cut(s) 213
BsuRI GGCC 6 cut(s) 183, 194, 255, 270, 291, 447
BtgI CCRYGG 3 cut(s) 256, 271, 292
BtsIMutI CAGTG 1 cut(s) 542
CaiI CAGNNNCTG 1 cut(s) 582
Cfr13I GGNCC 2 cut(s) 209, 221
Csp6I GTAC 1 cut(s) 487
CviAII CATG 1 cut(s) 400
CviQI GTAC 1 cut(s) 487
DdeI CTNAG 2 cut(s) 213, 417
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 4 cut(s) 181, 253, 289, 445
EagI CGGCCG 3 cut(s) 181, 253, 445
Eam1104I CTCTTC 1 cut(s) 95
Eam1105I GACNNNNNGTC 1 cut(s) 145
EarI CTCTTC 1 cut(s) 95
EciI GGCGGA 2 cut(s) 86, 486
EclXI CGGCCG 3 cut(s) 181, 253, 445
Eco130I CCWWGG 1 cut(s) 189
Eco47I GGWCC 2 cut(s) 209, 221
Eco52I CGGCCG 3 cut(s) 181, 253, 445
Eco81I CCTNAGG 1 cut(s) 213
Eco88I CYCGRG 1 cut(s) 490
EcoNI CCTNNNNNAGG 1 cut(s) 576
EcoO109I RGGNCCY 1 cut(s) 221
EcoT14I CCWWGG 1 cut(s) 189
ErhI CCWWGG 1 cut(s) 189
FaeI CATG 1 cut(s) 403
FaiI YATR 5 cut(s) 309, 327, 348, 401, 435
FaqI GGGAC 2 cut(s) 207, 422
FatI CATG 1 cut(s) 399
FauI CCCGC 2 cut(s) 272, 293
HaeIII GGCC 6 cut(s) 183, 194, 255, 270, 291, 447
HapII CCGG 6 cut(s) 18, 68, 127, 207, 243, 522
Hin1II CATG 1 cut(s) 403
HinfI GANTC 3 cut(s) 130, 146, 167
HpaII CCGG 6 cut(s) 18, 68, 127, 207, 243, 522
HphI GGTGA 5 cut(s) 37, 55, 155, 398, 554
Hpy166II GTNNAC 1 cut(s) 97
Hpy188I TCNGA 3 cut(s) 113, 172, 418
Hpy188III TCNNGA 4 cut(s) 127, 160, 243, 492
Hpy8I GTNNAC 1 cut(s) 97
Hpy99I CGWCG 3 cut(s) 143, 155, 182
HpyAV CCTTC 2 cut(s) 40, 113
HpyCH4III ACNGT 2 cut(s) 25, 143
HpyF10VI GCNNNNNNNGC 9 cut(s) 258, 267, 276, 297, 330, 381, 438, 465, 474
HpyF3I CTNAG 2 cut(s) 213, 417
Hsp92II CATG 1 cut(s) 403
KflI GGGWCCC 1 cut(s) 221
Kpn2I TCCGGA 2 cut(s) 126, 242
Kzo9I GATC 4 cut(s) 85, 108, 162, 239
LmnI GCTCC 1 cut(s) 303
Lsp1109I GCAGC 1 cut(s) 515
MaeIII GTNAC 3 cut(s) 202, 368, 461
MalI GATC 4 cut(s) 87, 110, 164, 241
MboI GATC 4 cut(s) 85, 108, 162, 239
MboII GAAGA 1 cut(s) 82
MflI RGATCY 2 cut(s) 85, 239
MhlI GDGCHC 1 cut(s) 572
MlyI GAGTC 3 cut(s) 124, 155, 176
MmeI TCCRAC 1 cut(s) 195
MroI TCCGGA 2 cut(s) 126, 242
MroXI GAANNNNTTC 2 cut(s) 32, 50
MspI CCGG 6 cut(s) 18, 68, 127, 207, 243, 522
MspR9I CCNGG 2 cut(s) 68, 523
MwoI GCNNNNNNNGC 9 cut(s) 258, 267, 276, 297, 330, 381, 438, 465, 474
NciI CCSGG 2 cut(s) 68, 523
NdeII GATC 4 cut(s) 85, 108, 162, 239
NlaIII CATG 1 cut(s) 403
NlaIV GGNNCC 3 cut(s) 222, 223, 241
NmeAIII GCCGAG 2 cut(s) 114, 473
NmuCI GTSAC 1 cut(s) 202
PcsI WCGNNNNNNNCGW 1 cut(s) 147
PdmI GAANNNNTTC 2 cut(s) 32, 50
PleI GAGTC 3 cut(s) 124, 154, 175
PpsI GAGTC 3 cut(s) 124, 154, 175
PpuMI RGGWCCY 1 cut(s) 221
Psp5II RGGWCCY 1 cut(s) 221
PspN4I GGNNCC 3 cut(s) 222, 223, 241
PspPI GGNCC 2 cut(s) 209, 221
PspPPI RGGWCCY 1 cut(s) 221
PstNI CAGNNNCTG 1 cut(s) 582
PsuI RGATCY 2 cut(s) 85, 239
RsaI GTAC 1 cut(s) 488
RsaNI GTAC 1 cut(s) 487
Sau3AI GATC 4 cut(s) 85, 108, 162, 239
Sau96I GGNCC 2 cut(s) 209, 221
SchI GAGTC 3 cut(s) 124, 155, 176
ScrFI CCNGG 2 cut(s) 68, 523
SduI GDGCHC 1 cut(s) 572
SetI ASST 9 cut(s) 214, 289, 308, 343, 364, 434, 454, 488, 499
SinI GGWCC 2 cut(s) 209, 221
StyD4I CCNGG 2 cut(s) 66, 521
StyI CCWWGG 1 cut(s) 189
TaaI ACNGT 2 cut(s) 25, 143
TaqI TCGA 3 cut(s) 107, 153, 165
TscAI CASTG 1 cut(s) 542
TseFI GTSAC 1 cut(s) 202
TseI GCWGC 1 cut(s) 528
Tsp45I GTSAC 1 cut(s) 202
TspDTI ATGAA 1 cut(s) 49
TspGWI ACGGA 1 cut(s) 139
TspRI CASTG 1 cut(s) 542
VpaK11BI GGWCC 2 cut(s) 209, 221
XagI CCTNNNNNAGG 1 cut(s) 576
XmnI GAANNNNTTC 2 cut(s) 32, 50
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.