RLG00000015370

Cold shock protein domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_laevigata
Chr3
OG0017069
Physical Location & Seq
Forward (+)
65127282 .. 65127881
600 bp
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UTR
Exon/CDS
Intron
RLM00000015370

Sequence Viewer

Length: 600 bp
ATGAGTGATAGGTTGACCGGAACGGTGAAGTGGTTCAGTGACCAGAAGGGGTTCGGCTTCATAACCCCGGCGGACGGCGGCGAGGATCTCTTCGTCCACCAGTCCTCGATCCGAACCGAAGGCTTCCGGACTCTCGGCGACGGCGAGTCCGTCGAGTTCCAGATCGAGACCGACAACGACGGCCGCACCAAGGCTGTTGATGTGACCGGACCGGAGGAGGGTCCCGTTCAGGGGAGAGGATCTGGAGGCGGCGGCCGTGGCGGTGGAGGCCGTGGTGGCGGGAGAGGTGGCCGTGGAGGCGGGAGCTACGGCGGTGGTGGAGGCTATGGCGGTGGGGGAGGTTATGGCGGCGGTGGCGGTGGATATGGAGGCGGTGGAGGTGGGAACTGTTTTAAGTGTGGTGAGGCTGGACACATGGCGAGGGACTGCTCGGAGGGAGGTGGTAGCTATGGAGGCGGCGGCCGAGGTGGAGGCGGTTACGGCGGCGGAGGCGGTGGTAGGTACTCGGGAGGTGGAGGCGGCGGCGCTGGTGCATCCAACGGCTGCTATCAGTGTGGCGAAACTGGTCATTTCGCAAGGGAGTGCCCTAACAGAGGCTGA
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

200

Amino Acids

18.88

Weight (kDa)

5.92

Isoelectric Point (pI)

42.17

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
CSD PF00313 6 - 70 6.8e-26 'Cold-shock' DNA-binding domain
zf-CCHC PF00098 129 - 144 4.1e-07 Zinc knuckle
zf-CCHC PF00098 181 - 197 1.7e-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 1 cut(s) 126
AclWI GGATC 3 cut(s) 93, 103, 247
AcoI YGGCCR 4 cut(s) 181, 253, 289, 460
AfaI GTAC 1 cut(s) 503
AfiI CCNNNNNNNGG 6 cut(s) 74, 190, 218, 230, 231, 593
AhdI GACNNNNNGTC 1 cut(s) 145
AluBI AGCT 2 cut(s) 306, 447
AluI AGCT 2 cut(s) 306, 447
Alw26I GTCTC 1 cut(s) 161
AlwI GGATC 3 cut(s) 93, 103, 247
AlwNI CAGNNNCTG 1 cut(s) 597
Ama87I CYCGRG 1 cut(s) 505
Aor13HI TCCGGA 1 cut(s) 126
AoxI GGCC 5 cut(s) 181, 253, 268, 289, 460
ApeKI GCWGC 1 cut(s) 543
Asp700I GAANNNNTTC 2 cut(s) 32, 50
AspLEI GCGC 1 cut(s) 527
AspS9I GGNCC 2 cut(s) 209, 221
AsuC2I CCSGG 1 cut(s) 68
AsuHPI GGTGA 2 cut(s) 37, 413
AvaI CYCGRG 1 cut(s) 505
AvaII GGWCC 2 cut(s) 209, 221
BaeGI GKGCMC 1 cut(s) 587
BbvI GCAGC 1 cut(s) 530
BceAI ACGGC 9 cut(s) 91, 157, 196, 240, 255, 276, 325, 496, 556
BcnI CCSGG 1 cut(s) 68
BcoDI GTCTC 1 cut(s) 161
BfoI RGCGCY 1 cut(s) 528
BglI GCCNNNNNGGC 2 cut(s) 276, 297
Bme1390I CCNGG 1 cut(s) 68
Bme18I GGWCC 2 cut(s) 209, 221
BmeRI GACNNNNNGTC 1 cut(s) 145
BmeT110I CYCGRG 1 cut(s) 505
BmgT120I GGNCC 2 cut(s) 209, 221
BmiI GGNNCC 2 cut(s) 222, 223
BmrFI CCNGG 1 cut(s) 68
BmsI GCATC 1 cut(s) 542
BpmI CTGGAG 1 cut(s) 264
BpuMI CCSGG 1 cut(s) 68
BsaI GGTCTC 1 cut(s) 161
BsaJI CCNNGG 6 cut(s) 66, 189, 256, 271, 292, 463
BsaWI WCCGGW 4 cut(s) 17, 126, 206, 211
Bsc4I CCNNNNNNNGG 6 cut(s) 74, 190, 218, 230, 231, 593
Bse1I ACTGG 2 cut(s) 100, 568
BseAI TCCGGA 1 cut(s) 126
BseDI CCNNGG 6 cut(s) 66, 189, 256, 271, 292, 463
BseGI GGATG 1 cut(s) 533
BseLI CCNNNNNNNGG 6 cut(s) 74, 190, 218, 230, 231, 593
BseNI ACTGG 2 cut(s) 100, 568
BseRI GAGGAG 1 cut(s) 230
BseSI GKGCMC 1 cut(s) 587
BseX3I CGGCCG 3 cut(s) 181, 253, 460
BseXI GCAGC 1 cut(s) 530
Bsh1285I CGRYCG 3 cut(s) 184, 256, 463
BshFI GGCC 5 cut(s) 183, 255, 270, 291, 462
BsiEI CGRYCG 3 cut(s) 184, 256, 463
BsiHKCI CYCGRG 1 cut(s) 505
BsiSI CCGG 5 cut(s) 18, 68, 127, 207, 212
BslFI GGGAC 2 cut(s) 207, 437
BslI CCNNNNNNNGG 6 cut(s) 74, 190, 218, 230, 231, 593
BsmAI GTCTC 1 cut(s) 161
BsmFI GGGAC 2 cut(s) 207, 437
BsnI GGCC 5 cut(s) 183, 255, 270, 291, 462
Bso31I GGTCTC 1 cut(s) 161
BsoBI CYCGRG 1 cut(s) 505
Bsp1286I GDGCHC 1 cut(s) 587
Bsp13I TCCGGA 1 cut(s) 126
Bsp143I GATC 4 cut(s) 85, 108, 162, 239
BspANI GGCC 5 cut(s) 183, 255, 270, 291, 462
BspEI TCCGGA 1 cut(s) 126
BspLI GGNNCC 2 cut(s) 222, 223
BspPI GGATC 3 cut(s) 93, 103, 247
BspTNI GGTCTC 1 cut(s) 161
BsrI ACTGG 2 cut(s) 100, 568
BssECI CCNNGG 6 cut(s) 66, 189, 256, 271, 292, 463
BssMI GATC 4 cut(s) 85, 108, 162, 239
BssT1I CCWWGG 1 cut(s) 189
Bst4CI ACNGT 2 cut(s) 25, 389
Bst6I CTCTTC 1 cut(s) 95
BstDSI CCRYGG 3 cut(s) 256, 271, 292
BstENI CCTNNNNNAGG 1 cut(s) 591
BstF5I GGATG 1 cut(s) 533
BstH2I RGCGCY 1 cut(s) 528
BstHHI GCGC 1 cut(s) 527
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, 256, 463
BstMWI GCNNNNNNNGC 8 cut(s) 258, 267, 276, 297, 354, 453, 480, 489
BstSCI CCNGG 1 cut(s) 66
BstSLI GKGCMC 1 cut(s) 587
BstV1I GCAGC 1 cut(s) 530
BstX2I RGATCY 2 cut(s) 85, 239
BstYI RGATCY 2 cut(s) 85, 239
BstZI CGGCCG 3 cut(s) 181, 253, 460
BsuRI GGCC 5 cut(s) 183, 255, 270, 291, 462
BtgI CCRYGG 3 cut(s) 256, 271, 292
BtsCI GGATG 1 cut(s) 533
BtsIMutI CAGTG 2 cut(s) 43, 557
CaiI CAGNNNCTG 1 cut(s) 597
CfoI GCGC 1 cut(s) 527
Cfr13I GGNCC 2 cut(s) 209, 221
CpoI CGGWCCG 1 cut(s) 209
Csp6I GTAC 1 cut(s) 502
CspI CGGWCCG 1 cut(s) 209
CviAII CATG 1 cut(s) 415
CviQI GTAC 1 cut(s) 502
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, 460
EagI CGGCCG 3 cut(s) 181, 253, 460
Eam1104I CTCTTC 1 cut(s) 95
Eam1105I GACNNNNNGTC 1 cut(s) 145
EarI CTCTTC 1 cut(s) 95
EciI GGCGGA 2 cut(s) 86, 501
EclXI CGGCCG 3 cut(s) 181, 253, 460
Eco130I CCWWGG 1 cut(s) 189
Eco31I GGTCTC 1 cut(s) 161
Eco47I GGWCC 2 cut(s) 209, 221
Eco52I CGGCCG 3 cut(s) 181, 253, 460
Eco88I CYCGRG 1 cut(s) 505
EcoNI CCTNNNNNAGG 1 cut(s) 591
EcoO109I RGGNCCY 1 cut(s) 221
EcoT14I CCWWGG 1 cut(s) 189
ErhI CCWWGG 1 cut(s) 189
FaeI CATG 1 cut(s) 418
FaiI YATR 6 cut(s) 62, 327, 345, 366, 416, 450
FaqI GGGAC 2 cut(s) 207, 437
FatI CATG 1 cut(s) 414
FauI CCCGC 2 cut(s) 272, 293
FokI GGATG 1 cut(s) 520
GlaI GCGC 1 cut(s) 526
GsuI CTGGAG 1 cut(s) 264
HaeII RGCGCY 1 cut(s) 528
HaeIII GGCC 5 cut(s) 183, 255, 270, 291, 462
HapII CCGG 5 cut(s) 18, 68, 127, 207, 212
HhaI GCGC 1 cut(s) 527
Hin1II CATG 1 cut(s) 418
Hin6I GCGC 1 cut(s) 525
HinP1I GCGC 1 cut(s) 525
HincII GTYRAC 1 cut(s) 15
HindII GTYRAC 1 cut(s) 15
HinfI GANTC 2 cut(s) 130, 146
HpaII CCGG 5 cut(s) 18, 68, 127, 207, 212
HphI GGTGA 2 cut(s) 37, 413
Hpy166II GTNNAC 2 cut(s) 15, 97
Hpy188I TCNGA 2 cut(s) 113, 433
Hpy188III TCNNGA 5 cut(s) 127, 160, 166, 243, 507
Hpy8I GTNNAC 2 cut(s) 15, 97
Hpy99I CGWCG 3 cut(s) 143, 155, 182
HpyAV CCTTC 2 cut(s) 40, 113
HpyCH4III ACNGT 2 cut(s) 25, 389
HpyCH4V TGCA 1 cut(s) 533
HpyF10VI GCNNNNNNNGC 8 cut(s) 258, 267, 276, 297, 354, 453, 480, 489
Hsp92II CATG 1 cut(s) 418
HspAI GCGC 1 cut(s) 525
KflI GGGWCCC 1 cut(s) 221
Kpn2I TCCGGA 1 cut(s) 126
Kzo9I GATC 4 cut(s) 85, 108, 162, 239
LmnI GCTCC 1 cut(s) 303
Lsp1109I GCAGC 1 cut(s) 530
LweI GCATC 1 cut(s) 542
MaeIII GTNAC 3 cut(s) 38, 202, 476
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) 587
MlyI GAGTC 2 cut(s) 124, 155
MmeI TCCRAC 1 cut(s) 561
MroI TCCGGA 1 cut(s) 126
MroXI GAANNNNTTC 2 cut(s) 32, 50
MseI TTAA 1 cut(s) 393
MspI CCGG 5 cut(s) 18, 68, 127, 207, 212
MspR9I CCNGG 1 cut(s) 68
MwoI GCNNNNNNNGC 8 cut(s) 258, 267, 276, 297, 354, 453, 480, 489
NciI CCSGG 1 cut(s) 68
NdeII GATC 4 cut(s) 85, 108, 162, 239
NlaIII CATG 1 cut(s) 418
NlaIV GGNNCC 2 cut(s) 222, 223
NmeAIII GCCGAG 2 cut(s) 114, 488
NmuCI GTSAC 2 cut(s) 38, 202
PcsI WCGNNNNNNNCGW 2 cut(s) 141, 147
PdmI GAANNNNTTC 2 cut(s) 32, 50
PleI GAGTC 2 cut(s) 124, 154
PpsI GAGTC 2 cut(s) 124, 154
PpuMI RGGWCCY 1 cut(s) 221
Psp5II RGGWCCY 1 cut(s) 221
PspN4I GGNNCC 2 cut(s) 222, 223
PspPI GGNCC 2 cut(s) 209, 221
PspPPI RGGWCCY 1 cut(s) 221
PstNI CAGNNNCTG 1 cut(s) 597
PsuI RGATCY 2 cut(s) 85, 239
RsaI GTAC 1 cut(s) 503
RsaNI GTAC 1 cut(s) 502
Rsr2I CGGWCCG 1 cut(s) 209
RsrII CGGWCCG 1 cut(s) 209
SaqAI TTAA 1 cut(s) 393
Sau3AI GATC 4 cut(s) 85, 108, 162, 239
Sau96I GGNCC 2 cut(s) 209, 221
SchI GAGTC 2 cut(s) 124, 155
ScrFI CCNGG 1 cut(s) 68
SduI GDGCHC 1 cut(s) 587
SfaNI GCATC 1 cut(s) 542
SinI GGWCC 2 cut(s) 209, 221
StyD4I CCNGG 1 cut(s) 66
StyI CCWWGG 1 cut(s) 189
TaaI ACNGT 2 cut(s) 25, 389
TaqI TCGA 3 cut(s) 107, 153, 165
TaqII GACCGA 1 cut(s) 185
Tru1I TTAA 1 cut(s) 393
Tru9I TTAA 1 cut(s) 393
TscAI CASTG 2 cut(s) 43, 557
TseFI GTSAC 2 cut(s) 38, 202
TseI GCWGC 1 cut(s) 543
Tsp45I GTSAC 2 cut(s) 38, 202
TspDTI ATGAA 1 cut(s) 49
TspGWI ACGGA 1 cut(s) 139
TspRI CASTG 2 cut(s) 43, 557
VpaK11BI GGWCC 2 cut(s) 209, 221
XagI CCTNNNNNAGG 1 cut(s) 591
XmnI GAANNNNTTC 2 cut(s) 32, 50
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.