Rh3AG246100

Cold shock protein domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr3A
OG0019907
Physical Location & Seq
Forward (+)
26247892 .. 26252820
4929 bp
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UTR
Exon/CDS
Intron
Rh3AG246100.1

Sequence Viewer

Length: 417 bp
ATGGATCATGGCATCAATGTTCCATCTGCTCTAGAATCCGAGAAGGCTATATTGCCTCCTAGTGACTATAAGAAAGTTAATCTGACACTTCACTATCGAAGTTTGAACCCAGATTCTGCACTTTTCCTAAACAAAATCTCTTCTTCCTCACACCGAATCTCCCAAAACCCAAATCTAGGTCATTCTTCCCCTCCACCATCACCACCTGATCGCTCTCTTTCCCCTCCCAAATTGACGACCATCACTTGCATGTCCTCCGGCAAGCCGACATCAGCCACAAATCGGTTAATCTCAGCCGTAGGGTTGAGTGAGAGGTTGACCGGAATGGTGAAGTGGTTCAATGACCAGAAGGGGTTCAACTTCACCACCCCGAAGAATGGCGGCGAGGATCTCTACGTCCACCTGTCCTCGATCTGA
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

138

Amino Acids

14.99

Weight (kDa)

9.37

Isoelectric Point (pI)

55.76

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
CSD PF00313 107 - 138 3.7e-09 'Cold-shock' DNA-binding domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Orthologous Genes (Group: OG0019907)

Species Orthologous Gene IDs
rosa_chinensis RchiOBHm_Chr3g0482111
rosa_laevigata RLG00000026065 RLG00000037055
rosa_multiflora Rmu_sc0007408.1_g000004 Rmu_sc0011150.1_g000001
rosa_samantha Rh3AG246100 Rh7BG243600

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 1 cut(s) 381
AclWI GGATC 2 cut(s) 12, 396
AfiI CCNNNNNNNGG 3 cut(s) 176, 282, 377
AgsI TTSAA 3 cut(s) 106, 340, 358
AlwI GGATC 2 cut(s) 12, 396
AlwNI CAGNNNCTG 1 cut(s) 116
Asp700I GAANNNNTTC 2 cut(s) 335, 353
AsuHPI GGTGA 3 cut(s) 192, 340, 355
BccI CCATC 3 cut(s) 31, 205, 248
BceAI ACGGC 1 cut(s) 281
BfaI CTAG 3 cut(s) 32, 60, 176
BisI GCNGC 1 cut(s) 382
BlsI GCNGC 1 cut(s) 383
BmsI GCATC 1 cut(s) 21
BsaWI WCCGGW 1 cut(s) 320
BsaXI ACNNNNNCTCC 2 cut(s) 143, 173
Bsc4I CCNNNNNNNGG 3 cut(s) 176, 282, 377
BseLI CCNNNNNNNGG 3 cut(s) 176, 282, 377
BseMII CTCAG 1 cut(s) 306
BsgI GTGCAG 1 cut(s) 102
BsiSI CCGG 2 cut(s) 258, 321
BslI CCNNNNNNNGG 3 cut(s) 176, 282, 377
Bsp143I GATC 4 cut(s) 4, 208, 388, 411
BspACI CCGC 1 cut(s) 381
BspCNI CTCAG 1 cut(s) 305
BspPI GGATC 2 cut(s) 12, 396
BssMI GATC 4 cut(s) 4, 208, 388, 411
Bst6I CTCTTC 1 cut(s) 145
BstC8I GCNNGC 1 cut(s) 263
BstDEI CTNAG 1 cut(s) 292
BstKTI GATC 4 cut(s) 7, 211, 391, 414
BstMBI GATC 4 cut(s) 4, 208, 388, 411
BstNSI RCATGY 1 cut(s) 253
BstX2I RGATCY 1 cut(s) 388
BstYI RGATCY 1 cut(s) 388
Cac8I GCNNGC 1 cut(s) 263
CaiI CAGNNNCTG 1 cut(s) 116
CviAII CATG 2 cut(s) 8, 250
CviJI RGCY 4 cut(s) 47, 265, 275, 296
CviKI_1 RGCY 4 cut(s) 47, 265, 275, 296
DdeI CTNAG 1 cut(s) 292
DpnI GATC 4 cut(s) 6, 210, 390, 413
DpnII GATC 4 cut(s) 4, 208, 388, 411
Eam1104I CTCTTC 1 cut(s) 145
EarI CTCTTC 1 cut(s) 145
FaeI CATG 2 cut(s) 11, 253
FaiI YATR 4 cut(s) 9, 50, 69, 251
FatI CATG 2 cut(s) 7, 249
Fnu4HI GCNGC 1 cut(s) 382
Fsp4HI GCNGC 1 cut(s) 382
FspBI CTAG 3 cut(s) 32, 60, 176
GluI GCNGC 1 cut(s) 382
HapII CCGG 2 cut(s) 258, 321
Hin1II CATG 2 cut(s) 11, 253
HincII GTYRAC 1 cut(s) 318
HindII GTYRAC 1 cut(s) 318
HinfI GANTC 3 cut(s) 35, 113, 156
HpaII CCGG 2 cut(s) 258, 321
HphI GGTGA 3 cut(s) 192, 340, 355
Hpy166II GTNNAC 2 cut(s) 318, 400
Hpy188I TCNGA 3 cut(s) 40, 84, 416
Hpy188III TCNNGA 1 cut(s) 32
Hpy8I GTNNAC 2 cut(s) 318, 400
HpyAV CCTTC 2 cut(s) 37, 343
HpyCH4IV ACGT 1 cut(s) 396
HpyCH4V TGCA 2 cut(s) 119, 249
HpyF3I CTNAG 1 cut(s) 292
HpySE526I ACGT 1 cut(s) 396
Hsp92II CATG 2 cut(s) 11, 253
Kzo9I GATC 4 cut(s) 4, 208, 388, 411
LpnPI CCDG 5 cut(s) 123, 219, 271, 334, 359
LweI GCATC 1 cut(s) 21
MaeI CTAG 3 cut(s) 32, 60, 176
MaeII ACGT 1 cut(s) 396
MaeIII GTNAC 1 cut(s) 62
MalI GATC 4 cut(s) 6, 210, 390, 413
MboI GATC 4 cut(s) 4, 208, 388, 411
MboII GAAGA 4 cut(s) 132, 135, 177, 385
MflI RGATCY 1 cut(s) 388
MluCI AATT 1 cut(s) 230
MnlI CCTC 7 cut(s) 66, 157, 201, 234, 265, 306, 379
MroXI GAANNNNTTC 2 cut(s) 335, 353
MseI TTAA 2 cut(s) 78, 287
MslI CAYNNNNRTG 1 cut(s) 248
MspI CCGG 2 cut(s) 258, 321
NdeII GATC 4 cut(s) 4, 208, 388, 411
NlaIII CATG 2 cut(s) 11, 253
NmuCI GTSAC 1 cut(s) 62
NspI RCATGY 1 cut(s) 253
PdmI GAANNNNTTC 2 cut(s) 335, 353
PfeI GAWTC 3 cut(s) 35, 113, 156
PkrI GCNGC 1 cut(s) 383
PstNI CAGNNNCTG 1 cut(s) 116
PsuI RGATCY 1 cut(s) 388
RseI CAYNNNNRTG 1 cut(s) 248
SaqAI TTAA 2 cut(s) 78, 287
SatI GCNGC 1 cut(s) 382
Sau3AI GATC 4 cut(s) 4, 208, 388, 411
SetI ASST 5 cut(s) 181, 208, 317, 399, 405
SfaNI GCATC 1 cut(s) 21
SmiMI CAYNNNNRTG 1 cut(s) 248
Sse9I AATT 1 cut(s) 230
SsiI CCGC 1 cut(s) 381
SspMI CTAG 3 cut(s) 32, 60, 176
TaiI ACGT 1 cut(s) 399
TaqI TCGA 2 cut(s) 97, 410
TasI AATT 1 cut(s) 230
TauI GCSGC 1 cut(s) 384
TfiI GAWTC 3 cut(s) 35, 113, 156
Tru1I TTAA 2 cut(s) 78, 287
Tru9I TTAA 2 cut(s) 78, 287
TseFI GTSAC 1 cut(s) 62
Tsp45I GTSAC 1 cut(s) 62
XbaI TCTAGA 1 cut(s) 31
XceI RCATGY 1 cut(s) 253
XmnI GAANNNNTTC 2 cut(s) 335, 353
XspI CTAG 3 cut(s) 32, 60, 176
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.