Rroxscaffold_2G00108200

3'-UTR-mediated mRNA destabilization

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000002
OG0006416
Physical Location & Seq
Forward (+)
32183599 .. 32186078
2480 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_2G00108200.1

Sequence Viewer

Length: 816 bp
ATGAGTAATCTTCAATCAACCTGCCAATTTTTCACTCCATTTCCGAGAGAGGGTCAAGAATTCGAAGCTGTATCGGATTTTGAACACCACCAAGCTTTCAAGAAACCCAGAGTCTCTAAGGTTGGGTCAGACTCAATGGTTATTGAGAGAAGATATAAGTGGTGGCATTACAAGACCCGACTGTGCAATAACTTCAAACGGGGTCGTTGCCTTTATGGTGAGGCGTGTCTCTATGCTCATGGCATTGAAGAAATCCGCAACACTTTGGGTAGTTCCGAAAATGAGAAGGGCATGTTGGGTAGGACTGAGAATGCTCATCACAGAACTTGTGATGAACTTCGACTTTGTAAGTTGTTCTTGAATGAGGGGAAATGCACATATGGAGAGAAATGCCGCTTTCGTCATGTTATTCCGAAGAGTATCAGAGATGAGTCAGTGATCATTTTGACTAGTGGGTCTAAAGGGTCTCAAATTAGTGGCTCTGGGCAATTTGGGGGCAAGAGGTCTTTGGATGTTGACACTAATGGAGTGAGTGGAGGCAGGCATTTTAGGCAACAGAGCTCTGTTGCAGCTGGGACAGGGATGCTGAGTAATACCTGCATAGCTAGTGGAACCTTTGCTCATGGACATGCCGTGCTCAGGAAGCTCTGTGGCTACACTACCATGGAGACTAAACATTTAAAGACTTTTACTACTTCTAGGGAATTGCAAGTTACGGACGGCAACTTCAACTGGAATGAACTTGAGAAAATGAGTCGCATCTATGCTGATTGGATTGAAGAAATTCCTCTTGCACATAGGAAGATGGAGTTCTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko04218 map04218
Pfam Domains
Protein Families
KH_1 W2 zf-CCCH zf-CCCH_2

Protein Analysis

271

Amino Acids

30.87

Weight (kDa)

9.07

Isoelectric Point (pI)

43.55

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
zf-CCCH PF00642 57 - 81 6.5e-07 Zinc finger C-x8-C-x5-C-x3-H type (and similar)
zf-CCCH_DUS3L PF25585 114 - 135 5.9e-06 DUS3L CCCH zinc finger domain
zf-CCCH_4 PF18044 114 - 135 6.3e-07 CCCH-type zinc finger
zf_CCCH_4 PF18345 116 - 135 6e-07 Zinc finger 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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 1 cut(s) 454
Acc36I ACCTGC 2 cut(s) 29, 605
AciI CCGC 2 cut(s) 256, 394
AcsI RAATTY 2 cut(s) 59, 783
AfiI CCNNNNNNNGG 2 cut(s) 50, 639
AgsI TTSAA 8 cut(s) 14, 83, 100, 196, 248, 361, 730, 779
AhlI ACTAGT 1 cut(s) 449
AjuI GAANNNNNNNTTGG 2 cut(s) 278, 310
AluBI AGCT 6 cut(s) 68, 95, 561, 572, 605, 646
AluI AGCT 6 cut(s) 68, 95, 561, 572, 605, 646
Alw21I GWGCWC 2 cut(s) 563, 639
Alw26I GTCTC 4 cut(s) 118, 233, 471, 662
ApeKI GCWGC 1 cut(s) 569
ApoI RAATTY 2 cut(s) 59, 783
Asp700I GAANNNNTTC 1 cut(s) 783
AsuHPI GGTGA 1 cut(s) 230
AsuII TTCGAA 1 cut(s) 63
BanII GRGCYC 1 cut(s) 563
Bbv12I GWGCWC 2 cut(s) 563, 639
BbvI GCAGC 1 cut(s) 581
BccI CCATC 1 cut(s) 799
BceAI ACGGC 2 cut(s) 617, 736
BclI TGATCA 1 cut(s) 438
BcoDI GTCTC 4 cut(s) 118, 233, 471, 662
BcuI ACTAGT 1 cut(s) 449
BfaI CTAG 3 cut(s) 450, 606, 699
BfuAI ACCTGC 2 cut(s) 29, 605
BisI GCNGC 2 cut(s) 394, 570
BlsI GCNGC 2 cut(s) 395, 571
BmiI GGNNCC 1 cut(s) 613
BmsI GCATC 2 cut(s) 573, 768
Bpu10I CCTNAGC 1 cut(s) 638
Bpu14I TTCGAA 1 cut(s) 63
BpuEI CTTGAG 1 cut(s) 764
BsaI GGTCTC 1 cut(s) 471
BsaJI CCNNGG 1 cut(s) 663
Bsc4I CCNNNNNNNGG 2 cut(s) 50, 639
Bse1I ACTGG 1 cut(s) 737
BseDI CCNNGG 1 cut(s) 663
BseGI GGATG 2 cut(s) 517, 588
BseLI CCNNNNNNNGG 2 cut(s) 50, 639
BseMII CTCAG 3 cut(s) 297, 578, 652
BseNI ACTGG 1 cut(s) 737
BseXI GCAGC 1 cut(s) 581
BseYI CCCAGC 1 cut(s) 572
BsiHKAI GWGCWC 2 cut(s) 563, 639
BslFI GGGAC 1 cut(s) 589
BslI CCNNNNNNNGG 2 cut(s) 50, 639
BsmAI GTCTC 4 cut(s) 118, 233, 471, 662
BsmFI GGGAC 1 cut(s) 589
BsmI GAATGC 1 cut(s) 316
Bso31I GGTCTC 1 cut(s) 471
Bsp119I TTCGAA 1 cut(s) 63
Bsp1286I GDGCHC 2 cut(s) 563, 639
Bsp143I GATC 1 cut(s) 438
Bsp19I CCATGG 1 cut(s) 663
BspACI CCGC 2 cut(s) 256, 394
BspCNI CTCAG 3 cut(s) 298, 579, 651
BspLI GGNNCC 1 cut(s) 613
BspMI ACCTGC 2 cut(s) 29, 605
BspT104I TTCGAA 1 cut(s) 63
BspTNI GGTCTC 1 cut(s) 471
BsrI ACTGG 1 cut(s) 737
BssECI CCNNGG 1 cut(s) 663
BssMI GATC 1 cut(s) 438
BssT1I CCWWGG 1 cut(s) 663
Bst4CI ACNGT 1 cut(s) 183
Bst6I CTCTTC 1 cut(s) 410
BstBI TTCGAA 1 cut(s) 63
BstC8I GCNNGC 1 cut(s) 542
BstDEI CTNAG 4 cut(s) 117, 306, 587, 638
BstDSI CCRYGG 1 cut(s) 663
BstF5I GGATG 2 cut(s) 517, 588
BstKTI GATC 1 cut(s) 441
BstMAI GTCTC 4 cut(s) 118, 233, 471, 662
BstMBI GATC 1 cut(s) 438
BstMWI GCNNNNNNNGC 2 cut(s) 550, 643
BstNSI RCATGY 2 cut(s) 295, 632
BstV1I GCAGC 1 cut(s) 581
BtgI CCRYGG 1 cut(s) 663
BtsCI GGATG 2 cut(s) 517, 588
BtsIMutI CAGTG 1 cut(s) 441
BveI ACCTGC 2 cut(s) 29, 605
Cac8I GCNNGC 1 cut(s) 542
CviAII CATG 6 cut(s) 239, 292, 404, 623, 629, 664
CviJI RGCY 8 cut(s) 68, 95, 480, 561, 572, 605, 646, 654
CviKI_1 RGCY 8 cut(s) 68, 95, 480, 561, 572, 605, 646, 654
DdeI CTNAG 4 cut(s) 117, 306, 587, 638
DpnI GATC 1 cut(s) 440
DpnII GATC 1 cut(s) 438
DraI TTTAAA 1 cut(s) 681
DrdI GACNNNNNNGTC 1 cut(s) 454
DseDI GACNNNNNNGTC 1 cut(s) 454
Eam1104I CTCTTC 1 cut(s) 410
EarI CTCTTC 1 cut(s) 410
Ecl136II GAGCTC 1 cut(s) 561
Eco130I CCWWGG 1 cut(s) 663
Eco24I GRGCYC 1 cut(s) 563
Eco31I GGTCTC 1 cut(s) 471
Eco53kI GAGCTC 1 cut(s) 561
EcoICRI GAGCTC 1 cut(s) 561
EcoRI GAATTC 1 cut(s) 59
EcoT14I CCWWGG 1 cut(s) 663
EcoT38I GRGCYC 1 cut(s) 563
ErhI CCWWGG 1 cut(s) 663
FaeI CATG 6 cut(s) 242, 295, 407, 626, 632, 667
FalI AAGNNNNNCTT 2 cut(s) 341, 373
FaqI GGGAC 1 cut(s) 589
FatI CATG 6 cut(s) 238, 291, 403, 622, 628, 663
FauNDI CATATG 1 cut(s) 379
FbaI TGATCA 1 cut(s) 438
Fnu4HI GCNGC 2 cut(s) 394, 570
FokI GGATG 2 cut(s) 524, 595
FriOI GRGCYC 1 cut(s) 563
Fsp4HI GCNGC 2 cut(s) 394, 570
FspBI CTAG 3 cut(s) 450, 606, 699
GluI GCNGC 2 cut(s) 394, 570
GsaI CCCAGC 1 cut(s) 576
Hin1II CATG 6 cut(s) 242, 295, 407, 626, 632, 667
HincII GTYRAC 1 cut(s) 517
HindII GTYRAC 1 cut(s) 517
HindIII AAGCTT 1 cut(s) 93
HinfI GANTC 4 cut(s) 111, 131, 431, 754
HphI GGTGA 1 cut(s) 230
Hpy166II GTNNAC 1 cut(s) 517
Hpy188I TCNGA 7 cut(s) 45, 76, 130, 277, 414, 425, 815
Hpy188III TCNNGA 4 cut(s) 56, 100, 358, 640
Hpy8I GTNNAC 1 cut(s) 517
HpyAV CCTTC 1 cut(s) 280
HpyCH4III ACNGT 1 cut(s) 183
HpyCH4V TGCA 6 cut(s) 186, 375, 569, 600, 709, 794
HpyF10VI GCNNNNNNNGC 2 cut(s) 550, 643
HpyF3I CTNAG 4 cut(s) 117, 306, 587, 638
Hsp92II CATG 6 cut(s) 242, 295, 407, 626, 632, 667
Ksp22I TGATCA 1 cut(s) 438
Kzo9I GATC 1 cut(s) 438
LpnPI CCDG 9 cut(s) 34, 121, 468, 526, 558, 564, 610, 625, 718
Lsp1109I GCAGC 1 cut(s) 581
LweI GCATC 2 cut(s) 573, 768
MaeI CTAG 3 cut(s) 450, 606, 699
MaeIII GTNAC 1 cut(s) 712
MalI GATC 1 cut(s) 440
MboI GATC 1 cut(s) 438
MboII GAAGA 5 cut(s) 162, 260, 427, 791, 814
MhlI GDGCHC 2 cut(s) 563, 639
MluCI AATT 6 cut(s) 26, 59, 471, 488, 704, 783
MlyI GAGTC 4 cut(s) 120, 125, 440, 763
MnlI CCTC 6 cut(s) 43, 214, 358, 495, 530, 798
MroXI GAANNNNTTC 1 cut(s) 783
MseI TTAA 1 cut(s) 680
MslI CAYNNNNRTG 2 cut(s) 627, 662
MspA1I CMGCKG 1 cut(s) 572
Mva1269I GAATGC 1 cut(s) 316
MwoI GCNNNNNNNGC 2 cut(s) 550, 643
NcoI CCATGG 1 cut(s) 663
NdeI CATATG 1 cut(s) 379
NdeII GATC 1 cut(s) 438
NlaIII CATG 6 cut(s) 242, 295, 407, 626, 632, 667
NlaIV GGNNCC 1 cut(s) 613
NspI RCATGY 2 cut(s) 295, 632
NspV TTCGAA 1 cut(s) 63
PctI GAATGC 1 cut(s) 316
PdmI GAANNNNTTC 1 cut(s) 783
PkrI GCNGC 2 cut(s) 395, 571
PleI GAGTC 4 cut(s) 119, 125, 439, 762
PpsI GAGTC 4 cut(s) 119, 125, 439, 762
Psp124BI GAGCTC 1 cut(s) 563
PspFI CCCAGC 1 cut(s) 572
PspN4I GGNNCC 1 cut(s) 613
PvuII CAGCTG 1 cut(s) 572
RseI CAYNNNNRTG 2 cut(s) 627, 662
SacI GAGCTC 1 cut(s) 563
SaqAI TTAA 1 cut(s) 680
SatI GCNGC 2 cut(s) 394, 570
Sau3AI GATC 1 cut(s) 438
SchI GAGTC 4 cut(s) 120, 125, 440, 763
SduI GDGCHC 2 cut(s) 563, 639
SfaNI GCATC 2 cut(s) 573, 768
SfuI TTCGAA 1 cut(s) 63
SmiMI CAYNNNNRTG 2 cut(s) 627, 662
SmlI CTYRAG 1 cut(s) 743
SmoI CTYRAG 1 cut(s) 743
SpeI ACTAGT 1 cut(s) 449
Sse9I AATT 6 cut(s) 26, 59, 471, 488, 704, 783
SsiI CCGC 2 cut(s) 256, 394
SspMI CTAG 3 cut(s) 450, 606, 699
SstI GAGCTC 1 cut(s) 563
StyI CCWWGG 1 cut(s) 663
TaaI ACNGT 1 cut(s) 183
TaqI TCGA 2 cut(s) 63, 340
TasI AATT 6 cut(s) 26, 59, 471, 488, 704, 783
TauI GCSGC 1 cut(s) 396
Tru1I TTAA 1 cut(s) 680
Tru9I TTAA 1 cut(s) 680
TscAI CASTG 1 cut(s) 441
TseI GCWGC 1 cut(s) 569
TspDTI ATGAA 2 cut(s) 348, 753
TspGWI ACGGA 1 cut(s) 731
TspRI CASTG 1 cut(s) 441
XapI RAATTY 2 cut(s) 59, 783
XceI RCATGY 2 cut(s) 295, 632
XmnI GAANNNNTTC 1 cut(s) 783
XspI CTAG 3 cut(s) 450, 606, 699
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.