Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3A

Orthogroup ID

OG0017335

Physical Location & Seq

Genomic Coordinates Reverse (-)

25536757 .. 25538421

Gene Structure 1665 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3AG242700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 909 bp

ATGGCTTCTTCTCGCCGCATTTTCGTTGGGAACATCCCTTATGATGCCACCGAGCAACAGGTCAAGGCTCTCTGCGAGGAGGTTGGCCCTGTTGTGACTTTCAGAATGGTTACAGATAAAGACACCGGGAAGCCAAAGGGTTTTGGGTTCTGTGAGTACAGGGATGAAGCGACGGCGTTTAGTGCGCTGCGAAATCTTCAGGATTGTGAGCTCAATGGCCGGCGTTTGAAGGTTAATTTTGCTGCTAATGATAAGGCCAATCATCAGCCGATTGGTCTCCAAGCAGCTGTTGATGCAGCCGCCGCAATGGCGGGAGCTCTAGGCGGTTCTCAGCAGCAGGCATTGGCTAATGATCCTTTGACAGTCCATCTGTCCAAAATGTCGAGGAATCAGTTGGCGCAAATGGTCTCGGAGATGAAGGGAATTGCTGTGGAAAATCAGGAGATGGCTCAGGAGCTGTTGCTTGCAAAGCCGCAGTTAAACAGGGCTCTGCTTCAGGCACAAATGATGCTAGGAATGGTCACACCACAAATGTTGGGACAGGTTAATATGAGGCCAATGCTTCCCTTCAATAATGGCCAGCCGCAGCAGCAGCAGCTCGTTCCCAAATCGGAACCAGTACAGATCTCGGAGCCTCAGACTCTGGTCACCCCACAAATGATGCAAAAGCGGGCAATGCCTCCATTGAATATGGGCCAGCAGCAGCAGCAGCAAGTTCCAAAATCAGAACCAGTGCAAATCTCTGAGCCTCAGATTCTTCCAACGGGGGTGGACCCTGCTTTGTTGCAACAAGTTTTGAGCCTACCTCCCAAAACGGTGGCTTCATTGGCACCCGAACTGCGACAACAGGTCATTCAACTCCAACAGATGTATAGGCAAGATCAGAGGATCCCTTGCAGCAGTGGATGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003676 GO:0003723 GO:0003729 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005847 GO:0005849 GO:0006139 GO:0006379 GO:0006396 GO:0006397 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009987 GO:0010467 GO:0016070 GO:0016071 GO:0016604 GO:0031123 GO:0031124 GO:0031974 GO:0031981 GO:0032991 GO:0034641 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044237 GO:0044238 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044464 GO:0046483 GO:0070013 GO:0071704 GO:0071920 GO:0090304 GO:0090305 GO:0090501 GO:0097159 GO:0098787 GO:0098789 GO:1901360 GO:1901363

KEGG Pathways

Metabolic & Signaling

ko03015 map03015

Pfam Domains

Protein Families

CSTF2_hinge CSTF_C RRM_1

Protein Analysis

302

Amino Acids

33.22

Weight (kDa)

8.34

Isoelectric Point (pI)

57.78

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RRM_1	PF00076	7 - 77	2.5e-20	RNA recognition motif
CSTF2_hinge	PF14327	113 - 182	3.5e-14	Hinge domain of cleavage stimulation factor subunit 2
CSTF_C	PF14304	260 - 293	4.5e-07	Transcription termination and cleavage factor C-terminal

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: OG0017335)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_6g22940 FvH4_6g23390
rosa_chinensis	RchiOBHm_Chr3g0481441
rosa_laevigata	RLG00000023400
rosa_multiflora	Rmu_sc0000064.1_g000026 Rmu_sc0021886.1_g000005
rosa_roxburghii	Rroxscaffold_6G00400450
rosa_rugosa	Rorug03G0191800
rosa_samantha	Rh3AG242700 Rh3BG277700 Rh3CG272700 Rh3DG269700
rosa_wichuraiana	Rw3G021690

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	829
AciI	CCGC	8 cut(s)	16, 300, 303, 311, 324, 473, 584, 670
AclWI	GGATC	3 cut(s)	347, 883, 896
AcoI	YGGCCR	2 cut(s)	217, 577
AcuI	CTGAAG	2 cut(s)	182, 479
AfaI	GTAC	2 cut(s)	158, 621
AgsI	TTSAA	4 cut(s)	229, 571, 688, 857
AhdI	GACNNNNNGTC	1 cut(s)	848
AluBI	AGCT	5 cut(s)	211, 287, 317, 457, 598
AluI	AGCT	5 cut(s)	211, 287, 317, 457, 598
Alw21I	GWGCWC	2 cut(s)	213, 319
Alw26I	GTCTC	2 cut(s)	281, 412
AlwI	GGATC	3 cut(s)	347, 883, 896
AlwNI	CAGNNNCTG	2 cut(s)	457, 643
AoxI	GGCC	6 cut(s)	85, 217, 255, 554, 577, 694
AspLEI	GCGC	2 cut(s)	187, 400
AspS9I	GGNCC	3 cut(s)	86, 694, 772
AsuC2I	CCSGG	1 cut(s)	127
AsuHPI	GGTGA	1 cut(s)	640
AvaII	GGWCC	1 cut(s)	772
BalI	TGGCCA	1 cut(s)	579
BamHI	GGATCC	1 cut(s)	888
BanI	GGYRCC	1 cut(s)	829
BanII	GRGCYC	3 cut(s)	213, 319, 490
Bbv12I	GWGCWC	2 cut(s)	213, 319
BccI	CCATC	2 cut(s)	375, 439
BceAI	ACGGC	1 cut(s)	189
BcnI	CCSGG	1 cut(s)	127
BcoDI	GTCTC	2 cut(s)	281, 412
BfaI	CTAG	2 cut(s)	320, 512
BglI	GCCNNNNNGGC	1 cut(s)	308
BglII	AGATCT	1 cut(s)	624
Bme1390I	CCNGG	1 cut(s)	127
Bme18I	GGWCC	1 cut(s)	772
BmeRI	GACNNNNNGTC	1 cut(s)	848
BmgT120I	GGNCC	3 cut(s)	86, 694, 772
BmiI	GGNNCC	5 cut(s)	615, 633, 774, 831, 890
BmrFI	CCNGG	1 cut(s)	127
BmsI	GCATC	4 cut(s)	34, 283, 498, 651
BoxI	GACNNNNGTC	1 cut(s)	644
BplI	GAGNNNNNCTC	2 cut(s)	790, 822
Bpu10I	CCTNAGC	1 cut(s)	450
BpuMI	CCSGG	1 cut(s)	127
BsaI	GGTCTC	2 cut(s)	281, 412
Bse118I	RCCGGY	1 cut(s)	219
Bse1I	ACTGG	2 cut(s)	617, 731
Bse3DI	GCAATG	2 cut(s)	312, 681
BseGI	GGATG	2 cut(s)	33, 169
BseMI	GCAATG	2 cut(s)	312, 681
BseMII	CTCAG	5 cut(s)	344, 464, 650, 735, 764
BseNI	ACTGG	2 cut(s)	617, 731
BseRI	GAGGAG	1 cut(s)	92
BshFI	GGCC	6 cut(s)	87, 219, 257, 556, 579, 696
BshNI	GGYRCC	1 cut(s)	829
BsiHKAI	GWGCWC	2 cut(s)	213, 319
BsiSI	CCGG	2 cut(s)	126, 220
BslFI	GGGAC	1 cut(s)	552
BsmAI	GTCTC	2 cut(s)	281, 412
BsmFI	GGGAC	1 cut(s)	552
BsnI	GGCC	6 cut(s)	87, 219, 257, 556, 579, 696
Bso31I	GGTCTC	2 cut(s)	281, 412
Bsp1286I	GDGCHC	3 cut(s)	213, 319, 490
Bsp143I	GATC	4 cut(s)	352, 624, 880, 888
BspACI	CCGC	8 cut(s)	16, 300, 303, 311, 324, 473, 584, 670
BspANI	GGCC	6 cut(s)	87, 219, 257, 556, 579, 696
BspCNI	CTCAG	5 cut(s)	343, 463, 649, 736, 763
BspLI	GGNNCC	5 cut(s)	615, 633, 774, 831, 890
BspPI	GGATC	3 cut(s)	347, 883, 896
BspT107I	GGYRCC	1 cut(s)	829
BspTNI	GGTCTC	2 cut(s)	281, 412
BsrDI	GCAATG	2 cut(s)	312, 681
BsrFI	RCCGGY	1 cut(s)	219
BsrI	ACTGG	2 cut(s)	617, 731
BssAI	RCCGGY	1 cut(s)	219
BssMI	GATC	4 cut(s)	352, 624, 880, 888
Bst4CI	ACNGT	2 cut(s)	364, 817
BstC8I	GCNNGC	6 cut(s)	221, 339, 465, 581, 672, 698
BstDEI	CTNAG	5 cut(s)	330, 450, 636, 744, 750
BstEII	GGTNACC	1 cut(s)	646
BstF5I	GGATG	2 cut(s)	33, 169
BstHHI	GCGC	2 cut(s)	187, 400
BstKTI	GATC	4 cut(s)	355, 627, 883, 891
BstMAI	GTCTC	2 cut(s)	281, 412
BstMBI	GATC	4 cut(s)	352, 624, 880, 888
BstPAI	GACNNNNGTC	1 cut(s)	644
BstPI	GGTNACC	1 cut(s)	646
BstSCI	CCNGG	1 cut(s)	125
BstX2I	RGATCY	2 cut(s)	624, 888
BstXI	CCANNNNNNTGG	1 cut(s)	817
BstYI	RGATCY	2 cut(s)	624, 888
BsuRI	GGCC	6 cut(s)	87, 219, 257, 556, 579, 696
BtsCI	GGATG	2 cut(s)	33, 169
BtsI	GCAGTG	1 cut(s)	907
BtsIMutI	CAGTG	2 cut(s)	738, 907
Cac8I	GCNNGC	6 cut(s)	221, 339, 465, 581, 672, 698
CaiI	CAGNNNCTG	2 cut(s)	457, 643
CfoI	GCGC	2 cut(s)	187, 400
Cfr10I	RCCGGY	1 cut(s)	219
Cfr13I	GGNCC	3 cut(s)	86, 694, 772
Csp6I	GTAC	2 cut(s)	157, 620
CspCI	CAANNNNNGTGG	4 cut(s)	516, 551, 750, 785
CviQI	GTAC	2 cut(s)	157, 620
DdeI	CTNAG	5 cut(s)	330, 450, 636, 744, 750
DpnI	GATC	4 cut(s)	354, 626, 882, 890
DpnII	GATC	4 cut(s)	352, 624, 880, 888
DriI	GACNNNNNGTC	1 cut(s)	848
EaeI	YGGCCR	2 cut(s)	217, 577
Eam1105I	GACNNNNNGTC	1 cut(s)	848
Ecl136II	GAGCTC	2 cut(s)	211, 317
Eco24I	GRGCYC	3 cut(s)	213, 319, 490
Eco31I	GGTCTC	2 cut(s)	281, 412
Eco47I	GGWCC	1 cut(s)	772
Eco53kI	GAGCTC	2 cut(s)	211, 317
Eco57I	CTGAAG	2 cut(s)	182, 479
Eco91I	GGTNACC	1 cut(s)	646
EcoICRI	GAGCTC	2 cut(s)	211, 317
EcoO65I	GGTNACC	1 cut(s)	646
EcoT38I	GRGCYC	3 cut(s)	213, 319, 490
FaiI	YATR	4 cut(s)	42, 551, 692, 873
FaqI	GGGAC	1 cut(s)	552
FauI	CCCGC	2 cut(s)	304, 663
FokI	GGATG	2 cut(s)	20, 176
FriOI	GRGCYC	3 cut(s)	213, 319, 490
FspBI	CTAG	2 cut(s)	320, 512
GlaI	GCGC	2 cut(s)	186, 399
HaeIII	GGCC	6 cut(s)	87, 219, 257, 556, 579, 696
HapII	CCGG	2 cut(s)	126, 220
HhaI	GCGC	2 cut(s)	187, 400
Hin6I	GCGC	2 cut(s)	185, 398
HinP1I	GCGC	2 cut(s)	185, 398
HinfI	GANTC	3 cut(s)	388, 640, 754
HpaII	CCGG	2 cut(s)	126, 220
HphI	GGTGA	1 cut(s)	640
Hpy166II	GTNNAC	1 cut(s)	772
Hpy188I	TCNGA	9 cut(s)	104, 412, 613, 631, 639, 727, 745, 753, 885
Hpy188III	TCNNGA	3 cut(s)	200, 440, 452
Hpy8I	GTNNAC	1 cut(s)	772
Hpy99I	CGWCG	1 cut(s)	175
HpyAV	CCTTC	3 cut(s)	223, 412, 577
HpyCH4III	ACNGT	2 cut(s)	364, 817
HpyCH4V	TGCA	6 cut(s)	296, 467, 664, 736, 787, 897
HpyF3I	CTNAG	5 cut(s)	330, 450, 636, 744, 750
HspAI	GCGC	2 cut(s)	185, 398
KroI	GCCGGC	1 cut(s)	219
KroNI	GCCGGC	1 cut(s)	221
Kzo9I	GATC	4 cut(s)	352, 624, 880, 888
LmnI	GCTCC	3 cut(s)	314, 454, 631
LweI	GCATC	4 cut(s)	34, 283, 498, 651
MaeI	CTAG	2 cut(s)	320, 512
MaeIII	GTNAC	4 cut(s)	94, 109, 520, 646
MalI	GATC	4 cut(s)	354, 626, 882, 890
MboI	GATC	4 cut(s)	352, 624, 880, 888
MboII	GAAGA	2 cut(s)	188, 749
MflI	RGATCY	2 cut(s)	624, 888
MhlI	GDGCHC	3 cut(s)	213, 319, 490
MlsI	TGGCCA	1 cut(s)	579
MluCI	AATT	2 cut(s)	235, 423
MluNI	TGGCCA	1 cut(s)	579
MlyI	GAGTC	1 cut(s)	634
MmeI	TCCRAC	2 cut(s)	785, 886
MnlI	CCTC	9 cut(s)	70, 73, 378, 546, 645, 690, 759, 816, 879
Mox20I	TGGCCA	1 cut(s)	579
MroNI	GCCGGC	1 cut(s)	219
MscI	TGGCCA	1 cut(s)	579
MseI	TTAA	3 cut(s)	234, 479, 546
Msp20I	TGGCCA	1 cut(s)	579
MspA1I	CMGCKG	1 cut(s)	287
MspI	CCGG	2 cut(s)	126, 220
MspR9I	CCNGG	1 cut(s)	127
NaeI	GCCGGC	1 cut(s)	221
NciI	CCSGG	1 cut(s)	127
NdeII	GATC	4 cut(s)	352, 624, 880, 888
NgoMIV	GCCGGC	1 cut(s)	219
NlaIV	GGNNCC	5 cut(s)	615, 633, 774, 831, 890
NmuCI	GTSAC	3 cut(s)	94, 520, 646
PdiI	GCCGGC	1 cut(s)	221
PfeI	GAWTC	2 cut(s)	388, 754
PleI	GAGTC	1 cut(s)	634
PpsI	GAGTC	1 cut(s)	634
PshAI	GACNNNNGTC	1 cut(s)	644
Psp124BI	GAGCTC	2 cut(s)	213, 319
PspEI	GGTNACC	1 cut(s)	646
PspN4I	GGNNCC	5 cut(s)	615, 633, 774, 831, 890
PspPI	GGNCC	3 cut(s)	86, 694, 772
PstNI	CAGNNNCTG	2 cut(s)	457, 643
PsuI	RGATCY	2 cut(s)	624, 888
PvuII	CAGCTG	1 cut(s)	287
RsaI	GTAC	2 cut(s)	158, 621
RsaNI	GTAC	2 cut(s)	157, 620
SacI	GAGCTC	2 cut(s)	213, 319
SaqAI	TTAA	3 cut(s)	234, 479, 546
Sau3AI	GATC	4 cut(s)	352, 624, 880, 888
Sau96I	GGNCC	3 cut(s)	86, 694, 772
SchI	GAGTC	1 cut(s)	634
ScrFI	CCNGG	1 cut(s)	127
SduI	GDGCHC	3 cut(s)	213, 319, 490
SfaNI	GCATC	4 cut(s)	34, 283, 498, 651
SinI	GGWCC	1 cut(s)	772
Sse9I	AATT	2 cut(s)	235, 423
SsiI	CCGC	8 cut(s)	16, 300, 303, 311, 324, 473, 584, 670
SspMI	CTAG	2 cut(s)	320, 512
SstI	GAGCTC	2 cut(s)	213, 319
StyD4I	CCNGG	1 cut(s)	125
TaaI	ACNGT	2 cut(s)	364, 817
TaqI	TCGA	1 cut(s)	383
TasI	AATT	2 cut(s)	235, 423
TatI	WGTACW	2 cut(s)	156, 619
TauI	GCSGC	5 cut(s)	18, 302, 305, 475, 586
TfiI	GAWTC	2 cut(s)	388, 754
Tru1I	TTAA	3 cut(s)	234, 479, 546
Tru9I	TTAA	3 cut(s)	234, 479, 546
TscAI	CASTG	2 cut(s)	738, 907
TseFI	GTSAC	3 cut(s)	94, 520, 646
Tsp45I	GTSAC	3 cut(s)	94, 520, 646
TspDTI	ATGAA	3 cut(s)	180, 431, 813
TspRI	CASTG	2 cut(s)	738, 907
VpaK11BI	GGWCC	1 cut(s)	772
XspI	CTAG	2 cut(s)	320, 512

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.