Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3C

Orthogroup ID

OG0017335

Physical Location & Seq

Genomic Coordinates Reverse (-)

27087172 .. 27088844

Gene Structure 1673 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3CG272700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 903 bp

ATGGCTTCTTCTCGCCGCATTTTCGTTGGGAACATCCCTTATGATGCCACCGAGCAACAGGTCAAGGCTCTCTGCGAGGAGGTTGGCCCTGTTGTGACTTTCAGAATGGTTACGGATAAAGACACCGGGAAGCCAAAGGGTTTTGGGTTCTGTGAGTACAGGGATGAAGCGACGGCGTTTAGTGCGCTGCGAAATCTTCAGGATTGTGAGCTCAATGGCCGGCGTTTGAAGGTTAATTTTGCTGCTAATGATAAGGCCAATCATCAGCCGATTGGTCTCCAAGCAGCCGTTGATGCAGCCGCCGCAATGGCGGGAGCTCTAGGTGGTTCTCAGCAGCAGGCATTGGCTAATGATCCTTTGACAGTCCACCTGTCCAAAATGTCGAGGAATCAGTTGGCGCAAATGGTCTCGGAGATGAAGGGAATTGCTGTGGAAAATAAGGAGATGGCTCAGGAGCTGTTGCTTGCAAAGCCGCAGTTAAACAGGGCTCTGCTTCAGGCACAAATGATGCTAGGAATGGTCACACCACAAATGTTGGCACAGGTTAATATGAGGCCAATGCGTCCCTTCAATAATGGCCAGCCGCAGCAGCAGCAGCGGCTCGTTCCCAAATCGGAACCAGTACAGATCTCGGAGCCTCAGACTCTGGTCACCCCACAAATGATGCAAAAGAGGCCAATGCCTCCATTGAATATGGGCCAGCAGCAAGTTCCAAAATCAGAACCAGTGCAAATCTCTGAGCCTCAGATTCTTCCAACGGGGGTGGACCCTGCTTTGTTGCAACAAGTTTTGAGCCTACCTCCCGAAACGGTGGCTTCATTGGTACCCGAGCTGCGACAACAGGTCATTCAACTCCAACAGATGTATAGGCAAGATCAGAGGATCCCTTGCAGCAGTGGATAA

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

300

Amino Acids

33.1

Weight (kDa)

8.68

Isoelectric Point (pI)

57.29

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	5.2e-14	Hinge domain of cleavage stimulation factor subunit 2
CSTF_C	PF14304	258 - 291	1.9e-06	Transcription termination and cleavage factor C-terminal

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

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Genomic Context

Gene Family Tree

Species Filter

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Align Labels (Cladogram)

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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)
Acc65I	GGTACC	1 cut(s)	823
AccB1I	GGYRCC	1 cut(s)	823
AciI	CCGC	7 cut(s)	16, 300, 303, 311, 473, 584, 598
AclWI	GGATC	3 cut(s)	347, 877, 890
AcoI	YGGCCR	2 cut(s)	217, 577
AcuI	CTGAAG	2 cut(s)	182, 479
AfaI	GTAC	3 cut(s)	158, 624, 825
AgsI	TTSAA	4 cut(s)	229, 571, 691, 851
AhdI	GACNNNNNGTC	1 cut(s)	842
AluBI	AGCT	4 cut(s)	211, 317, 457, 832
AluI	AGCT	4 cut(s)	211, 317, 457, 832
Alw21I	GWGCWC	2 cut(s)	213, 319
Alw26I	GTCTC	2 cut(s)	281, 412
AlwI	GGATC	3 cut(s)	347, 877, 890
AlwNI	CAGNNNCTG	2 cut(s)	457, 646
Ama87I	CYCGRG	1 cut(s)	827
AoxI	GGCC	7 cut(s)	85, 217, 255, 554, 577, 674, 697
Asp718I	GGTACC	1 cut(s)	823
AspLEI	GCGC	2 cut(s)	187, 400
AspS9I	GGNCC	3 cut(s)	86, 697, 766
AsuC2I	CCSGG	1 cut(s)	127
AsuHPI	GGTGA	1 cut(s)	643
AvaI	CYCGRG	1 cut(s)	827
AvaII	GGWCC	1 cut(s)	766
BalI	TGGCCA	1 cut(s)	579
BamHI	GGATCC	1 cut(s)	882
BanI	GGYRCC	1 cut(s)	823
BanII	GRGCYC	3 cut(s)	213, 319, 490
Bbv12I	GWGCWC	2 cut(s)	213, 319
BccI	CCATC	1 cut(s)	439
BceAI	ACGGC	2 cut(s)	189, 272
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)	627
Bme1390I	CCNGG	1 cut(s)	127
Bme18I	GGWCC	1 cut(s)	766
BmeRI	GACNNNNNGTC	1 cut(s)	842
BmeT110I	CYCGRG	1 cut(s)	827
BmgT120I	GGNCC	3 cut(s)	86, 697, 766
BmiI	GGNNCC	5 cut(s)	618, 636, 768, 825, 884
BmrFI	CCNGG	1 cut(s)	127
BmsI	GCATC	4 cut(s)	34, 283, 498, 654
BoxI	GACNNNNGTC	1 cut(s)	647
BplI	GAGNNNNNCTC	2 cut(s)	784, 816
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)	620, 725
Bse3DI	GCAATG	1 cut(s)	312
BseGI	GGATG	2 cut(s)	33, 169
BseMI	GCAATG	1 cut(s)	312
BseMII	CTCAG	5 cut(s)	344, 464, 653, 729, 758
BseNI	ACTGG	2 cut(s)	620, 725
BseRI	GAGGAG	1 cut(s)	92
BshFI	GGCC	7 cut(s)	87, 219, 257, 556, 579, 676, 699
BshNI	GGYRCC	1 cut(s)	823
BsiHKAI	GWGCWC	2 cut(s)	213, 319
BsiHKCI	CYCGRG	1 cut(s)	827
BsiSI	CCGG	2 cut(s)	126, 220
BslFI	GGGAC	1 cut(s)	549
BsmAI	GTCTC	2 cut(s)	281, 412
BsmFI	GGGAC	1 cut(s)	549
BsnI	GGCC	7 cut(s)	87, 219, 257, 556, 579, 676, 699
Bso31I	GGTCTC	2 cut(s)	281, 412
BsoBI	CYCGRG	1 cut(s)	827
Bsp1286I	GDGCHC	3 cut(s)	213, 319, 490
Bsp143I	GATC	4 cut(s)	352, 627, 874, 882
BspACI	CCGC	7 cut(s)	16, 300, 303, 311, 473, 584, 598
BspANI	GGCC	7 cut(s)	87, 219, 257, 556, 579, 676, 699
BspCNI	CTCAG	5 cut(s)	343, 463, 652, 730, 757
BspLI	GGNNCC	5 cut(s)	618, 636, 768, 825, 884
BspPI	GGATC	3 cut(s)	347, 877, 890
BspT107I	GGYRCC	1 cut(s)	823
BspTNI	GGTCTC	2 cut(s)	281, 412
BsrDI	GCAATG	1 cut(s)	312
BsrFI	RCCGGY	1 cut(s)	219
BsrI	ACTGG	2 cut(s)	620, 725
BssAI	RCCGGY	1 cut(s)	219
BssMI	GATC	4 cut(s)	352, 627, 874, 882
Bst4CI	ACNGT	2 cut(s)	364, 811
BstC8I	GCNNGC	5 cut(s)	221, 339, 465, 581, 701
BstDEI	CTNAG	5 cut(s)	330, 450, 639, 738, 744
BstEII	GGTNACC	1 cut(s)	649
BstF5I	GGATG	2 cut(s)	33, 169
BstHHI	GCGC	2 cut(s)	187, 400
BstKTI	GATC	4 cut(s)	355, 630, 877, 885
BstMAI	GTCTC	2 cut(s)	281, 412
BstMBI	GATC	4 cut(s)	352, 627, 874, 882
BstPAI	GACNNNNGTC	1 cut(s)	647
BstPI	GGTNACC	1 cut(s)	649
BstSCI	CCNGG	1 cut(s)	125
BstX2I	RGATCY	2 cut(s)	627, 882
BstYI	RGATCY	2 cut(s)	627, 882
BsuRI	GGCC	7 cut(s)	87, 219, 257, 556, 579, 676, 699
BtsCI	GGATG	2 cut(s)	33, 169
BtsI	GCAGTG	1 cut(s)	901
BtsIMutI	CAGTG	2 cut(s)	732, 901
Cac8I	GCNNGC	5 cut(s)	221, 339, 465, 581, 701
CaiI	CAGNNNCTG	2 cut(s)	457, 646
CfoI	GCGC	2 cut(s)	187, 400
Cfr10I	RCCGGY	1 cut(s)	219
Cfr13I	GGNCC	3 cut(s)	86, 697, 766
CseI	GACGC	1 cut(s)	551
Csp6I	GTAC	3 cut(s)	157, 623, 824
CspCI	CAANNNNNGTGG	4 cut(s)	516, 551, 744, 779
CviQI	GTAC	3 cut(s)	157, 623, 824
DdeI	CTNAG	5 cut(s)	330, 450, 639, 738, 744
DpnI	GATC	4 cut(s)	354, 629, 876, 884
DpnII	GATC	4 cut(s)	352, 627, 874, 882
DriI	GACNNNNNGTC	1 cut(s)	842
EaeI	YGGCCR	2 cut(s)	217, 577
Eam1105I	GACNNNNNGTC	1 cut(s)	842
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)	766
Eco53kI	GAGCTC	2 cut(s)	211, 317
Eco57I	CTGAAG	2 cut(s)	182, 479
Eco88I	CYCGRG	1 cut(s)	827
Eco91I	GGTNACC	1 cut(s)	649
EcoICRI	GAGCTC	2 cut(s)	211, 317
EcoO65I	GGTNACC	1 cut(s)	649
EcoT38I	GRGCYC	3 cut(s)	213, 319, 490
FaiI	YATR	4 cut(s)	42, 551, 695, 867
FaqI	GGGAC	1 cut(s)	549
FauI	CCCGC	1 cut(s)	304
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	7 cut(s)	87, 219, 257, 556, 579, 676, 699
HapII	CCGG	2 cut(s)	126, 220
HgaI	GACGC	1 cut(s)	551
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, 643, 748
HpaII	CCGG	2 cut(s)	126, 220
HphI	GGTGA	1 cut(s)	643
Hpy166II	GTNNAC	2 cut(s)	367, 766
Hpy188I	TCNGA	9 cut(s)	104, 412, 616, 634, 642, 721, 739, 747, 879
Hpy188III	TCNNGA	3 cut(s)	200, 452, 803
Hpy8I	GTNNAC	2 cut(s)	367, 766
Hpy99I	CGWCG	1 cut(s)	175
HpyAV	CCTTC	3 cut(s)	223, 412, 577
HpyCH4III	ACNGT	2 cut(s)	364, 811
HpyCH4V	TGCA	6 cut(s)	296, 467, 667, 730, 781, 891
HpyF3I	CTNAG	5 cut(s)	330, 450, 639, 738, 744
HspAI	GCGC	2 cut(s)	185, 398
KpnI	GGTACC	1 cut(s)	827
KroI	GCCGGC	1 cut(s)	219
KroNI	GCCGGC	1 cut(s)	221
Kzo9I	GATC	4 cut(s)	352, 627, 874, 882
LmnI	GCTCC	3 cut(s)	314, 454, 634
LweI	GCATC	4 cut(s)	34, 283, 498, 654
MaeI	CTAG	2 cut(s)	320, 512
MaeIII	GTNAC	4 cut(s)	94, 109, 520, 649
MalI	GATC	4 cut(s)	354, 629, 876, 884
MboI	GATC	4 cut(s)	352, 627, 874, 882
MboII	GAAGA	2 cut(s)	188, 743
MflI	RGATCY	2 cut(s)	627, 882
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)	637
MmeI	TCCRAC	2 cut(s)	779, 880
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)	598
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, 627, 874, 882
NgoMIV	GCCGGC	1 cut(s)	219
NlaIV	GGNNCC	5 cut(s)	618, 636, 768, 825, 884
NmuCI	GTSAC	3 cut(s)	94, 520, 649
PdiI	GCCGGC	1 cut(s)	221
PfeI	GAWTC	2 cut(s)	388, 748
PleI	GAGTC	1 cut(s)	637
PpsI	GAGTC	1 cut(s)	637
PshAI	GACNNNNGTC	1 cut(s)	647
Psp124BI	GAGCTC	2 cut(s)	213, 319
PspEI	GGTNACC	1 cut(s)	649
PspN4I	GGNNCC	5 cut(s)	618, 636, 768, 825, 884
PspPI	GGNCC	3 cut(s)	86, 697, 766
PstNI	CAGNNNCTG	2 cut(s)	457, 646
PsuI	RGATCY	2 cut(s)	627, 882
RsaI	GTAC	3 cut(s)	158, 624, 825
RsaNI	GTAC	3 cut(s)	157, 623, 824
SacI	GAGCTC	2 cut(s)	213, 319
SaqAI	TTAA	3 cut(s)	234, 479, 546
Sau3AI	GATC	4 cut(s)	352, 627, 874, 882
Sau96I	GGNCC	3 cut(s)	86, 697, 766
SchI	GAGTC	1 cut(s)	637
ScrFI	CCNGG	1 cut(s)	127
SduI	GDGCHC	3 cut(s)	213, 319, 490
SfaNI	GCATC	4 cut(s)	34, 283, 498, 654
SinI	GGWCC	1 cut(s)	766
Sse9I	AATT	2 cut(s)	235, 423
SsiI	CCGC	7 cut(s)	16, 300, 303, 311, 473, 584, 598
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, 811
TaqI	TCGA	1 cut(s)	383
TasI	AATT	2 cut(s)	235, 423
TatI	WGTACW	2 cut(s)	156, 622
TauI	GCSGC	6 cut(s)	18, 302, 305, 475, 586, 601
TfiI	GAWTC	2 cut(s)	388, 748
Tru1I	TTAA	3 cut(s)	234, 479, 546
Tru9I	TTAA	3 cut(s)	234, 479, 546
TscAI	CASTG	2 cut(s)	732, 901
TseFI	GTSAC	3 cut(s)	94, 520, 649
Tsp45I	GTSAC	3 cut(s)	94, 520, 649
TspDTI	ATGAA	3 cut(s)	180, 431, 807
TspGWI	ACGGA	1 cut(s)	128
TspRI	CASTG	2 cut(s)	732, 901
VpaK11BI	GGWCC	1 cut(s)	766
XspI	CTAG	2 cut(s)	320, 512

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