Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3A

Orthogroup ID

OG0005944

Physical Location & Seq

Genomic Coordinates Reverse (-)

22030078 .. 22048143

Gene Structure 18066 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3AG217400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 924 bp

ATGGCGGTCTCCGAGGAGGAGTGTTCCTCCGCCAACTCCAGATCATCCTCGCCCTCCACCTCCAGCACCTCTCACTACCTCTCCAAGTGCCTCCTCTGTGGCACCGTCGTTCTCCACGCCCTCCACGGTCACATCCGCTTCCCCAACTCCCGCGACATCATTTTCGGCAAGGAGAAATCGATAGAGATGGTGATAATCGGTGAAGATGGGATCGTACAGTCTGTGTGTGAGCAGCCTGTGTTTGGCACCATTAAAGACATTGCCGTCCTACCTTGGAATGACGGATTCCGAACCCGAAACCTCCAGATGCCGGGCAAGGATCTTTTGGTGGTTGTTTCGGATTCCGGGAAGCTCTCGGTTCTATCTTTCTGCAATGAAATGCACAGGTTTTTTCCTGTGACACAAGTTCAACTTTCTAATCCTGGACACTCGAGGAATCAGCTTGCAAGAATGCTAGCCATTGATTCAAGATATCATCTGTTGCTTCTTGCTCTGTTTCTGCGAGAGAACAAACACCAAGACAAGAAACATGCAATTTTCGTGAAAACCCTAACTGGGAAGGCCATCACTCTCGAGGTTGAGAGCAGCAATACTATCGATAATGTCAAAGCCAAGACCCAGTATAAGGAAGGCATCCCTCCTGATCAACAGAGATTGATTTGTGCCGGTAAGCAATTGGAAGATGGTAGCACTCTAGCAGATTATAACATCCAAAAGGAGTCATCTCTTCACCTGGCTTTGAGGCTGAGGGGAGGAACTATGATTAAGGTGAAGGCTCTTACCGGGAATGAAATTGAGATTCATATTGAACCGACTGACACCATTGACCGAATCAAGGAAAGGGTTGAGGAGAAAGAGGGAGTTCCTCCATTGCAACAAAGATCCACTGACCTTGCAATGGTGTGTGATTTGTTTGAGATTTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0000151 GO:0003006 GO:0003674 GO:0003676 GO:0003677 GO:0003684 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006139 GO:0006259 GO:0006281 GO:0006289 GO:0006508 GO:0006511 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0007275 GO:0008150 GO:0008152 GO:0009056 GO:0009057 GO:0009790 GO:0009791 GO:0009793 GO:0009987 GO:0010154 GO:0010498 GO:0019538 GO:0019941 GO:0022414 GO:0030163 GO:0031461 GO:0032501 GO:0032502 GO:0032991 GO:0033554 GO:0034641 GO:0043161 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043632 GO:0044237 GO:0044238 GO:0044248 GO:0044257 GO:0044260 GO:0044265 GO:0044267 GO:0044424 GO:0044464 GO:0046483 GO:0048316 GO:0048608 GO:0048731 GO:0048856 GO:0050896 GO:0051603 GO:0051716 GO:0061458 GO:0071704 GO:0090304 GO:0097159 GO:1901360 GO:1901363 GO:1901564 GO:1901565 GO:1901575 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko03040 map03040

Pfam Domains

Protein Families

CPSF_A MMS1_N

Protein Analysis

307

Amino Acids

34.22

Weight (kDa)

6.6

Isoelectric Point (pI)

54.96

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Beta-prop_RSE1_1st	PF10433	37 - 164	1.1e-23	RSE1/DDB1/CPSF1 first beta-propeller
ubiquitin	PF00240	179 - 250	3e-25	Ubiquitin family
Rad60-SLD	PF11976	179 - 245	3.6e-11	Ubiquitin-2 like Rad60 SUMO-like
ubiquitin	PF00240	255 - 294	3.6e-09	Ubiquitin family

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0005944)

Species	Orthologous Gene IDs
rosa_laevigata	RLG00000023647 RLG00000023653 RLG00000023665
rosa_multiflora	Rmu_sc0000968.1_g000012 Rmu_sc0001262.1_g000012 Rmu_sc0001518.1_g000014 Rmu_sc0002766.1_g000007 Rmu_sc0003078.1_g000002 Rmu_sc0005657.1_g000062 Rmu_sc0005657.1_g000063 Rmu_sc0012126.1_g000001 Rmu_sc0030925.1_g000001
rosa_roxburghii	Rroxscaffold_2G00108950 Rroxscaffold_6G00403400
rosa_rugosa	Rorug01G0021800 Rorug01G0146300.1 Rorug03G0358800.1 Rorug05G0241400 Rorug07G0101300
rosa_samantha	Rh1AG149600 Rh1BG381400 Rh1CG140700 Rh1CG395300 Rh3AG216500 Rh3AG217400 Rh3BG249600 Rh3CG245900 Rh6DG353100

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	705
AasI	GACNNNNNNGTC	1 cut(s)	263
AccB1I	GGYRCC	2 cut(s)	101, 245
AccII	CGCG	1 cut(s)	153
AciI	CCGC	4 cut(s)	5, 30, 136, 151
AclWI	GGATC	3 cut(s)	218, 327, 876
AfaI	GTAC	1 cut(s)	216
AfiI	CCNNNNNNNGG	6 cut(s)	242, 310, 555, 625, 835, 898
AgsI	TTSAA	3 cut(s)	410, 468, 809
AjnI	CCWGG	2 cut(s)	421, 732
AluBI	AGCT	2 cut(s)	352, 442
AluI	AGCT	2 cut(s)	352, 442
Alw26I	GTCTC	1 cut(s)	13
AlwI	GGATC	3 cut(s)	218, 327, 876
Ama87I	CYCGRG	2 cut(s)	430, 572
AoxI	GGCC	1 cut(s)	561
ApeKI	GCWGC	2 cut(s)	232, 585
ArsI	GACNNNNNNTTYG	2 cut(s)	146, 178
AsuC2I	CCSGG	3 cut(s)	312, 346, 784
AsuHPI	GGTGA	4 cut(s)	202, 212, 722, 781
AsuNHI	GCTAGC	1 cut(s)	454
AvaI	CYCGRG	2 cut(s)	430, 572
BanI	GGYRCC	2 cut(s)	101, 245
BbvCI	CCTCAGC	1 cut(s)	746
BbvI	GCAGC	2 cut(s)	244, 597
BccI	CCATC	4 cut(s)	181, 200, 572, 677
BceAI	ACGGC	1 cut(s)	248
BcgI	CGANNNNNNTGC	2 cut(s)	577, 611
BciT130I	CCWGG	2 cut(s)	423, 734
BclI	TGATCA	1 cut(s)	643
BcnI	CCSGG	3 cut(s)	312, 346, 784
BcoDI	GTCTC	1 cut(s)	13
BfaI	CTAG	2 cut(s)	455, 695
BisI	GCNGC	2 cut(s)	233, 586
BlsI	GCNGC	2 cut(s)	234, 587
Bme1390I	CCNGG	5 cut(s)	312, 346, 423, 734, 784
BmeT110I	CYCGRG	2 cut(s)	430, 572
BmiI	GGNNCC	2 cut(s)	103, 247
BmrFI	CCNGG	5 cut(s)	312, 346, 423, 734, 784
BmrI	ACTGGG	2 cut(s)	564, 613
BmsI	GCATC	2 cut(s)	297, 642
BmtI	GCTAGC	1 cut(s)	458
BmuI	ACTGGG	2 cut(s)	564, 613
BplI	GAGNNNNNCTC	2 cut(s)	11, 43
BpmI	CTGGAG	3 cut(s)	22, 46, 287
Bpu10I	CCTNAGC	1 cut(s)	746
BpuMI	CCSGG	3 cut(s)	312, 346, 784
Bsa29I	ATCGAT	2 cut(s)	179, 597
BsaI	GGTCTC	1 cut(s)	13
BsaJI	CCNNGG	3 cut(s)	12, 124, 272
BsaXI	ACNNNNNCTCC	2 cut(s)	65, 95
Bsc4I	CCNNNNNNNGG	6 cut(s)	242, 310, 555, 625, 835, 898
Bse118I	RCCGGY	1 cut(s)	665
Bse1I	ACTGG	2 cut(s)	559, 619
Bse3DI	GCAATG	4 cut(s)	258, 379, 869, 903
BseBI	CCWGG	2 cut(s)	423, 734
BseCI	ATCGAT	2 cut(s)	179, 597
BseDI	CCNNGG	3 cut(s)	12, 124, 272
BseGI	GGATG	4 cut(s)	44, 132, 633, 708
BseLI	CCNNNNNNNGG	6 cut(s)	242, 310, 555, 625, 835, 898
BseMI	GCAATG	4 cut(s)	258, 379, 869, 903
BseMII	CTCAG	1 cut(s)	737
BseNI	ACTGG	2 cut(s)	559, 619
BseRI	GAGGAG	4 cut(s)	29, 32, 83, 863
BseXI	GCAGC	2 cut(s)	244, 597
Bsh1236I	CGCG	1 cut(s)	153
BshFI	GGCC	1 cut(s)	563
BshNI	GGYRCC	2 cut(s)	101, 245
BshVI	ATCGAT	2 cut(s)	179, 597
BsiHKCI	CYCGRG	2 cut(s)	430, 572
BsiSI	CCGG	4 cut(s)	311, 345, 666, 783
BslI	CCNNNNNNNGG	6 cut(s)	242, 310, 555, 625, 835, 898
BsmAI	GTCTC	1 cut(s)	13
BsmI	GAATGC	1 cut(s)	456
BsnI	GGCC	1 cut(s)	563
Bso31I	GGTCTC	1 cut(s)	13
BsoBI	CYCGRG	2 cut(s)	430, 572
Bsp143I	GATC	5 cut(s)	41, 210, 319, 643, 881
BspACI	CCGC	4 cut(s)	5, 30, 136, 151
BspANI	GGCC	1 cut(s)	563
BspCNI	CTCAG	1 cut(s)	738
BspDI	ATCGAT	2 cut(s)	179, 597
BspFNI	CGCG	1 cut(s)	153
BspLI	GGNNCC	2 cut(s)	103, 247
BspOI	GCTAGC	1 cut(s)	458
BspPI	GGATC	3 cut(s)	218, 327, 876
BspT107I	GGYRCC	2 cut(s)	101, 245
BspTNI	GGTCTC	1 cut(s)	13
BsrDI	GCAATG	4 cut(s)	258, 379, 869, 903
BsrFI	RCCGGY	1 cut(s)	665
BsrI	ACTGG	2 cut(s)	559, 619
BssAI	RCCGGY	1 cut(s)	665
BssECI	CCNNGG	3 cut(s)	12, 124, 272
BssMI	GATC	5 cut(s)	41, 210, 319, 643, 881
BssT1I	CCWWGG	1 cut(s)	272
Bst2UI	CCWGG	2 cut(s)	423, 734
Bst4CI	ACNGT	3 cut(s)	106, 128, 219
Bst6I	CTCTTC	1 cut(s)	732
BstC8I	GCNNGC	2 cut(s)	444, 456
BstDEI	CTNAG	1 cut(s)	746
BstDSI	CCRYGG	1 cut(s)	124
BstF5I	GGATG	4 cut(s)	44, 132, 633, 708
BstFNI	CGCG	1 cut(s)	153
BstKTI	GATC	5 cut(s)	44, 213, 322, 646, 884
BstMAI	GTCTC	1 cut(s)	13
BstMBI	GATC	5 cut(s)	41, 210, 319, 643, 881
BstNI	CCWGG	2 cut(s)	423, 734
BstNSI	RCATGY	1 cut(s)	533
BstSCI	CCNGG	5 cut(s)	310, 344, 421, 732, 782
BstUI	CGCG	1 cut(s)	153
BstV1I	GCAGC	2 cut(s)	244, 597
BstX2I	RGATCY	2 cut(s)	319, 881
BstYI	RGATCY	2 cut(s)	319, 881
Bsu15I	ATCGAT	2 cut(s)	179, 597
BsuRI	GGCC	1 cut(s)	563
BsuTUI	ATCGAT	2 cut(s)	179, 597
BtgI	CCRYGG	1 cut(s)	124
BtsCI	GGATG	4 cut(s)	44, 132, 633, 708
BtsIMutI	CAGTG	1 cut(s)	885
Cac8I	GCNNGC	2 cut(s)	444, 456
Cfr10I	RCCGGY	1 cut(s)	665
ClaI	ATCGAT	2 cut(s)	179, 597
Csp6I	GTAC	1 cut(s)	215
CspCI	CAANNNNNGTGG	2 cut(s)	874, 909
CviAII	CATG	1 cut(s)	530
CviJI	RGCY	9 cut(s)	235, 352, 442, 458, 563, 611, 737, 745, 776
CviKI_1	RGCY	9 cut(s)	235, 352, 442, 458, 563, 611, 737, 745, 776
CviQI	GTAC	1 cut(s)	215
DdeI	CTNAG	1 cut(s)	746
DpnI	GATC	5 cut(s)	43, 212, 321, 645, 883
DpnII	GATC	5 cut(s)	41, 210, 319, 643, 881
DrdI	GACNNNNNNGTC	1 cut(s)	263
DseDI	GACNNNNNNGTC	1 cut(s)	263
Eam1104I	CTCTTC	1 cut(s)	732
EarI	CTCTTC	1 cut(s)	732
EciI	GGCGGA	1 cut(s)	19
Eco130I	CCWWGG	1 cut(s)	272
Eco31I	GGTCTC	1 cut(s)	13
Eco32I	GATATC	1 cut(s)	473
Eco88I	CYCGRG	2 cut(s)	430, 572
EcoRII	CCWGG	2 cut(s)	421, 732
EcoRV	GATATC	1 cut(s)	473
EcoT14I	CCWWGG	1 cut(s)	272
ErhI	CCWWGG	1 cut(s)	272
FaeI	CATG	1 cut(s)	533
FaiI	YATR	5 cut(s)	531, 624, 705, 761, 804
FalI	AAGNNNNNCTT	2 cut(s)	396, 428
FatI	CATG	1 cut(s)	529
FauI	CCCGC	1 cut(s)	158
FbaI	TGATCA	1 cut(s)	643
Fnu4HI	GCNGC	2 cut(s)	233, 586
FokI	GGATG	4 cut(s)	31, 119, 620, 695
Fsp4HI	GCNGC	2 cut(s)	233, 586
FspBI	CTAG	2 cut(s)	455, 695
GluI	GCNGC	2 cut(s)	233, 586
GsuI	CTGGAG	3 cut(s)	22, 46, 287
HaeIII	GGCC	1 cut(s)	563
HapII	CCGG	4 cut(s)	311, 345, 666, 783
Hin1II	CATG	1 cut(s)	533
HinfI	GANTC	7 cut(s)	285, 341, 436, 464, 719, 799, 831
HpaII	CCGG	4 cut(s)	311, 345, 666, 783
HphI	GGTGA	4 cut(s)	202, 212, 722, 781
Hpy188I	TCNGA	3 cut(s)	13, 290, 340
Hpy188III	TCNNGA	6 cut(s)	39, 304, 468, 541, 572, 641
Hpy99I	CGWCG	1 cut(s)	110
HpyAV	CCTTC	3 cut(s)	553, 623, 766
HpyCH4III	ACNGT	3 cut(s)	106, 128, 219
HpyCH4V	TGCA	6 cut(s)	372, 382, 446, 533, 874, 896
HpyF3I	CTNAG	1 cut(s)	746
Hsp92II	CATG	1 cut(s)	533
Ksp22I	TGATCA	1 cut(s)	643
Kzo9I	GATC	5 cut(s)	41, 210, 319, 643, 881
Lsp1109I	GCAGC	2 cut(s)	244, 597
LweI	GCATC	2 cut(s)	297, 642
MaeI	CTAG	2 cut(s)	455, 695
MaeIII	GTNAC	2 cut(s)	128, 397
MalI	GATC	5 cut(s)	43, 212, 321, 645, 883
MboI	GATC	5 cut(s)	41, 210, 319, 643, 881
MboII	GAAGA	3 cut(s)	215, 692, 719
MfeI	CAATTG	1 cut(s)	674
MflI	RGATCY	2 cut(s)	319, 881
MluCI	AATT	3 cut(s)	534, 674, 792
MlyI	GAGTC	1 cut(s)	728
MseI	TTAA	2 cut(s)	252, 765
MspI	CCGG	4 cut(s)	311, 345, 666, 783
MspR9I	CCNGG	5 cut(s)	312, 346, 423, 734, 784
MunI	CAATTG	1 cut(s)	674
Mva1269I	GAATGC	1 cut(s)	456
MvaI	CCWGG	2 cut(s)	423, 734
MvnI	CGCG	1 cut(s)	153
NciI	CCSGG	3 cut(s)	312, 346, 784
NdeII	GATC	5 cut(s)	41, 210, 319, 643, 881
NheI	GCTAGC	1 cut(s)	454
NlaIII	CATG	1 cut(s)	533
NlaIV	GGNNCC	2 cut(s)	103, 247
NmuCI	GTSAC	2 cut(s)	128, 397
NspI	RCATGY	1 cut(s)	533
PaeR7I	CTCGAG	2 cut(s)	430, 572
PctI	GAATGC	1 cut(s)	456
PfeI	GAWTC	6 cut(s)	285, 341, 436, 464, 799, 831
PfoI	TCCNGGA	2 cut(s)	344, 421
PkrI	GCNGC	2 cut(s)	234, 587
PleI	GAGTC	1 cut(s)	727
PpsI	GAGTC	1 cut(s)	727
PsiI	TTATAA	1 cut(s)	705
Psp6I	CCWGG	2 cut(s)	421, 732
PspGI	CCWGG	2 cut(s)	421, 732
PspN4I	GGNNCC	2 cut(s)	103, 247
PspXI	VCTCGAGB	1 cut(s)	430
PsuI	RGATCY	2 cut(s)	319, 881
RsaI	GTAC	1 cut(s)	216
RsaNI	GTAC	1 cut(s)	215
SaqAI	TTAA	2 cut(s)	252, 765
SatI	GCNGC	2 cut(s)	233, 586
Sau3AI	GATC	5 cut(s)	41, 210, 319, 643, 881
SchI	GAGTC	1 cut(s)	728
ScrFI	CCNGG	5 cut(s)	312, 346, 423, 734, 784
SfaNI	GCATC	2 cut(s)	297, 642
Sfr274I	CTCGAG	2 cut(s)	430, 572
SlaI	CTCGAG	2 cut(s)	430, 572
SmlI	CTYRAG	2 cut(s)	430, 572
SmoI	CTYRAG	2 cut(s)	430, 572
Sse9I	AATT	3 cut(s)	534, 674, 792
SsiI	CCGC	4 cut(s)	5, 30, 136, 151
SspMI	CTAG	2 cut(s)	455, 695
StyD4I	CCNGG	5 cut(s)	310, 344, 421, 732, 782
StyI	CCWWGG	1 cut(s)	272
TaaI	ACNGT	3 cut(s)	106, 128, 219
TaqI	TCGA	4 cut(s)	179, 431, 573, 597
TaqII	GACCGA	1 cut(s)	843
TasI	AATT	3 cut(s)	534, 674, 792
TfiI	GAWTC	6 cut(s)	285, 341, 436, 464, 799, 831
Tru1I	TTAA	2 cut(s)	252, 765
Tru9I	TTAA	2 cut(s)	252, 765
TscAI	CASTG	1 cut(s)	892
TseFI	GTSAC	2 cut(s)	128, 397
TseI	GCWGC	2 cut(s)	232, 585
Tsp45I	GTSAC	2 cut(s)	128, 397
TspDTI	ATGAA	3 cut(s)	390, 791, 804
TspGWI	ACGGA	1 cut(s)	297
TspRI	CASTG	1 cut(s)	892
XceI	RCATGY	1 cut(s)	533
XhoI	CTCGAG	2 cut(s)	430, 572
XspI	CTAG	2 cut(s)	455, 695

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