Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3B

Orthogroup ID

OG0005944

Physical Location & Seq

Genomic Coordinates Forward (+)

23822086 .. 23824605

Gene Structure 2520 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3BG249600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 627 bp

ATGTGGCAATACGTGTGGCCTTTGCCCACATGTGTTGTGGTGAAAGCCATCGTCAATGGCGGTCTCCGAGGAGGAGTATTCCTCCGCCAACTCCAGATCATCCTCGAGAAATCGATAGAGTTGGTGATCATTGGTGAAAACGGGATTGTACAGTCTGTGTGTGAGCAGCCTGTGTTTGGCACCATTAAAGACATTGCTGTCCTACCTTGGAATGACGGATTCCGAACCCGAAACCGCCAGATGCCGGGCAAGGATCTTTTGGTGGTTGTTTCGGATTCTGGGAAGCTCTCGGTTCTATCTTTCTGCAATGAAATGCACAGGTTTTTCCCTGTGACACAAGTTCAACTTTCTAATCCTGGAAACTCGAGGAATCAGCTTGCAAGAATGCTAGCCATTGATTCAAGATATCATCTGTTGCTTCTTGCTCTGTTTCTGCGAGAGAACAAACACCAAGACAAGAAACATGCAATTTTCGTGAAAACCCTAACTGGGAAGGCCATCACTCTCGAGGTTGAGAGCAGCAATACTATCGATAATGTCAAAGCCAAGACCCAGAATAAGGAAGGCGTCCCTCCTGATCAACAGAGATTGATTTTTGCCAGTAATTGGAAGATGGTAGAACTCTAG

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

208

Amino Acids

23.49

Weight (kDa)

9.48

Isoelectric Point (pI)

37.29

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Beta-prop_RSE1_1st	PF10433	35 - 142	5.7e-18	RSE1/DDB1/CPSF1 first beta-propeller
ubiquitin	PF00240	157 - 200	1.1e-13	Ubiquitin family

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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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)
AasI	GACNNNNNNGTC	1 cut(s)	197
AccB1I	GGYRCC	1 cut(s)	179
AccB7I	CCANNNNNTGG	1 cut(s)	606
AciI	CCGC	3 cut(s)	60, 85, 235
AclWI	GGATC	1 cut(s)	261
AcyI	GRCGYC	1 cut(s)	567
AfaI	GTAC	1 cut(s)	150
AfiI	CCNNNNNNNGG	5 cut(s)	176, 244, 489, 559, 606
AflIII	ACRYGT	2 cut(s)	12, 29
AgsI	TTSAA	2 cut(s)	344, 402
AjnI	CCWGG	1 cut(s)	355
AluBI	AGCT	2 cut(s)	286, 376
AluI	AGCT	2 cut(s)	286, 376
Alw26I	GTCTC	1 cut(s)	68
AlwI	GGATC	1 cut(s)	261
Ama87I	CYCGRG	3 cut(s)	104, 364, 506
AoxI	GGCC	2 cut(s)	17, 495
ApeKI	GCWGC	2 cut(s)	166, 519
AsuC2I	CCSGG	1 cut(s)	246
AsuHPI	GGTGA	3 cut(s)	52, 136, 146
AsuNHI	GCTAGC	1 cut(s)	388
AvaI	CYCGRG	3 cut(s)	104, 364, 506
BanI	GGYRCC	1 cut(s)	179
BbvI	GCAGC	2 cut(s)	178, 531
BccI	CCATC	3 cut(s)	56, 506, 607
BcgI	CGANNNNNNTGC	2 cut(s)	511, 545
BciT130I	CCWGG	1 cut(s)	357
BclI	TGATCA	2 cut(s)	126, 577
BcnI	CCSGG	1 cut(s)	246
BcoDI	GTCTC	1 cut(s)	68
BfaI	CTAG	2 cut(s)	389, 625
BisI	GCNGC	2 cut(s)	167, 520
BlsI	GCNGC	2 cut(s)	168, 521
Bme1390I	CCNGG	2 cut(s)	246, 357
BmeT110I	CYCGRG	3 cut(s)	104, 364, 506
BmiI	GGNNCC	1 cut(s)	181
BmrFI	CCNGG	2 cut(s)	246, 357
BmrI	ACTGGG	1 cut(s)	498
BmsI	GCATC	1 cut(s)	231
BmtI	GCTAGC	1 cut(s)	392
BmuI	ACTGGG	1 cut(s)	498
BplI	GAGNNNNNCTC	2 cut(s)	66, 98
BpmI	CTGGAG	1 cut(s)	77
BpuMI	CCSGG	1 cut(s)	246
Bsa29I	ATCGAT	2 cut(s)	113, 531
BsaAI	YACGTR	1 cut(s)	13
BsaHI	GRCGYC	1 cut(s)	567
BsaI	GGTCTC	1 cut(s)	68
BsaJI	CCNNGG	2 cut(s)	67, 206
Bsc4I	CCNNNNNNNGG	5 cut(s)	176, 244, 489, 559, 606
Bse1I	ACTGG	2 cut(s)	493, 600
Bse3DI	GCAATG	2 cut(s)	192, 313
BseBI	CCWGG	1 cut(s)	357
BseCI	ATCGAT	2 cut(s)	113, 531
BseDI	CCNNGG	2 cut(s)	67, 206
BseGI	GGATG	1 cut(s)	99
BseLI	CCNNNNNNNGG	5 cut(s)	176, 244, 489, 559, 606
BseMI	GCAATG	2 cut(s)	192, 313
BseNI	ACTGG	2 cut(s)	493, 600
BseRI	GAGGAG	2 cut(s)	84, 87
BseXI	GCAGC	2 cut(s)	178, 531
BshFI	GGCC	2 cut(s)	19, 497
BshNI	GGYRCC	1 cut(s)	179
BshVI	ATCGAT	2 cut(s)	113, 531
BsiHKCI	CYCGRG	3 cut(s)	104, 364, 506
BsiSI	CCGG	1 cut(s)	245
BslFI	GGGAC	1 cut(s)	554
BslI	CCNNNNNNNGG	5 cut(s)	176, 244, 489, 559, 606
BsmAI	GTCTC	1 cut(s)	68
BsmFI	GGGAC	1 cut(s)	554
BsmI	GAATGC	1 cut(s)	390
BsnI	GGCC	2 cut(s)	19, 497
Bso31I	GGTCTC	1 cut(s)	68
BsoBI	CYCGRG	3 cut(s)	104, 364, 506
Bsp1407I	TGTACA	1 cut(s)	148
Bsp143I	GATC	4 cut(s)	96, 126, 253, 577
BspACI	CCGC	3 cut(s)	60, 85, 235
BspANI	GGCC	2 cut(s)	19, 497
BspDI	ATCGAT	2 cut(s)	113, 531
BspLI	GGNNCC	1 cut(s)	181
BspOI	GCTAGC	1 cut(s)	392
BspPI	GGATC	1 cut(s)	261
BspT107I	GGYRCC	1 cut(s)	179
BspTNI	GGTCTC	1 cut(s)	68
BsrDI	GCAATG	2 cut(s)	192, 313
BsrGI	TGTACA	1 cut(s)	148
BsrI	ACTGG	2 cut(s)	493, 600
BssECI	CCNNGG	2 cut(s)	67, 206
BssMI	GATC	4 cut(s)	96, 126, 253, 577
BssNI	GRCGYC	1 cut(s)	567
BssT1I	CCWWGG	1 cut(s)	206
Bst2UI	CCWGG	1 cut(s)	357
Bst4CI	ACNGT	1 cut(s)	153
BstACI	GRCGYC	1 cut(s)	567
BstAUI	TGTACA	1 cut(s)	148
BstBAI	YACGTR	1 cut(s)	13
BstC8I	GCNNGC	2 cut(s)	378, 390
BstF5I	GGATG	1 cut(s)	99
BstKTI	GATC	4 cut(s)	99, 129, 256, 580
BstMAI	GTCTC	1 cut(s)	68
BstMBI	GATC	4 cut(s)	96, 126, 253, 577
BstNI	CCWGG	1 cut(s)	357
BstNSI	RCATGY	2 cut(s)	33, 467
BstSCI	CCNGG	2 cut(s)	244, 355
BstV1I	GCAGC	2 cut(s)	178, 531
BstX2I	RGATCY	1 cut(s)	253
BstYI	RGATCY	1 cut(s)	253
Bsu15I	ATCGAT	2 cut(s)	113, 531
BsuRI	GGCC	2 cut(s)	19, 497
BsuTUI	ATCGAT	2 cut(s)	113, 531
BtsCI	GGATG	1 cut(s)	99
Cac8I	GCNNGC	2 cut(s)	378, 390
ClaI	ATCGAT	2 cut(s)	113, 531
CseI	GACGC	1 cut(s)	556
Csp6I	GTAC	1 cut(s)	149
CspCI	CAANNNNNGTGG	3 cut(s)	16, 31, 51
CviAII	CATG	2 cut(s)	30, 464
CviJI	RGCY	8 cut(s)	19, 47, 169, 286, 376, 392, 497, 545
CviKI_1	RGCY	8 cut(s)	19, 47, 169, 286, 376, 392, 497, 545
CviQI	GTAC	1 cut(s)	149
DpnI	GATC	4 cut(s)	98, 128, 255, 579
DpnII	GATC	4 cut(s)	96, 126, 253, 577
DrdI	GACNNNNNNGTC	1 cut(s)	197
DseDI	GACNNNNNNGTC	1 cut(s)	197
EciI	GGCGGA	1 cut(s)	74
Eco130I	CCWWGG	1 cut(s)	206
Eco31I	GGTCTC	1 cut(s)	68
Eco32I	GATATC	1 cut(s)	407
Eco88I	CYCGRG	3 cut(s)	104, 364, 506
EcoRII	CCWGG	1 cut(s)	355
EcoRV	GATATC	1 cut(s)	407
EcoT14I	CCWWGG	1 cut(s)	206
ErhI	CCWWGG	1 cut(s)	206
FaeI	CATG	2 cut(s)	33, 467
FaiI	YATR	2 cut(s)	31, 465
FalI	AAGNNNNNCTT	2 cut(s)	330, 362
FaqI	GGGAC	1 cut(s)	554
FatI	CATG	2 cut(s)	29, 463
FbaI	TGATCA	2 cut(s)	126, 577
Fnu4HI	GCNGC	2 cut(s)	167, 520
FokI	GGATG	1 cut(s)	86
Fsp4HI	GCNGC	2 cut(s)	167, 520
FspBI	CTAG	2 cut(s)	389, 625
GluI	GCNGC	2 cut(s)	167, 520
GsuI	CTGGAG	1 cut(s)	77
HaeIII	GGCC	2 cut(s)	19, 497
HapII	CCGG	1 cut(s)	245
HgaI	GACGC	1 cut(s)	556
Hin1I	GRCGYC	1 cut(s)	567
Hin1II	CATG	2 cut(s)	33, 467
HinfI	GANTC	4 cut(s)	219, 275, 370, 398
HpaII	CCGG	1 cut(s)	245
HphI	GGTGA	3 cut(s)	52, 136, 146
Hpy188I	TCNGA	3 cut(s)	68, 224, 274
Hpy188III	TCNNGA	6 cut(s)	94, 106, 402, 475, 506, 575
HpyAV	CCTTC	2 cut(s)	487, 557
HpyCH4III	ACNGT	1 cut(s)	153
HpyCH4IV	ACGT	1 cut(s)	12
HpyCH4V	TGCA	4 cut(s)	306, 316, 380, 467
HpySE526I	ACGT	1 cut(s)	12
Hsp92I	GRCGYC	1 cut(s)	567
Hsp92II	CATG	2 cut(s)	33, 467
Ksp22I	TGATCA	2 cut(s)	126, 577
Kzo9I	GATC	4 cut(s)	96, 126, 253, 577
Lsp1109I	GCAGC	2 cut(s)	178, 531
LweI	GCATC	1 cut(s)	231
MaeI	CTAG	2 cut(s)	389, 625
MaeII	ACGT	1 cut(s)	12
MaeIII	GTNAC	1 cut(s)	331
MalI	GATC	4 cut(s)	98, 128, 255, 579
MboI	GATC	4 cut(s)	96, 126, 253, 577
MboII	GAAGA	1 cut(s)	622
MflI	RGATCY	1 cut(s)	253
MluCI	AATT	2 cut(s)	468, 604
MnlI	CCTC	7 cut(s)	62, 65, 92, 113, 360, 502, 582
MseI	TTAA	1 cut(s)	186
MspI	CCGG	1 cut(s)	245
MspR9I	CCNGG	2 cut(s)	246, 357
Mva1269I	GAATGC	1 cut(s)	390
MvaI	CCWGG	1 cut(s)	357
NciI	CCSGG	1 cut(s)	246
NdeII	GATC	4 cut(s)	96, 126, 253, 577
NheI	GCTAGC	1 cut(s)	388
NlaIII	CATG	2 cut(s)	33, 467
NlaIV	GGNNCC	1 cut(s)	181
NmuCI	GTSAC	1 cut(s)	331
NspI	RCATGY	2 cut(s)	33, 467
PaeR7I	CTCGAG	3 cut(s)	104, 364, 506
PciI	ACATGT	1 cut(s)	29
PctI	GAATGC	1 cut(s)	390
PfeI	GAWTC	4 cut(s)	219, 275, 370, 398
PflMI	CCANNNNNTGG	1 cut(s)	606
PfoI	TCCNGGA	1 cut(s)	355
PkrI	GCNGC	2 cut(s)	168, 521
Ppu21I	YACGTR	1 cut(s)	13
PscI	ACATGT	1 cut(s)	29
Psp6I	CCWGG	1 cut(s)	355
PspGI	CCWGG	1 cut(s)	355
PspN4I	GGNNCC	1 cut(s)	181
PspXI	VCTCGAGB	1 cut(s)	364
PsuI	RGATCY	1 cut(s)	253
RsaI	GTAC	1 cut(s)	150
RsaNI	GTAC	1 cut(s)	149
SaqAI	TTAA	1 cut(s)	186
SatI	GCNGC	2 cut(s)	167, 520
Sau3AI	GATC	4 cut(s)	96, 126, 253, 577
ScrFI	CCNGG	2 cut(s)	246, 357
SetI	ASST	6 cut(s)	15, 208, 288, 323, 378, 513
SfaNI	GCATC	1 cut(s)	231
Sfr274I	CTCGAG	3 cut(s)	104, 364, 506
SlaI	CTCGAG	3 cut(s)	104, 364, 506
SmlI	CTYRAG	3 cut(s)	104, 364, 506
SmoI	CTYRAG	3 cut(s)	104, 364, 506
Sse9I	AATT	2 cut(s)	468, 604
SsiI	CCGC	3 cut(s)	60, 85, 235
SspMI	CTAG	2 cut(s)	389, 625
StyD4I	CCNGG	2 cut(s)	244, 355
StyI	CCWWGG	1 cut(s)	206
TaaI	ACNGT	1 cut(s)	153
TaiI	ACGT	1 cut(s)	15
TaqI	TCGA	5 cut(s)	105, 113, 365, 507, 531
TasI	AATT	2 cut(s)	468, 604
TatI	WGTACW	1 cut(s)	148
TfiI	GAWTC	4 cut(s)	219, 275, 370, 398
Tru1I	TTAA	1 cut(s)	186
Tru9I	TTAA	1 cut(s)	186
TseFI	GTSAC	1 cut(s)	331
TseI	GCWGC	2 cut(s)	166, 519
Tsp45I	GTSAC	1 cut(s)	331
TspDTI	ATGAA	1 cut(s)	324
TspGWI	ACGGA	1 cut(s)	231
Van91I	CCANNNNNTGG	1 cut(s)	606
XceI	RCATGY	2 cut(s)	33, 467
XcmI	CCANNNNNNNNNTGG	1 cut(s)	34
XhoI	CTCGAG	3 cut(s)	104, 364, 506
XspI	CTAG	2 cut(s)	389, 625

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