Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3A

Orthogroup ID

OG0005944

Physical Location & Seq

Genomic Coordinates Forward (+)

21917815 .. 21938860

Gene Structure 21046 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3AG216500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 684 bp

ATGGCGGTCTCCGAGGAGGAGTGTTCCTTCGCCAACTCCAGATCATCCACGCCTTCCACCTCCAGCAGCTCTCACTACCTCTCCAAGTGCCTCCTTCGTGGCACCGTCGTTCTCCACGTCCTCCACGGTCACATCCGCTTCCCCAACTCCCGCGACATCGTTTTCGGCAAGGAGAAATCAATAGAGTTGGTGATAATCGGTGAAGACGAGATTGTACAGTCTGTGTGTGAGCAGCCTGTGTTTGGCACCATTAAAGACATTGCCGTCCTACCATGGAATGACGGATTCCAAACCCGAAACCTCCAGGTGTCTAGCTCAATTCAACGAGTTCAGCCTTTTGTTTCGAGAATTAACTATTACATTGAGAAAAATAAATTTTGTGCTCATGTTGGTGTAGATGTCATGTCGGGCAAGGATCTTTTGGTCGTTGTTTCGGATTCCGGGAAGCTCTCGGTTCTATCTTTCTGCAATGAAATGCACAGGTTTTTTCCTGTGACACAAGTTCAACTTTCTAATCCTGGAAACTCGAGGAATCAGCTTGCAAGAATGCTAGCCATTGATTCAAGACCAAGTCACCATGCTAGCACAAGGTGGACTCCATTTGATGTCAATGTTCTATCAAACATACCAAAAACCAACATATACTGCCTTCTCAAAAAATGCATGATAGCATTCTGGCAGTAG

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

227

Amino Acids

25.51

Weight (kDa)

8.7

Isoelectric Point (pI)

61.46

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Beta-prop_RSE1_1st	PF10433	37 - 189	2.8e-22	RSE1/DDB1/CPSF1 first beta-propeller

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)

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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)	263
AccB1I	GGYRCC	2 cut(s)	101, 245
AccII	CGCG	1 cut(s)	153
AciI	CCGC	3 cut(s)	5, 136, 151
AclWI	GGATC	1 cut(s)	423
AcsI	RAATTY	1 cut(s)	374
AdeI	CACNNNGTG	1 cut(s)	591
AfaI	GTAC	1 cut(s)	216
AfiI	CCNNNNNNNGG	1 cut(s)	242
AgsI	TTSAA	3 cut(s)	323, 506, 564
AjiI	CACGTC	1 cut(s)	118
AjnI	CCWGG	2 cut(s)	303, 517
AluBI	AGCT	4 cut(s)	69, 315, 448, 538
AluI	AGCT	4 cut(s)	69, 315, 448, 538
Alw21I	GWGCWC	1 cut(s)	385
Alw26I	GTCTC	1 cut(s)	13
AlwI	GGATC	1 cut(s)	423
Ama87I	CYCGRG	1 cut(s)	526
ApeKI	GCWGC	2 cut(s)	66, 232
ApoI	RAATTY	1 cut(s)	374
ArsI	GACNNNNNNTTYG	2 cut(s)	146, 178
AsuC2I	CCSGG	1 cut(s)	442
AsuHPI	GGTGA	3 cut(s)	202, 212, 566
AsuNHI	GCTAGC	2 cut(s)	550, 581
AvaI	CYCGRG	1 cut(s)	526
BanI	GGYRCC	2 cut(s)	101, 245
BbsI	GAAGAC	1 cut(s)	210
Bbv12I	GWGCWC	1 cut(s)	385
BbvI	GCAGC	2 cut(s)	78, 244
BceAI	ACGGC	1 cut(s)	248
BciT130I	CCWGG	2 cut(s)	305, 519
BcnI	CCSGG	1 cut(s)	442
BcoDI	GTCTC	1 cut(s)	13
BfaI	CTAG	3 cut(s)	312, 551, 582
BisI	GCNGC	2 cut(s)	67, 233
BlsI	GCNGC	2 cut(s)	68, 234
Bme1390I	CCNGG	3 cut(s)	305, 442, 519
BmeT110I	CYCGRG	1 cut(s)	526
BmgBI	CACGTC	1 cut(s)	118
BmiI	GGNNCC	2 cut(s)	103, 247
BmrFI	CCNGG	3 cut(s)	305, 442, 519
BmtI	GCTAGC	2 cut(s)	554, 585
BpiI	GAAGAC	1 cut(s)	210
BpmI	CTGGAG	3 cut(s)	22, 46, 287
BpuMI	CCSGG	1 cut(s)	442
BsaI	GGTCTC	1 cut(s)	13
BsaJI	CCNNGG	3 cut(s)	12, 124, 272
BsaXI	ACNNNNNCTCC	2 cut(s)	65, 95
Bsc4I	CCNNNNNNNGG	1 cut(s)	242
Bse3DI	GCAATG	2 cut(s)	258, 475
BseBI	CCWGG	2 cut(s)	305, 519
BseDI	CCNNGG	3 cut(s)	12, 124, 272
BseGI	GGATG	2 cut(s)	44, 132
BseLI	CCNNNNNNNGG	1 cut(s)	242
BseMI	GCAATG	2 cut(s)	258, 475
BseRI	GAGGAG	2 cut(s)	29, 32
BseXI	GCAGC	2 cut(s)	78, 244
Bsh1236I	CGCG	1 cut(s)	153
BshNI	GGYRCC	2 cut(s)	101, 245
BsiHKAI	GWGCWC	1 cut(s)	385
BsiHKCI	CYCGRG	1 cut(s)	526
BsiSI	CCGG	1 cut(s)	441
BslI	CCNNNNNNNGG	1 cut(s)	242
BsmAI	GTCTC	1 cut(s)	13
BsmI	GAATGC	2 cut(s)	552, 671
Bso31I	GGTCTC	1 cut(s)	13
BsoBI	CYCGRG	1 cut(s)	526
Bsp1286I	GDGCHC	1 cut(s)	385
Bsp1407I	TGTACA	1 cut(s)	214
Bsp143I	GATC	2 cut(s)	41, 415
Bsp19I	CCATGG	1 cut(s)	272
BspACI	CCGC	3 cut(s)	5, 136, 151
BspFNI	CGCG	1 cut(s)	153
BspLI	GGNNCC	2 cut(s)	103, 247
BspOI	GCTAGC	2 cut(s)	554, 585
BspPI	GGATC	1 cut(s)	423
BspT107I	GGYRCC	2 cut(s)	101, 245
BspTNI	GGTCTC	1 cut(s)	13
BsrDI	GCAATG	2 cut(s)	258, 475
BsrGI	TGTACA	1 cut(s)	214
BssECI	CCNNGG	3 cut(s)	12, 124, 272
BssMI	GATC	2 cut(s)	41, 415
BssT1I	CCWWGG	1 cut(s)	272
Bst2UI	CCWGG	2 cut(s)	305, 519
Bst4CI	ACNGT	3 cut(s)	106, 128, 219
BstAUI	TGTACA	1 cut(s)	214
BstC8I	GCNNGC	3 cut(s)	540, 552, 583
BstDSI	CCRYGG	2 cut(s)	124, 272
BstF5I	GGATG	2 cut(s)	44, 132
BstFNI	CGCG	1 cut(s)	153
BstKTI	GATC	2 cut(s)	44, 418
BstMAI	GTCTC	1 cut(s)	13
BstMBI	GATC	2 cut(s)	41, 415
BstNI	CCWGG	2 cut(s)	305, 519
BstSCI	CCNGG	3 cut(s)	303, 440, 517
BstUI	CGCG	1 cut(s)	153
BstV1I	GCAGC	2 cut(s)	78, 244
BstV2I	GAAGAC	1 cut(s)	210
BstX2I	RGATCY	1 cut(s)	415
BstYI	RGATCY	1 cut(s)	415
BtgI	CCRYGG	2 cut(s)	124, 272
BtrI	CACGTC	1 cut(s)	118
BtsCI	GGATG	2 cut(s)	44, 132
Cac8I	GCNNGC	3 cut(s)	540, 552, 583
Csp6I	GTAC	1 cut(s)	215
CviAII	CATG	5 cut(s)	273, 386, 403, 578, 664
CviJI	RGCY	7 cut(s)	69, 235, 315, 334, 448, 538, 554
CviKI_1	RGCY	7 cut(s)	69, 235, 315, 334, 448, 538, 554
CviQI	GTAC	1 cut(s)	215
DpnI	GATC	2 cut(s)	43, 417
DpnII	GATC	2 cut(s)	41, 415
DraIII	CACNNNGTG	1 cut(s)	591
DrdI	GACNNNNNNGTC	1 cut(s)	263
DseDI	GACNNNNNNGTC	1 cut(s)	263
Eco130I	CCWWGG	1 cut(s)	272
Eco31I	GGTCTC	1 cut(s)	13
Eco88I	CYCGRG	1 cut(s)	526
EcoRII	CCWGG	2 cut(s)	303, 517
EcoT14I	CCWWGG	1 cut(s)	272
EcoT22I	ATGCAT	1 cut(s)	665
ErhI	CCWWGG	1 cut(s)	272
FaeI	CATG	5 cut(s)	276, 389, 406, 581, 667
FaiI	YATR	8 cut(s)	274, 387, 404, 579, 626, 641, 643, 665
FalI	AAGNNNNNCTT	2 cut(s)	492, 524
FatI	CATG	5 cut(s)	272, 385, 402, 577, 663
FauI	CCCGC	1 cut(s)	158
Fnu4HI	GCNGC	2 cut(s)	67, 233
FokI	GGATG	2 cut(s)	31, 119
Fsp4HI	GCNGC	2 cut(s)	67, 233
FspBI	CTAG	3 cut(s)	312, 551, 582
GluI	GCNGC	2 cut(s)	67, 233
GsuI	CTGGAG	3 cut(s)	22, 46, 287
HapII	CCGG	1 cut(s)	441
Hin1II	CATG	5 cut(s)	276, 389, 406, 581, 667
HinfI	GANTC	5 cut(s)	285, 437, 532, 560, 595
HpaII	CCGG	1 cut(s)	441
HphI	GGTGA	3 cut(s)	202, 212, 566
Hpy166II	GTNNAC	1 cut(s)	594
Hpy188I	TCNGA	2 cut(s)	13, 436
Hpy188III	TCNNGA	3 cut(s)	39, 345, 564
Hpy8I	GTNNAC	1 cut(s)	594
Hpy99I	CGWCG	1 cut(s)	110
HpyAV	CCTTC	4 cut(s)	37, 63, 104, 659
HpyCH4III	ACNGT	3 cut(s)	106, 128, 219
HpyCH4IV	ACGT	1 cut(s)	117
HpyCH4V	TGCA	4 cut(s)	468, 478, 542, 663
HpySE526I	ACGT	1 cut(s)	117
Hsp92II	CATG	5 cut(s)	276, 389, 406, 581, 667
Kzo9I	GATC	2 cut(s)	41, 415
Lsp1109I	GCAGC	2 cut(s)	78, 244
MaeI	CTAG	3 cut(s)	312, 551, 582
MaeII	ACGT	1 cut(s)	117
MaeIII	GTNAC	3 cut(s)	128, 493, 572
MalI	GATC	2 cut(s)	43, 417
MboI	GATC	2 cut(s)	41, 415
MboII	GAAGA	1 cut(s)	215
MflI	RGATCY	1 cut(s)	415
MhlI	GDGCHC	1 cut(s)	385
MluCI	AATT	3 cut(s)	318, 348, 374
MlyI	GAGTC	1 cut(s)	589
MnlI	CCTC	8 cut(s)	7, 10, 70, 89, 101, 131, 311, 522
Mph1103I	ATGCAT	1 cut(s)	665
MseI	TTAA	2 cut(s)	252, 351
MslI	CAYNNNNRTG	1 cut(s)	390
MspI	CCGG	1 cut(s)	441
MspR9I	CCNGG	3 cut(s)	305, 442, 519
Mva1269I	GAATGC	2 cut(s)	552, 671
MvaI	CCWGG	2 cut(s)	305, 519
MvnI	CGCG	1 cut(s)	153
NciI	CCSGG	1 cut(s)	442
NcoI	CCATGG	1 cut(s)	272
NdeII	GATC	2 cut(s)	41, 415
NheI	GCTAGC	2 cut(s)	550, 581
NlaIII	CATG	5 cut(s)	276, 389, 406, 581, 667
NlaIV	GGNNCC	2 cut(s)	103, 247
NmuCI	GTSAC	3 cut(s)	128, 493, 572
NsiI	ATGCAT	1 cut(s)	665
PaeR7I	CTCGAG	1 cut(s)	526
PcsI	WCGNNNNNNNCGW	2 cut(s)	114, 204
PctI	GAATGC	2 cut(s)	552, 671
PfeI	GAWTC	4 cut(s)	285, 437, 532, 560
PflFI	GACNNNGTC	1 cut(s)	570
PfoI	TCCNGGA	2 cut(s)	440, 517
PkrI	GCNGC	2 cut(s)	68, 234
PleI	GAGTC	1 cut(s)	589
PpsI	GAGTC	1 cut(s)	589
Psp6I	CCWGG	2 cut(s)	303, 517
PspGI	CCWGG	2 cut(s)	303, 517
PspN4I	GGNNCC	2 cut(s)	103, 247
PspXI	VCTCGAGB	1 cut(s)	526
PsuI	RGATCY	1 cut(s)	415
PsyI	GACNNNGTC	1 cut(s)	570
RsaI	GTAC	1 cut(s)	216
RsaNI	GTAC	1 cut(s)	215
RseI	CAYNNNNRTG	1 cut(s)	390
SaqAI	TTAA	2 cut(s)	252, 351
SatI	GCNGC	2 cut(s)	67, 233
Sau3AI	GATC	2 cut(s)	41, 415
SchI	GAGTC	1 cut(s)	589
ScrFI	CCNGG	3 cut(s)	305, 442, 519
SduI	GDGCHC	1 cut(s)	385
Sfr274I	CTCGAG	1 cut(s)	526
SlaI	CTCGAG	1 cut(s)	526
SmiMI	CAYNNNNRTG	1 cut(s)	390
SmlI	CTYRAG	1 cut(s)	526
SmoI	CTYRAG	1 cut(s)	526
Sse9I	AATT	3 cut(s)	318, 348, 374
SsiI	CCGC	3 cut(s)	5, 136, 151
SspMI	CTAG	3 cut(s)	312, 551, 582
StyD4I	CCNGG	3 cut(s)	303, 440, 517
StyI	CCWWGG	1 cut(s)	272
TaaI	ACNGT	3 cut(s)	106, 128, 219
TaiI	ACGT	1 cut(s)	120
TaqI	TCGA	2 cut(s)	344, 527
TasI	AATT	3 cut(s)	318, 348, 374
TatI	WGTACW	1 cut(s)	214
TfiI	GAWTC	4 cut(s)	285, 437, 532, 560
Tru1I	TTAA	2 cut(s)	252, 351
Tru9I	TTAA	2 cut(s)	252, 351
TseFI	GTSAC	3 cut(s)	128, 493, 572
TseI	GCWGC	2 cut(s)	66, 232
Tsp45I	GTSAC	3 cut(s)	128, 493, 572
TspDTI	ATGAA	1 cut(s)	486
TspGWI	ACGGA	1 cut(s)	297
Tth111I	GACNNNGTC	1 cut(s)	570
XapI	RAATTY	1 cut(s)	374
XhoI	CTCGAG	1 cut(s)	526
XspI	CTAG	3 cut(s)	312, 551, 582
Zsp2I	ATGCAT	1 cut(s)	665

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