Basic Information

Type: gene

Biological Identity

Species

rosa_wichuraiana

Chromosome

Chr3

Orthogroup ID

OG0007416

Physical Location & Seq

Genomic Coordinates Forward (+)

19557191 .. 19558453

Gene Structure 1263 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rw3G017770.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 711 bp

ATGGAGGGTCTCAAAGAGATTCAAAAGCTGGAGGGCCACACTGATAGGGTGTGGAGCCTCGCGTGGAACCCACTCTCCGGTCTCGACGGAGCTCCCCTTAAGCTCGCTTCATGCAGTGGCGATAAGACCGTTCGTATTTGGGAACACAAACCTTCCAACTCCTGGGAATGCCAGGTAGTCCTGGATGATCCGCACACCAGGACCGTCCGATCATGCGATTGGTCGCCATCCGGGAAGCTACTGGCCACTGCCAGCTTCGATGGCACCACCGCAATTTTTCAGGACGTTGGGGATGATTATGAGTGCGTTTCGACTCTAGAGGAGCAAAATGCCAAAGAGAAGTTGCTCTTTGTTCAGTTGCCTCCTACTCTACCATTGGTCAAGCGACCTACTAGTGCAAAGGGGAAAGAGAAAGTCAGAAGCTCAGCACCATCAGAGAAGGTAGGTGCTGCAAGGAAGGGCGGTAGTTTGGAAGAGTTATCTGAGGGGTATATGGGGAAGATGCAGGTTTACAAGAGTGGAGCAGTCAAGTTCAAGCTAGGAGATGCACTGTATGATGTTTCACCCGGTTCAGATTGTACATTTGCTCAAGATGTTGCTGCAATCAACACTGCAGCGAGAAAGTGTTGTGTTCTTGGAGAGCTTGGCCAGCGAGTTGTTATAACTCCTGATGTGGATTCCCTACTAGACGCAACGATTGAGTTGGACTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0001817 GO:0001819 GO:0002682 GO:0002684 GO:0003674 GO:0003682 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0005737 GO:0005829 GO:0008150 GO:0016604 GO:0016607 GO:0030880 GO:0031347 GO:0031349 GO:0031974 GO:0031981 GO:0032479 GO:0032481 GO:0032648 GO:0032728 GO:0032991 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044451 GO:0044464 GO:0045088 GO:0045089 GO:0048518 GO:0048583 GO:0048584 GO:0050776 GO:0050778 GO:0050789 GO:0051239 GO:0051240 GO:0055029 GO:0061695 GO:0065007 GO:0070013 GO:0080134 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko04623 ko05169 map00230 map00240 map01100 map03020 map04623 map05169

Pfam Domains

Protein Families

RNA_pol_Rpc4

Protein Analysis

236

Amino Acids

25.56

Weight (kDa)

5.24

Isoelectric Point (pI)

38.6

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
WD40	PF00400	5 - 47	4.6e-09	WD domain, G-beta repeat
Beta-prop_WDR5	PF25175	5 - 107	2.5e-13	WDR5 beta-propeller domain
WD40_CDC20-Fz	PF24807	5 - 85	9.4e-08	CDC20/Fizzy WD40 domain
Beta-prop_THOC3	PF25174	6 - 52	3.8e-07	THOC3 beta-propeller domain
WD40_Prp19	PF24814	6 - 119	1e-11	Prp19 WD40 domain
Beta-prop_WDR3_1st	PF25173	7 - 93	3.7e-07	WDR3 first beta-propeller domain
Beta-prop_Aladin	PF25460	16 - 99	2.9e-06	Aladin seven-bladed propeller
Beta-prop_EML_2	PF23414	18 - 95	5.5e-06	Echinoderm microtubule-associated protein second beta-propeller
Beta-prop_CAF1B_HIR1	PF24105	30 - 115	1.4e-07	CAF1B/HIR1 beta-propeller domain
WD40	PF00400	57 - 92	1.9e-06	WD domain, G-beta repeat
RNA_pol_Rpc4	PF05132	113 - 225	8.4e-27	RNA polymerase III RPC4

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Align Labels (Cladogram)

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Publication-ready

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Orthologous Genes (Group: OG0007416)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT2G26060 AT2G26060 AT4G32990 AT4G32990
fragaria_vesca	FvH4_6g18650
malus_domestica	MD12G1035900.v1.1 MD14G1022600.v1.1
prunus_persica	Prupe.7G110600_v2.0.a1 Prupe.7G110600_v2.0.a1
pyrus_communis	pycom08g05600 pycom12g02370 pycom14g02160
rosa_chinensis	RchiOBHm_Chr3g0473611
rosa_laevigata	RLG00000024000
rosa_multiflora	Rmu_sc0003069.1_g000012 Rmu_sc0021612.1_g000001 Rmu_sc0033628.1_g000001
rosa_roxburghii	Rroxscaffold_6G00408020
rosa_rugosa	Rorug03G0133100
rosa_samantha	Rh3AG184700 Rh3BG212700 Rh3CG209500 Rh3DG208800
rosa_wichuraiana	Rw3G015950 Rw3G017770

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	662
Acc36I	ACCTGC	1 cut(s)	496
AccB1I	GGYRCC	1 cut(s)	263
AccB7I	CCANNNNNTGG	1 cut(s)	162
AccII	CGCG	1 cut(s)	62
AciI	CCGC	3 cut(s)	191, 270, 462
AclWI	GGATC	1 cut(s)	182
AcoI	YGGCCR	2 cut(s)	243, 646
AfaI	GTAC	1 cut(s)	580
AfiI	CCNNNNNNNGG	2 cut(s)	77, 162
AflII	CTTAAG	1 cut(s)	98
AgsI	TTSAA	2 cut(s)	23, 535
AhlI	ACTAGT	1 cut(s)	392
AjnI	CCWGG	4 cut(s)	161, 171, 180, 197
AloI	GAACNNNNNNTCC	2 cut(s)	59, 91
AluBI	AGCT	8 cut(s)	28, 92, 103, 238, 255, 423, 538, 643
AluI	AGCT	8 cut(s)	28, 92, 103, 238, 255, 423, 538, 643
Alw21I	GWGCWC	1 cut(s)	94
Alw26I	GTCTC	2 cut(s)	14, 86
AlwI	GGATC	1 cut(s)	182
AoxI	GGCC	3 cut(s)	34, 243, 646
ApeKI	GCWGC	3 cut(s)	449, 599, 614
AspS9I	GGNCC	2 cut(s)	34, 201
AsuC2I	CCSGG	2 cut(s)	232, 567
AsuHPI	GGTGA	1 cut(s)	555
AvaII	GGWCC	1 cut(s)	201
BalI	TGGCCA	2 cut(s)	245, 648
BanI	GGYRCC	1 cut(s)	263
BanII	GRGCYC	1 cut(s)	94
Bbv12I	GWGCWC	1 cut(s)	94
BbvI	GCAGC	3 cut(s)	436, 586, 626
BccI	CCATC	3 cut(s)	235, 254, 439
BciT130I	CCWGG	4 cut(s)	163, 173, 182, 199
BcnI	CCSGG	2 cut(s)	232, 567
BcoDI	GTCTC	2 cut(s)	14, 86
BcuI	ACTAGT	1 cut(s)	392
BfaI	CTAG	4 cut(s)	317, 393, 539, 686
BfmI	CTRYAG	1 cut(s)	612
BfrI	CTTAAG	1 cut(s)	98
BfuAI	ACCTGC	1 cut(s)	496
BisI	GCNGC	3 cut(s)	450, 600, 615
BlpI	GCTNAGC	1 cut(s)	424
BlsI	GCNGC	3 cut(s)	451, 601, 616
Bme1390I	CCNGG	6 cut(s)	163, 173, 182, 199, 232, 567
Bme18I	GGWCC	1 cut(s)	201
BmgT120I	GGNCC	2 cut(s)	34, 201
BmiI	GGNNCC	3 cut(s)	56, 68, 265
BmrFI	CCNGG	6 cut(s)	163, 173, 182, 199, 232, 567
BmsI	GCATC	2 cut(s)	492, 535
BpmI	CTGGAG	1 cut(s)	50
Bpu1102I	GCTNAGC	1 cut(s)	424
BpuEI	CTTGAG	1 cut(s)	573
BpuMI	CCSGG	2 cut(s)	232, 567
BsaI	GGTCTC	2 cut(s)	14, 86
BsaJI	CCNNGG	1 cut(s)	162
BsaWI	WCCGGW	1 cut(s)	77
BsaXI	ACNNNNNCTCC	2 cut(s)	59, 89
Bsc4I	CCNNNNNNNGG	2 cut(s)	77, 162
Bse1I	ACTGG	1 cut(s)	246
BseBI	CCWGG	4 cut(s)	163, 173, 182, 199
BseDI	CCNNGG	1 cut(s)	162
BseGI	GGATG	3 cut(s)	190, 227, 298
BseLI	CCNNNNNNNGG	2 cut(s)	77, 162
BseMII	CTCAG	2 cut(s)	438, 474
BseNI	ACTGG	1 cut(s)	246
BseRI	GAGGAG	1 cut(s)	335
BseXI	GCAGC	3 cut(s)	436, 586, 626
Bsh1236I	CGCG	1 cut(s)	62
BshFI	GGCC	3 cut(s)	36, 245, 648
BshNI	GGYRCC	1 cut(s)	263
BsiHKAI	GWGCWC	1 cut(s)	94
BsiSI	CCGG	3 cut(s)	78, 231, 567
BslI	CCNNNNNNNGG	2 cut(s)	77, 162
BsmAI	GTCTC	2 cut(s)	14, 86
BsmI	GAATGC	1 cut(s)	173
BsnI	GGCC	3 cut(s)	36, 245, 648
Bso31I	GGTCTC	2 cut(s)	14, 86
Bsp1286I	GDGCHC	1 cut(s)	94
Bsp1407I	TGTACA	1 cut(s)	578
Bsp143I	GATC	2 cut(s)	187, 209
Bsp1720I	GCTNAGC	1 cut(s)	424
BspACI	CCGC	3 cut(s)	191, 270, 462
BspANI	GGCC	3 cut(s)	36, 245, 648
BspCNI	CTCAG	2 cut(s)	437, 475
BspFNI	CGCG	1 cut(s)	62
BspLI	GGNNCC	3 cut(s)	56, 68, 265
BspMAI	CTGCAG	1 cut(s)	616
BspMI	ACCTGC	1 cut(s)	496
BspPI	GGATC	1 cut(s)	182
BspT107I	GGYRCC	1 cut(s)	263
BspTI	CTTAAG	1 cut(s)	98
BspTNI	GGTCTC	2 cut(s)	14, 86
BsrGI	TGTACA	1 cut(s)	578
BsrI	ACTGG	1 cut(s)	246
BssECI	CCNNGG	1 cut(s)	162
BssMI	GATC	2 cut(s)	187, 209
Bst2UI	CCWGG	4 cut(s)	163, 173, 182, 199
Bst4CI	ACNGT	3 cut(s)	130, 205, 552
Bst6I	CTCTTC	1 cut(s)	468
BstAFI	CTTAAG	1 cut(s)	98
BstAUI	TGTACA	1 cut(s)	578
BstC8I	GCNNGC	3 cut(s)	105, 253, 650
BstDEI	CTNAG	2 cut(s)	424, 483
BstF5I	GGATG	3 cut(s)	190, 227, 298
BstFNI	CGCG	1 cut(s)	62
BstKTI	GATC	2 cut(s)	190, 212
BstMAI	GTCTC	2 cut(s)	14, 86
BstMBI	GATC	2 cut(s)	187, 209
BstMWI	GCNNNNNNNGC	2 cut(s)	261, 649
BstNI	CCWGG	4 cut(s)	163, 173, 182, 199
BstSCI	CCNGG	6 cut(s)	161, 171, 180, 197, 230, 565
BstSFI	CTRYAG	1 cut(s)	612
BstUI	CGCG	1 cut(s)	62
BstV1I	GCAGC	3 cut(s)	436, 586, 626
BsuRI	GGCC	3 cut(s)	36, 245, 648
BtsCI	GGATG	3 cut(s)	190, 227, 298
BtsI	GCAGTG	3 cut(s)	121, 246, 609
BtsIMutI	CAGTG	5 cut(s)	39, 121, 246, 548, 609
BveI	ACCTGC	1 cut(s)	496
Cac8I	GCNNGC	3 cut(s)	105, 253, 650
Cfr13I	GGNCC	2 cut(s)	34, 201
CseI	GACGC	1 cut(s)	698
Csp6I	GTAC	1 cut(s)	579
CviAII	CATG	2 cut(s)	111, 213
CviQI	GTAC	1 cut(s)	579
DdeI	CTNAG	2 cut(s)	424, 483
DpnI	GATC	2 cut(s)	189, 211
DpnII	GATC	2 cut(s)	187, 209
EaeI	YGGCCR	2 cut(s)	243, 646
Eam1104I	CTCTTC	1 cut(s)	468
EarI	CTCTTC	1 cut(s)	468
Ecl136II	GAGCTC	1 cut(s)	92
Eco24I	GRGCYC	1 cut(s)	94
Eco31I	GGTCTC	2 cut(s)	14, 86
Eco47I	GGWCC	1 cut(s)	201
Eco53kI	GAGCTC	1 cut(s)	92
EcoICRI	GAGCTC	1 cut(s)	92
EcoRII	CCWGG	4 cut(s)	161, 171, 180, 197
EcoT38I	GRGCYC	1 cut(s)	94
FaeI	CATG	2 cut(s)	114, 216
FaiI	YATR	7 cut(s)	112, 214, 300, 492, 494, 555, 662
FalI	AAGNNNNNCTT	2 cut(s)	332, 364
FatI	CATG	2 cut(s)	110, 212
Fnu4HI	GCNGC	3 cut(s)	450, 600, 615
FokI	GGATG	3 cut(s)	197, 214, 305
FriOI	GRGCYC	1 cut(s)	94
Fsp4HI	GCNGC	3 cut(s)	450, 600, 615
FspBI	CTAG	4 cut(s)	317, 393, 539, 686
GluI	GCNGC	3 cut(s)	450, 600, 615
GsuI	CTGGAG	1 cut(s)	50
HaeIII	GGCC	3 cut(s)	36, 245, 648
HapII	CCGG	3 cut(s)	78, 231, 567
HgaI	GACGC	1 cut(s)	698
Hin1II	CATG	2 cut(s)	114, 216
HinfI	GANTC	3 cut(s)	19, 313, 677
HpaII	CCGG	3 cut(s)	78, 231, 567
HphI	GGTGA	1 cut(s)	555
Hpy166II	GTNNAC	1 cut(s)	511
Hpy188I	TCNGA	5 cut(s)	209, 419, 436, 484, 574
Hpy188III	TCNNGA	5 cut(s)	83, 281, 317, 590, 668
Hpy8I	GTNNAC	1 cut(s)	511
Hpy99I	CGWCG	1 cut(s)	89
HpyAV	CCTTC	3 cut(s)	162, 433, 451
HpyCH4III	ACNGT	3 cut(s)	130, 205, 552
HpyCH4IV	ACGT	1 cut(s)	285
HpyCH4V	TGCA	7 cut(s)	114, 398, 452, 505, 548, 602, 614
HpyF10VI	GCNNNNNNNGC	2 cut(s)	261, 649
HpyF3I	CTNAG	2 cut(s)	424, 483
HpySE526I	ACGT	1 cut(s)	285
Hsp92II	CATG	2 cut(s)	114, 216
Kzo9I	GATC	2 cut(s)	187, 209
LmnI	GCTCC	5 cut(s)	54, 89, 97, 322, 521
Lsp1109I	GCAGC	3 cut(s)	436, 586, 626
LweI	GCATC	2 cut(s)	492, 535
MaeI	CTAG	4 cut(s)	317, 393, 539, 686
MaeII	ACGT	1 cut(s)	285
MalI	GATC	2 cut(s)	189, 211
MboI	GATC	2 cut(s)	187, 209
MboII	GAAGA	2 cut(s)	485, 511
MhlI	GDGCHC	1 cut(s)	94
MlsI	TGGCCA	2 cut(s)	245, 648
MluCI	AATT	1 cut(s)	273
MluNI	TGGCCA	2 cut(s)	245, 648
MlyI	GAGTC	1 cut(s)	307
MmeI	TCCRAC	2 cut(s)	180, 684
MnlI	CCTC	5 cut(s)	25, 68, 313, 372, 478
Mox20I	TGGCCA	2 cut(s)	245, 648
MscI	TGGCCA	2 cut(s)	245, 648
MseI	TTAA	1 cut(s)	99
Msp20I	TGGCCA	2 cut(s)	245, 648
MspCI	CTTAAG	1 cut(s)	98
MspI	CCGG	3 cut(s)	78, 231, 567
MspR9I	CCNGG	6 cut(s)	163, 173, 182, 199, 232, 567
Mva1269I	GAATGC	1 cut(s)	173
MvaI	CCWGG	4 cut(s)	163, 173, 182, 199
MvnI	CGCG	1 cut(s)	62
MwoI	GCNNNNNNNGC	2 cut(s)	261, 649
NciI	CCSGG	2 cut(s)	232, 567
NdeII	GATC	2 cut(s)	187, 209
NlaIII	CATG	2 cut(s)	114, 216
NlaIV	GGNNCC	3 cut(s)	56, 68, 265
PctI	GAATGC	1 cut(s)	173
PfeI	GAWTC	2 cut(s)	19, 677
PflMI	CCANNNNNTGG	1 cut(s)	162
PfoI	TCCNGGA	2 cut(s)	180, 230
PkrI	GCNGC	3 cut(s)	451, 601, 616
PleI	GAGTC	1 cut(s)	307
PpsI	GAGTC	1 cut(s)	307
PsiI	TTATAA	1 cut(s)	662
Psp124BI	GAGCTC	1 cut(s)	94
Psp6I	CCWGG	4 cut(s)	161, 171, 180, 197
PspGI	CCWGG	4 cut(s)	161, 171, 180, 197
PspN4I	GGNNCC	3 cut(s)	56, 68, 265
PspPI	GGNCC	2 cut(s)	34, 201
PstI	CTGCAG	1 cut(s)	616
RsaI	GTAC	1 cut(s)	580
RsaNI	GTAC	1 cut(s)	579
SacI	GAGCTC	1 cut(s)	94
SaqAI	TTAA	1 cut(s)	99
SatI	GCNGC	3 cut(s)	450, 600, 615
Sau3AI	GATC	2 cut(s)	187, 209
Sau96I	GGNCC	2 cut(s)	34, 201
SchI	GAGTC	1 cut(s)	307
ScrFI	CCNGG	6 cut(s)	163, 173, 182, 199, 232, 567
SduI	GDGCHC	1 cut(s)	94
SfaNI	GCATC	2 cut(s)	492, 535
SfcI	CTRYAG	1 cut(s)	612
SinI	GGWCC	1 cut(s)	201
SmlI	CTYRAG	2 cut(s)	98, 588
SmoI	CTYRAG	2 cut(s)	98, 588
SpeI	ACTAGT	1 cut(s)	392
Sse9I	AATT	1 cut(s)	273
SsiI	CCGC	3 cut(s)	191, 270, 462
SspMI	CTAG	4 cut(s)	317, 393, 539, 686
SstI	GAGCTC	1 cut(s)	94
StyD4I	CCNGG	6 cut(s)	161, 171, 180, 197, 230, 565
TaaI	ACNGT	3 cut(s)	130, 205, 552
TaiI	ACGT	1 cut(s)	288
TaqI	TCGA	3 cut(s)	84, 258, 311
TasI	AATT	1 cut(s)	273
TatI	WGTACW	1 cut(s)	578
TfiI	GAWTC	2 cut(s)	19, 677
Tru1I	TTAA	1 cut(s)	99
Tru9I	TTAA	1 cut(s)	99
TscAI	CASTG	5 cut(s)	46, 121, 253, 555, 616
TseI	GCWGC	3 cut(s)	449, 599, 614
TspDTI	ATGAA	1 cut(s)	99
TspGWI	ACGGA	1 cut(s)	102
TspRI	CASTG	5 cut(s)	46, 121, 253, 555, 616
Van91I	CCANNNNNTGG	1 cut(s)	162
Vha464I	CTTAAG	1 cut(s)	98
VpaK11BI	GGWCC	1 cut(s)	201
XbaI	TCTAGA	1 cut(s)	316
XspI	CTAG	4 cut(s)	317, 393, 539, 686

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