Basic Information

Type: gene

Biological Identity

Species

rosa_wichuraiana

Chromosome

Chr4

Orthogroup ID

OG0001390

Physical Location & Seq

Genomic Coordinates Forward (+)

2148117 .. 2149497

Gene Structure 1381 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rw4G001120.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 474 bp

ATGAAGATACTAAAGGCTGATGTCGGAGCACTTGATAATTTTGAAGTGCTCGAATTCCTAAAATCTAAAGGGGCCTCAAAGAATGATCTATCACGGGTGGCAAGAGTTACACAATCGGAGTATAAGGTTTTCGATTATTTGGTTGATACTCCTGCTGGTACTCACACAAGAGAGAGTGTTGAAGAGTTCAAGGAGAAGTGTAGACAATATGACCTTGGGAATGATAAGATCCTCAATATTATTAACACTAGGCCAGCTTCAGTGGTTGAAATATATGCGATCGTGGAGGATAATGCTGATGAGCTAGTAGAGCTGGTTGCAGAGGTCTTGACTCCTCCAACCGTCGCATCCCCTAAACCTGAAGCCGATACTAATGAGATTGATGCAGAGACCATGAACGTAGAACAAATTGAACAAAATGATGGCAATAAAGAAAAACCTGAATTTGGGGAAGCACCAATGGAGACTAGTTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0003674 GO:0003824 GO:0003899 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0005737 GO:0005886 GO:0006139 GO:0006351 GO:0006352 GO:0006383 GO:0006384 GO:0006725 GO:0006807 GO:0007568 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009360 GO:0009987 GO:0010467 GO:0016020 GO:0016070 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019438 GO:0030424 GO:0030425 GO:0030880 GO:0031974 GO:0031981 GO:0032502 GO:0032774 GO:0032991 GO:0034062 GO:0034641 GO:0034645 GO:0034654 GO:0036477 GO:0042575 GO:0042995 GO:0043005 GO:0043025 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044297 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044463 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0071944 GO:0090304 GO:0097447 GO:0097458 GO:0097659 GO:0097747 GO:0120025 GO:0120038 GO:0140098 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

RNA_pol_Rpb4

Protein Analysis

157

Amino Acids

17.49

Weight (kDa)

4.39

Isoelectric Point (pI)

30.98

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb4	PF03874	11 - 100	1.8e-10	RNA polymerase Rpb4

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

Font Size (px)

Line Width

Align Labels (Cladogram)

Image

Tree File

Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0001390)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT5G62950 AT5G62950 AT5G62950 AT5G62950 AT5G62950 AT5G62950 AT5G62950
fragaria_vesca	FvH4_4g01070 FvH4_4g01070 FvH4_5g27570
malus_domestica	MD13G1198900.v1.1
prunus_persica	Prupe.1G020700_v2.0.a1 Prupe.1G020700_v2.0.a1 Prupe.1G020700_v2.0.a1 Prupe.1G020700_v2.0.a1
pyrus_communis	pycom13g17270
rosa_chinensis	RchiOBHm_Chr4g0387641 RchiOBHm_Chr6g0280701
rosa_laevigata	RLG00000010104 RLG00000013035
rosa_multiflora	Rmu_sc0000976.1_g000021 Rmu_sc0003953.1_g000006
rosa_roxburghii	Rroxscaffold_7G00187720
rosa_rugosa	Rorug03G0311800 Rorug03G0311900 Rorug03G0312000 Rorug03G0312100 Rorug06G0133900 Rorug06G0133900 Rorug06G0133900 Rorug06G0134000
rosa_samantha	Rh4AG017400 Rh4BG012200 Rh4CG018600 Rh4DG013200 Rh6AG246600 Rh6BG248900 Rh6CG250000 Rh6DG241500
rosa_wichuraiana	Rw4G001120 Rw6G021350

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	1 cut(s)	202
AclWI	GGATC	1 cut(s)	223
AcsI	RAATTY	2 cut(s)	53, 443
AcuI	CTGAAG	2 cut(s)	243, 381
AfaI	GTAC	1 cut(s)	160
AfiI	CCNNNNNNNGG	1 cut(s)	446
AgsI	TTSAA	5 cut(s)	44, 182, 190, 269, 413
AhlI	ACTAGT	1 cut(s)	467
AluBI	AGCT	3 cut(s)	257, 304, 313
AluI	AGCT	3 cut(s)	257, 304, 313
Alw21I	GWGCWC	2 cut(s)	31, 51
Alw26I	GTCTC	2 cut(s)	383, 458
AlwI	GGATC	1 cut(s)	223
AoxI	GGCC	2 cut(s)	72, 251
ApoI	RAATTY	2 cut(s)	53, 443
AspS9I	GGNCC	1 cut(s)	72
Bbv12I	GWGCWC	2 cut(s)	31, 51
BccI	CCATC	1 cut(s)	416
BcoDI	GTCTC	2 cut(s)	383, 458
BcuI	ACTAGT	1 cut(s)	467
BfaI	CTAG	3 cut(s)	249, 305, 468
BmgT120I	GGNCC	1 cut(s)	72
BmiI	GGNNCC	1 cut(s)	73
BmsI	GCATC	2 cut(s)	356, 373
BsaI	GGTCTC	1 cut(s)	383
BsaJI	CCNNGG	1 cut(s)	214
Bsc4I	CCNNNNNNNGG	1 cut(s)	446
BseDI	CCNNGG	1 cut(s)	214
BseGI	GGATG	1 cut(s)	347
BseLI	CCNNNNNNNGG	1 cut(s)	446
BseRI	GAGGAG	1 cut(s)	324
Bsh1285I	CGRYCG	1 cut(s)	282
BshFI	GGCC	2 cut(s)	74, 253
BsiEI	CGRYCG	1 cut(s)	282
BsiHKAI	GWGCWC	2 cut(s)	31, 51
BslI	CCNNNNNNNGG	1 cut(s)	446
BsmAI	GTCTC	2 cut(s)	383, 458
BsnI	GGCC	2 cut(s)	74, 253
Bso31I	GGTCTC	1 cut(s)	383
Bsp1286I	GDGCHC	2 cut(s)	31, 51
Bsp143I	GATC	3 cut(s)	85, 228, 279
BspANI	GGCC	2 cut(s)	74, 253
BspLI	GGNNCC	1 cut(s)	73
BspPI	GGATC	1 cut(s)	223
BspTNI	GGTCTC	1 cut(s)	383
BssECI	CCNNGG	1 cut(s)	214
BssMI	GATC	3 cut(s)	85, 228, 279
BssT1I	CCWWGG	1 cut(s)	214
Bst4CI	ACNGT	1 cut(s)	343
Bst6I	CTCTTC	1 cut(s)	177
BstC8I	GCNNGC	1 cut(s)	255
BstF5I	GGATG	1 cut(s)	347
BstKTI	GATC	3 cut(s)	88, 231, 282
BstMAI	GTCTC	2 cut(s)	383, 458
BstMBI	GATC	3 cut(s)	85, 228, 279
BstMCI	CGRYCG	1 cut(s)	282
BstMWI	GCNNNNNNNGC	1 cut(s)	310
BstX2I	RGATCY	1 cut(s)	228
BstYI	RGATCY	1 cut(s)	228
BsuRI	GGCC	2 cut(s)	74, 253
BtsCI	GGATG	1 cut(s)	347
BtsIMutI	CAGTG	1 cut(s)	267
Cac8I	GCNNGC	1 cut(s)	255
Cfr13I	GGNCC	1 cut(s)	72
Csp6I	GTAC	1 cut(s)	159
CviAII	CATG	1 cut(s)	394
CviJI	RGCY	7 cut(s)	17, 74, 253, 257, 304, 313, 365
CviKI_1	RGCY	7 cut(s)	17, 74, 253, 257, 304, 313, 365
CviQI	GTAC	1 cut(s)	159
DpnI	GATC	3 cut(s)	87, 230, 281
DpnII	GATC	3 cut(s)	85, 228, 279
Eam1104I	CTCTTC	1 cut(s)	177
EarI	CTCTTC	1 cut(s)	177
Eco130I	CCWWGG	1 cut(s)	214
Eco31I	GGTCTC	1 cut(s)	383
Eco57I	CTGAAG	2 cut(s)	243, 381
EcoO109I	RGGNCCY	1 cut(s)	72
EcoRI	GAATTC	1 cut(s)	53
EcoT14I	CCWWGG	1 cut(s)	214
ErhI	CCWWGG	1 cut(s)	214
FaeI	CATG	1 cut(s)	397
FaiI	YATR	5 cut(s)	123, 210, 274, 276, 395
FatI	CATG	1 cut(s)	393
FblI	GTMKAC	1 cut(s)	202
FokI	GGATG	1 cut(s)	334
FspBI	CTAG	3 cut(s)	249, 305, 468
HaeIII	GGCC	2 cut(s)	74, 253
Hin1II	CATG	1 cut(s)	397
HinfI	GANTC	1 cut(s)	331
Hpy166II	GTNNAC	1 cut(s)	203
Hpy188I	TCNGA	2 cut(s)	26, 118
Hpy188III	TCNNGA	1 cut(s)	328
Hpy8I	GTNNAC	1 cut(s)	203
Hpy99I	CGWCG	1 cut(s)	347
HpyCH4III	ACNGT	1 cut(s)	343
HpyCH4IV	ACGT	1 cut(s)	399
HpyCH4V	TGCA	2 cut(s)	320, 386
HpyF10VI	GCNNNNNNNGC	1 cut(s)	310
HpySE526I	ACGT	1 cut(s)	399
Hsp92II	CATG	1 cut(s)	397
Kzo9I	GATC	3 cut(s)	85, 228, 279
LmnI	GCTCC	1 cut(s)	26
LpnPI	CCDG	6 cut(s)	141, 165, 267, 299, 372, 453
LweI	GCATC	2 cut(s)	356, 373
MaeI	CTAG	3 cut(s)	249, 305, 468
MaeII	ACGT	1 cut(s)	399
MaeIII	GTNAC	1 cut(s)	106
MalI	GATC	3 cut(s)	87, 230, 281
MboI	GATC	3 cut(s)	85, 228, 279
MboII	GAAGA	2 cut(s)	16, 194
MflI	RGATCY	1 cut(s)	228
MhlI	GDGCHC	2 cut(s)	31, 51
MluCI	AATT	4 cut(s)	37, 53, 408, 443
MlyI	GAGTC	1 cut(s)	325
MmeI	TCCRAC	2 cut(s)	4, 362
MnlI	CCTC	5 cut(s)	85, 242, 280, 316, 345
MseI	TTAA	1 cut(s)	243
MwoI	GCNNNNNNNGC	1 cut(s)	310
NdeII	GATC	3 cut(s)	85, 228, 279
NlaIII	CATG	1 cut(s)	397
NlaIV	GGNNCC	1 cut(s)	73
Ple19I	CGATCG	1 cut(s)	282
PleI	GAGTC	1 cut(s)	325
PpsI	GAGTC	1 cut(s)	325
PspN4I	GGNNCC	1 cut(s)	73
PspPI	GGNCC	1 cut(s)	72
PsuI	RGATCY	1 cut(s)	228
PvuI	CGATCG	1 cut(s)	282
RsaI	GTAC	1 cut(s)	160
RsaNI	GTAC	1 cut(s)	159
SaqAI	TTAA	1 cut(s)	243
Sau3AI	GATC	3 cut(s)	85, 228, 279
Sau96I	GGNCC	1 cut(s)	72
SchI	GAGTC	1 cut(s)	325
SduI	GDGCHC	2 cut(s)	31, 51
SetI	ASST	9 cut(s)	129, 216, 259, 306, 315, 327, 361, 402, 442
SfaNI	GCATC	2 cut(s)	356, 373
SpeI	ACTAGT	1 cut(s)	467
Sse9I	AATT	4 cut(s)	37, 53, 408, 443
SspI	AATATT	1 cut(s)	238
SspMI	CTAG	3 cut(s)	249, 305, 468
StyI	CCWWGG	1 cut(s)	214
TaaI	ACNGT	1 cut(s)	343
TaiI	ACGT	1 cut(s)	402
TaqI	TCGA	2 cut(s)	51, 132
TasI	AATT	4 cut(s)	37, 53, 408, 443
Tru1I	TTAA	1 cut(s)	243
Tru9I	TTAA	1 cut(s)	243
TscAI	CASTG	1 cut(s)	267
TspDTI	ATGAA	2 cut(s)	17, 410
TspRI	CASTG	1 cut(s)	267
XapI	RAATTY	2 cut(s)	53, 443
XmiI	GTMKAC	1 cut(s)	202
XspI	CTAG	3 cut(s)	249, 305, 468

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