Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6B

Orthogroup ID

OG0001390

Physical Location & Seq

Genomic Coordinates Reverse (-)

46033668 .. 46038919

Gene Structure 5252 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6BG248900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 456 bp

ATGTCGGAGCACTTGGACAATTTTGAAGTGCTCGAATTCCTAAAATCTAAAGGGGCCTCAAAGAATGATCTATCACGGGTGGCAAGAGTTACACAATCAGAGTATAAGGTTTTCGATTATTTGGTTGATACTCCTGCTGGTACTCACACAAGAGAGAGTGTTGAAGAGTTCAAGGAGAAGTGTAGACAATATGACCTTGGGAATGATAAGATCCTCAATATTATTAACACTAGGCCAGCTTCAGTGGTTGAAATATATGCGATCGTGGAGGATAATGCTGATGAGCTAGTAGAGCTGGTTGCAGAGGTCTTGACTCCTCCAACTGTACCATCCCCTAAACCTGAAGCTGATACTAATGAGATTGATGCAGAGACCATGAACGTGGAACAAATTGAACAAAATGATGGCAATAAAGAAAAACCTGAATTTGGGGAAGCACCAATGGAGACTAGTTGA

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

151

Amino Acids

16.98

Weight (kDa)

4.35

Isoelectric Point (pI)

39.59

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb4	PF03874	5 - 94	2.5e-10	RNA polymerase Rpb4

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: 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)	184
AclWI	GGATC	1 cut(s)	205
AcsI	RAATTY	2 cut(s)	35, 425
AcuI	CTGAAG	2 cut(s)	225, 363
AfaI	GTAC	2 cut(s)	142, 327
AfiI	CCNNNNNNNGG	1 cut(s)	428
AgsI	TTSAA	5 cut(s)	26, 164, 172, 251, 395
AhlI	ACTAGT	1 cut(s)	449
AluBI	AGCT	4 cut(s)	239, 286, 295, 347
AluI	AGCT	4 cut(s)	239, 286, 295, 347
Alw21I	GWGCWC	2 cut(s)	12, 33
Alw26I	GTCTC	2 cut(s)	365, 440
AlwI	GGATC	1 cut(s)	205
AoxI	GGCC	2 cut(s)	54, 233
ApoI	RAATTY	2 cut(s)	35, 425
AspS9I	GGNCC	1 cut(s)	54
Bbv12I	GWGCWC	2 cut(s)	12, 33
BccI	CCATC	2 cut(s)	337, 398
BcoDI	GTCTC	2 cut(s)	365, 440
BcuI	ACTAGT	1 cut(s)	449
BfaI	CTAG	3 cut(s)	231, 287, 450
BmgT120I	GGNCC	1 cut(s)	54
BmiI	GGNNCC	1 cut(s)	55
BmsI	GCATC	1 cut(s)	355
BsaI	GGTCTC	1 cut(s)	365
BsaJI	CCNNGG	1 cut(s)	196
Bsc4I	CCNNNNNNNGG	1 cut(s)	428
BseDI	CCNNGG	1 cut(s)	196
BseGI	GGATG	1 cut(s)	329
BseLI	CCNNNNNNNGG	1 cut(s)	428
BseRI	GAGGAG	1 cut(s)	306
Bsh1285I	CGRYCG	1 cut(s)	264
BshFI	GGCC	2 cut(s)	56, 235
BsiEI	CGRYCG	1 cut(s)	264
BsiHKAI	GWGCWC	2 cut(s)	12, 33
BslI	CCNNNNNNNGG	1 cut(s)	428
BsmAI	GTCTC	2 cut(s)	365, 440
BsnI	GGCC	2 cut(s)	56, 235
Bso31I	GGTCTC	1 cut(s)	365
Bsp1286I	GDGCHC	2 cut(s)	12, 33
Bsp143I	GATC	3 cut(s)	67, 210, 261
BspANI	GGCC	2 cut(s)	56, 235
BspLI	GGNNCC	1 cut(s)	55
BspPI	GGATC	1 cut(s)	205
BspTNI	GGTCTC	1 cut(s)	365
BssECI	CCNNGG	1 cut(s)	196
BssMI	GATC	3 cut(s)	67, 210, 261
BssT1I	CCWWGG	1 cut(s)	196
Bst4CI	ACNGT	1 cut(s)	325
Bst6I	CTCTTC	1 cut(s)	159
BstC8I	GCNNGC	1 cut(s)	237
BstF5I	GGATG	1 cut(s)	329
BstKTI	GATC	3 cut(s)	70, 213, 264
BstMAI	GTCTC	2 cut(s)	365, 440
BstMBI	GATC	3 cut(s)	67, 210, 261
BstMCI	CGRYCG	1 cut(s)	264
BstMWI	GCNNNNNNNGC	1 cut(s)	292
BstX2I	RGATCY	1 cut(s)	210
BstXI	CCANNNNNNTGG	1 cut(s)	382
BstYI	RGATCY	1 cut(s)	210
BsuRI	GGCC	2 cut(s)	56, 235
BtsCI	GGATG	1 cut(s)	329
BtsIMutI	CAGTG	1 cut(s)	249
Cac8I	GCNNGC	1 cut(s)	237
Cfr13I	GGNCC	1 cut(s)	54
Csp6I	GTAC	2 cut(s)	141, 326
CviAII	CATG	1 cut(s)	376
CviJI	RGCY	6 cut(s)	56, 235, 239, 286, 295, 347
CviKI_1	RGCY	6 cut(s)	56, 235, 239, 286, 295, 347
CviQI	GTAC	2 cut(s)	141, 326
DpnI	GATC	3 cut(s)	69, 212, 263
DpnII	GATC	3 cut(s)	67, 210, 261
Eam1104I	CTCTTC	1 cut(s)	159
EarI	CTCTTC	1 cut(s)	159
Eco130I	CCWWGG	1 cut(s)	196
Eco31I	GGTCTC	1 cut(s)	365
Eco57I	CTGAAG	2 cut(s)	225, 363
EcoO109I	RGGNCCY	1 cut(s)	54
EcoRI	GAATTC	1 cut(s)	35
EcoT14I	CCWWGG	1 cut(s)	196
ErhI	CCWWGG	1 cut(s)	196
FaeI	CATG	1 cut(s)	379
FaiI	YATR	5 cut(s)	105, 192, 256, 258, 377
FatI	CATG	1 cut(s)	375
FblI	GTMKAC	1 cut(s)	184
FokI	GGATG	1 cut(s)	316
FspBI	CTAG	3 cut(s)	231, 287, 450
HaeIII	GGCC	2 cut(s)	56, 235
Hin1II	CATG	1 cut(s)	379
HinfI	GANTC	1 cut(s)	313
Hpy166II	GTNNAC	1 cut(s)	185
Hpy188I	TCNGA	2 cut(s)	7, 100
Hpy188III	TCNNGA	1 cut(s)	310
Hpy8I	GTNNAC	1 cut(s)	185
HpyCH4III	ACNGT	1 cut(s)	325
HpyCH4IV	ACGT	1 cut(s)	381
HpyCH4V	TGCA	2 cut(s)	302, 368
HpyF10VI	GCNNNNNNNGC	1 cut(s)	292
HpySE526I	ACGT	1 cut(s)	381
Hsp92II	CATG	1 cut(s)	379
Kzo9I	GATC	3 cut(s)	67, 210, 261
LmnI	GCTCC	1 cut(s)	7
LpnPI	CCDG	6 cut(s)	123, 147, 249, 281, 354, 435
LweI	GCATC	1 cut(s)	355
MaeI	CTAG	3 cut(s)	231, 287, 450
MaeII	ACGT	1 cut(s)	381
MaeIII	GTNAC	1 cut(s)	88
MalI	GATC	3 cut(s)	69, 212, 263
MboI	GATC	3 cut(s)	67, 210, 261
MboII	GAAGA	1 cut(s)	176
MflI	RGATCY	1 cut(s)	210
MhlI	GDGCHC	2 cut(s)	12, 33
MluCI	AATT	4 cut(s)	19, 35, 390, 425
MlyI	GAGTC	1 cut(s)	307
MmeI	TCCRAC	1 cut(s)	344
MnlI	CCTC	5 cut(s)	67, 224, 262, 298, 327
MseI	TTAA	1 cut(s)	225
MslI	CAYNNNNRTG	1 cut(s)	380
MwoI	GCNNNNNNNGC	1 cut(s)	292
NdeII	GATC	3 cut(s)	67, 210, 261
NlaIII	CATG	1 cut(s)	379
NlaIV	GGNNCC	1 cut(s)	55
Ple19I	CGATCG	1 cut(s)	264
PleI	GAGTC	1 cut(s)	307
PpsI	GAGTC	1 cut(s)	307
PspN4I	GGNNCC	1 cut(s)	55
PspPI	GGNCC	1 cut(s)	54
PsuI	RGATCY	1 cut(s)	210
PvuI	CGATCG	1 cut(s)	264
RsaI	GTAC	2 cut(s)	142, 327
RsaNI	GTAC	2 cut(s)	141, 326
RseI	CAYNNNNRTG	1 cut(s)	380
SaqAI	TTAA	1 cut(s)	225
Sau3AI	GATC	3 cut(s)	67, 210, 261
Sau96I	GGNCC	1 cut(s)	54
SchI	GAGTC	1 cut(s)	307
SduI	GDGCHC	2 cut(s)	12, 33
SfaNI	GCATC	1 cut(s)	355
SmiMI	CAYNNNNRTG	1 cut(s)	380
SpeI	ACTAGT	1 cut(s)	449
Sse9I	AATT	4 cut(s)	19, 35, 390, 425
SspI	AATATT	1 cut(s)	220
SspMI	CTAG	3 cut(s)	231, 287, 450
StyI	CCWWGG	1 cut(s)	196
TaaI	ACNGT	1 cut(s)	325
TaiI	ACGT	1 cut(s)	384
TaqI	TCGA	2 cut(s)	33, 114
TasI	AATT	4 cut(s)	19, 35, 390, 425
Tru1I	TTAA	1 cut(s)	225
Tru9I	TTAA	1 cut(s)	225
TscAI	CASTG	1 cut(s)	249
TspDTI	ATGAA	1 cut(s)	392
TspRI	CASTG	1 cut(s)	249
XapI	RAATTY	2 cut(s)	35, 425
XmiI	GTMKAC	1 cut(s)	184
XspI	CTAG	3 cut(s)	231, 287, 450

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