Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000007

Orthogroup ID

OG0001390

Physical Location & Seq

Genomic Coordinates Forward (+)

27132478 .. 27135403

Gene Structure 2926 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_7G00187720.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 495 bp

ATGCTCGAAACACTCGCGATAGAAGGCCAACTAAAGGCTGATGTCAGAGCACTTGACAATTTTGAAGTGCTCGAATTCCTAAAATCTAAAGGGGCCTCAAAGAATGATCTATCACGGGTGGCAAGAGTTACACAATCAGAGTATAAGGTTTTCGATTATTTGGTTGATACTCCTGCTGGCACTCACACAAGAGAGAGTGTTGAAGAGTTCAAGGAGAAGTGTAGACAATATGACCTTGGGAATGATAAGATCCTCAATATTATTAACACTAGGCCAGCTTCAGTGGTTGAAATATATGCGATCGTGGAGGATAATGCTGATGAGCTAGTAGAGCTGGTTGCAGAGGTCTTGACTCCTCCAACTGTACCATCCCCTAAACCTGAAGCTGATACTAATGAGATTGATGCAGAGACCATGAACGTGGAACAAATTGAACAAAATGATGGCAATAAAGAAAAACCTGAATTTGGGGAAGCACCAATGGAGACTAGTTGA

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

164

Amino Acids

18.33

Weight (kDa)

4.35

Isoelectric Point (pI)

35.49

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb4	PF03874	18 - 107	2.1e-10	RNA polymerase Rpb4

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

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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)	223
AccII	CGCG	1 cut(s)	17
AclWI	GGATC	1 cut(s)	244
AcsI	RAATTY	2 cut(s)	74, 464
AcuI	CTGAAG	2 cut(s)	264, 402
AfaI	GTAC	1 cut(s)	366
AfiI	CCNNNNNNNGG	2 cut(s)	34, 467
AgsI	TTSAA	5 cut(s)	65, 203, 211, 290, 434
AhlI	ACTAGT	1 cut(s)	488
AluBI	AGCT	4 cut(s)	278, 325, 334, 386
AluI	AGCT	4 cut(s)	278, 325, 334, 386
Alw21I	GWGCWC	2 cut(s)	52, 72
Alw26I	GTCTC	2 cut(s)	404, 479
AlwI	GGATC	1 cut(s)	244
AoxI	GGCC	3 cut(s)	25, 93, 272
ApoI	RAATTY	2 cut(s)	74, 464
AspS9I	GGNCC	1 cut(s)	93
Bbv12I	GWGCWC	2 cut(s)	52, 72
BccI	CCATC	2 cut(s)	376, 437
BcoDI	GTCTC	2 cut(s)	404, 479
BcuI	ACTAGT	1 cut(s)	488
BfaI	CTAG	3 cut(s)	270, 326, 489
BmgT120I	GGNCC	1 cut(s)	93
BmiI	GGNNCC	1 cut(s)	94
BmsI	GCATC	1 cut(s)	394
BsaI	GGTCTC	1 cut(s)	404
BsaJI	CCNNGG	1 cut(s)	235
Bsc4I	CCNNNNNNNGG	2 cut(s)	34, 467
BseDI	CCNNGG	1 cut(s)	235
BseGI	GGATG	1 cut(s)	368
BseLI	CCNNNNNNNGG	2 cut(s)	34, 467
BseRI	GAGGAG	1 cut(s)	345
Bsh1236I	CGCG	1 cut(s)	17
Bsh1285I	CGRYCG	1 cut(s)	303
BshFI	GGCC	3 cut(s)	27, 95, 274
BsiEI	CGRYCG	1 cut(s)	303
BsiHKAI	GWGCWC	2 cut(s)	52, 72
BslI	CCNNNNNNNGG	2 cut(s)	34, 467
BsmAI	GTCTC	2 cut(s)	404, 479
BsnI	GGCC	3 cut(s)	27, 95, 274
Bso31I	GGTCTC	1 cut(s)	404
Bsp1286I	GDGCHC	2 cut(s)	52, 72
Bsp143I	GATC	3 cut(s)	106, 249, 300
Bsp68I	TCGCGA	1 cut(s)	17
BspANI	GGCC	3 cut(s)	27, 95, 274
BspFNI	CGCG	1 cut(s)	17
BspLI	GGNNCC	1 cut(s)	94
BspPI	GGATC	1 cut(s)	244
BspTNI	GGTCTC	1 cut(s)	404
BssECI	CCNNGG	1 cut(s)	235
BssMI	GATC	3 cut(s)	106, 249, 300
BssT1I	CCWWGG	1 cut(s)	235
Bst4CI	ACNGT	1 cut(s)	364
Bst6I	CTCTTC	1 cut(s)	198
BstC8I	GCNNGC	2 cut(s)	178, 276
BstF5I	GGATG	1 cut(s)	368
BstFNI	CGCG	1 cut(s)	17
BstKTI	GATC	3 cut(s)	109, 252, 303
BstMAI	GTCTC	2 cut(s)	404, 479
BstMBI	GATC	3 cut(s)	106, 249, 300
BstMCI	CGRYCG	1 cut(s)	303
BstMWI	GCNNNNNNNGC	1 cut(s)	331
BstUI	CGCG	1 cut(s)	17
BstX2I	RGATCY	1 cut(s)	249
BstXI	CCANNNNNNTGG	1 cut(s)	421
BstYI	RGATCY	1 cut(s)	249
BsuRI	GGCC	3 cut(s)	27, 95, 274
BtsCI	GGATG	1 cut(s)	368
BtsIMutI	CAGTG	1 cut(s)	288
BtuMI	TCGCGA	1 cut(s)	17
Cac8I	GCNNGC	2 cut(s)	178, 276
Cfr13I	GGNCC	1 cut(s)	93
Csp6I	GTAC	1 cut(s)	365
CviAII	CATG	1 cut(s)	415
CviJI	RGCY	8 cut(s)	27, 38, 95, 274, 278, 325, 334, 386
CviKI_1	RGCY	8 cut(s)	27, 38, 95, 274, 278, 325, 334, 386
CviQI	GTAC	1 cut(s)	365
DpnI	GATC	3 cut(s)	108, 251, 302
DpnII	GATC	3 cut(s)	106, 249, 300
Eam1104I	CTCTTC	1 cut(s)	198
EarI	CTCTTC	1 cut(s)	198
Eco130I	CCWWGG	1 cut(s)	235
Eco31I	GGTCTC	1 cut(s)	404
Eco57I	CTGAAG	2 cut(s)	264, 402
EcoO109I	RGGNCCY	1 cut(s)	93
EcoRI	GAATTC	1 cut(s)	74
EcoT14I	CCWWGG	1 cut(s)	235
ErhI	CCWWGG	1 cut(s)	235
FaeI	CATG	1 cut(s)	418
FaiI	YATR	5 cut(s)	144, 231, 295, 297, 416
FatI	CATG	1 cut(s)	414
FblI	GTMKAC	1 cut(s)	223
FokI	GGATG	1 cut(s)	355
FspBI	CTAG	3 cut(s)	270, 326, 489
HaeIII	GGCC	3 cut(s)	27, 95, 274
Hin1II	CATG	1 cut(s)	418
HinfI	GANTC	1 cut(s)	352
Hpy166II	GTNNAC	1 cut(s)	224
Hpy188I	TCNGA	2 cut(s)	47, 139
Hpy188III	TCNNGA	2 cut(s)	16, 349
Hpy8I	GTNNAC	1 cut(s)	224
HpyAV	CCTTC	1 cut(s)	17
HpyCH4III	ACNGT	1 cut(s)	364
HpyCH4IV	ACGT	1 cut(s)	420
HpyCH4V	TGCA	2 cut(s)	341, 407
HpyF10VI	GCNNNNNNNGC	1 cut(s)	331
HpySE526I	ACGT	1 cut(s)	420
Hsp92II	CATG	1 cut(s)	418
Kzo9I	GATC	3 cut(s)	106, 249, 300
LpnPI	CCDG	6 cut(s)	162, 186, 288, 320, 393, 474
LweI	GCATC	1 cut(s)	394
MaeI	CTAG	3 cut(s)	270, 326, 489
MaeII	ACGT	1 cut(s)	420
MaeIII	GTNAC	1 cut(s)	127
MalI	GATC	3 cut(s)	108, 251, 302
MboI	GATC	3 cut(s)	106, 249, 300
MboII	GAAGA	1 cut(s)	215
MflI	RGATCY	1 cut(s)	249
MhlI	GDGCHC	2 cut(s)	52, 72
MluCI	AATT	4 cut(s)	58, 74, 429, 464
MlyI	GAGTC	1 cut(s)	346
MmeI	TCCRAC	1 cut(s)	383
MnlI	CCTC	5 cut(s)	106, 263, 301, 337, 366
MseI	TTAA	1 cut(s)	264
MslI	CAYNNNNRTG	1 cut(s)	419
MvnI	CGCG	1 cut(s)	17
MwoI	GCNNNNNNNGC	1 cut(s)	331
NdeII	GATC	3 cut(s)	106, 249, 300
NlaIII	CATG	1 cut(s)	418
NlaIV	GGNNCC	1 cut(s)	94
NruI	TCGCGA	1 cut(s)	17
Ple19I	CGATCG	1 cut(s)	303
PleI	GAGTC	1 cut(s)	346
PpsI	GAGTC	1 cut(s)	346
PspN4I	GGNNCC	1 cut(s)	94
PspPI	GGNCC	1 cut(s)	93
PsuI	RGATCY	1 cut(s)	249
PvuI	CGATCG	1 cut(s)	303
RruI	TCGCGA	1 cut(s)	17
RsaI	GTAC	1 cut(s)	366
RsaNI	GTAC	1 cut(s)	365
RseI	CAYNNNNRTG	1 cut(s)	419
SaqAI	TTAA	1 cut(s)	264
Sau3AI	GATC	3 cut(s)	106, 249, 300
Sau96I	GGNCC	1 cut(s)	93
SchI	GAGTC	1 cut(s)	346
SduI	GDGCHC	2 cut(s)	52, 72
SfaNI	GCATC	1 cut(s)	394
SmiMI	CAYNNNNRTG	1 cut(s)	419
SpeI	ACTAGT	1 cut(s)	488
Sse9I	AATT	4 cut(s)	58, 74, 429, 464
SspI	AATATT	1 cut(s)	259
SspMI	CTAG	3 cut(s)	270, 326, 489
StyI	CCWWGG	1 cut(s)	235
TaaI	ACNGT	1 cut(s)	364
TaiI	ACGT	1 cut(s)	423
TaqI	TCGA	3 cut(s)	6, 72, 153
TasI	AATT	4 cut(s)	58, 74, 429, 464
Tru1I	TTAA	1 cut(s)	264
Tru9I	TTAA	1 cut(s)	264
TscAI	CASTG	1 cut(s)	288
TspDTI	ATGAA	1 cut(s)	431
TspRI	CASTG	1 cut(s)	288
XapI	RAATTY	2 cut(s)	74, 464
XmiI	GTMKAC	1 cut(s)	223
XspI	CTAG	3 cut(s)	270, 326, 489

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