Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6D

Orthogroup ID

OG0001390

Physical Location & Seq

Genomic Coordinates Reverse (-)

42854225 .. 42855608

Gene Structure 1384 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6DG241500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 480 bp

ATGAAGATACTAAAGGCTGATGTCGGAGCACTTGACAATTTTGAAGTGCTCGAATTCCTAAAATCTAAAGGGGCCTCAAAGAATGATCTATCACGGGTGGCAAGAGTTACACAATCAGAGTATAAGGTTTTCGATTATTTGGTTGATACTCCTGCTGGTACTCACACAAGAGAGAGTGTTGAAGAGTTCAAGGAGAAGTGTAGACAATATGACCTTGGGAATGATAAGATCCTCAATATTATTAACACTAGGCCAGCTTCAGTGGTTGAAATATATGCGATCGTGGAGGATAATGCTGATGAGCTAGTAGAGCTGGTTGCAGAGGTCTTGACTCCTCCAACTGTACCATCCCCTAAACCTGAAGCCGATACTAATGAGATTGATGCAGAGACCATGAACGTGGAACAAATTGAACAAAATGATGGCAATAAAGAAAAACCTGAATTTGGGGAAGCACCAATGGAGCCGTTAAATATATGA

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

159

Amino Acids

17.77

Weight (kDa)

4.39

Isoelectric Point (pI)

37.11

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb4	PF03874	11 - 100	1.9e-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)	202
AclWI	GGATC	1 cut(s)	223
AcsI	RAATTY	2 cut(s)	53, 443
AcuI	CTGAAG	2 cut(s)	243, 381
AfaI	GTAC	2 cut(s)	160, 345
AfiI	CCNNNNNNNGG	1 cut(s)	446
AgsI	TTSAA	5 cut(s)	44, 182, 190, 269, 413
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	1 cut(s)	383
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	2 cut(s)	355, 416
BceAI	ACGGC	1 cut(s)	451
BcoDI	GTCTC	1 cut(s)	383
BfaI	CTAG	2 cut(s)	249, 305
BmgT120I	GGNCC	1 cut(s)	72
BmiI	GGNNCC	2 cut(s)	73, 465
BmsI	GCATC	1 cut(s)	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	1 cut(s)	383
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	2 cut(s)	73, 465
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	1 cut(s)	383
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
BstXI	CCANNNNNNTGG	1 cut(s)	400
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	2 cut(s)	159, 344
CviAII	CATG	1 cut(s)	394
CviJI	RGCY	8 cut(s)	17, 74, 253, 257, 304, 313, 365, 466
CviKI_1	RGCY	8 cut(s)	17, 74, 253, 257, 304, 313, 365, 466
CviQI	GTAC	2 cut(s)	159, 344
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	7 cut(s)	123, 210, 274, 276, 395, 476, 478
FatI	CATG	1 cut(s)	393
FblI	GTMKAC	1 cut(s)	202
FokI	GGATG	1 cut(s)	334
FspBI	CTAG	2 cut(s)	249, 305
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
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	2 cut(s)	26, 463
LpnPI	CCDG	6 cut(s)	141, 165, 267, 299, 372, 453
LweI	GCATC	1 cut(s)	373
MaeI	CTAG	2 cut(s)	249, 305
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	2 cut(s)	243, 470
MslI	CAYNNNNRTG	1 cut(s)	398
MwoI	GCNNNNNNNGC	1 cut(s)	310
NdeII	GATC	3 cut(s)	85, 228, 279
NlaIII	CATG	1 cut(s)	397
NlaIV	GGNNCC	2 cut(s)	73, 465
Ple19I	CGATCG	1 cut(s)	282
PleI	GAGTC	1 cut(s)	325
PpsI	GAGTC	1 cut(s)	325
PspN4I	GGNNCC	2 cut(s)	73, 465
PspPI	GGNCC	1 cut(s)	72
PsuI	RGATCY	1 cut(s)	228
PvuI	CGATCG	1 cut(s)	282
RsaI	GTAC	2 cut(s)	160, 345
RsaNI	GTAC	2 cut(s)	159, 344
RseI	CAYNNNNRTG	1 cut(s)	398
SaqAI	TTAA	2 cut(s)	243, 470
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	1 cut(s)	373
SmiMI	CAYNNNNRTG	1 cut(s)	398
Sse9I	AATT	4 cut(s)	37, 53, 408, 443
SspI	AATATT	1 cut(s)	238
SspMI	CTAG	2 cut(s)	249, 305
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	2 cut(s)	243, 470
Tru9I	TTAA	2 cut(s)	243, 470
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	2 cut(s)	249, 305

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