Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4D

Orthogroup ID

OG0001390

Physical Location & Seq

Genomic Coordinates Forward (+)

2063770 .. 2069410

Gene Structure 5641 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4DG013200.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 390 bp

ATGAAGATACTAAAGGCTGATGTCGGAGCACTTGACAATTTTGAAGTGCTCGAATTCCTAAAATCTAAAGGGGCCTCAAAGAATGATCTATCACGGGTGGCAAGAGTTACACAATCGGAGTATAAGGTTTTTGATTATTTGGTTGATACTCCTGCTGGTACTCACACAAGAGAGAGTGTTGAAGAGTTCAAGGAGAAGTGTAGACAATATGACCTTGGGAATGATAAGATCCTCAATATTATTAACACTAGGCCAGCTTCAGTGGTTGAAATATATGCGGTGTGTTATTACTATTTGCTTCTACTTCGCTGTTCATCATTATGTGAGCTTTTCTCTGTGTTTTTTCGTTTTTTCCTTAAATTCATAATCTTGTATCATCTCTCCTGGTGA

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

129

Amino Acids

15.07

Weight (kDa)

7.63

Isoelectric Point (pI)

29.22

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb4	PF03874	11 - 94	1.4e-08	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

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
AciI	CCGC	1 cut(s)	278
AclWI	GGATC	1 cut(s)	223
AcsI	RAATTY	2 cut(s)	53, 359
AcuI	CTGAAG	1 cut(s)	243
AfaI	GTAC	1 cut(s)	160
AgsI	TTSAA	4 cut(s)	44, 182, 190, 269
AjnI	CCWGG	1 cut(s)	383
AluBI	AGCT	2 cut(s)	257, 328
AluI	AGCT	2 cut(s)	257, 328
Alw21I	GWGCWC	2 cut(s)	31, 51
AlwI	GGATC	1 cut(s)	223
AoxI	GGCC	2 cut(s)	72, 251
ApoI	RAATTY	2 cut(s)	53, 359
AspS9I	GGNCC	1 cut(s)	72
Bbv12I	GWGCWC	2 cut(s)	31, 51
BciT130I	CCWGG	1 cut(s)	385
BfaI	CTAG	1 cut(s)	249
Bme1390I	CCNGG	1 cut(s)	385
BmgT120I	GGNCC	1 cut(s)	72
BmiI	GGNNCC	1 cut(s)	73
BmrFI	CCNGG	1 cut(s)	385
BplI	GAGNNNNNCTC	2 cut(s)	317, 349
BsaJI	CCNNGG	1 cut(s)	214
BseBI	CCWGG	1 cut(s)	385
BseDI	CCNNGG	1 cut(s)	214
BshFI	GGCC	2 cut(s)	74, 253
BsiHKAI	GWGCWC	2 cut(s)	31, 51
BsnI	GGCC	2 cut(s)	74, 253
Bsp1286I	GDGCHC	2 cut(s)	31, 51
Bsp143I	GATC	2 cut(s)	85, 228
BspACI	CCGC	1 cut(s)	278
BspANI	GGCC	2 cut(s)	74, 253
BspLI	GGNNCC	1 cut(s)	73
BspPI	GGATC	1 cut(s)	223
BssECI	CCNNGG	1 cut(s)	214
BssMI	GATC	2 cut(s)	85, 228
BssT1I	CCWWGG	1 cut(s)	214
Bst2UI	CCWGG	1 cut(s)	385
Bst6I	CTCTTC	1 cut(s)	177
BstC8I	GCNNGC	1 cut(s)	255
BstKTI	GATC	2 cut(s)	88, 231
BstMBI	GATC	2 cut(s)	85, 228
BstNI	CCWGG	1 cut(s)	385
BstSCI	CCNGG	1 cut(s)	383
BstX2I	RGATCY	1 cut(s)	228
BstYI	RGATCY	1 cut(s)	228
BsuRI	GGCC	2 cut(s)	74, 253
BtsIMutI	CAGTG	1 cut(s)	267
Cac8I	GCNNGC	1 cut(s)	255
Cfr13I	GGNCC	1 cut(s)	72
Csp6I	GTAC	1 cut(s)	159
CviJI	RGCY	5 cut(s)	17, 74, 253, 257, 328
CviKI_1	RGCY	5 cut(s)	17, 74, 253, 257, 328
CviQI	GTAC	1 cut(s)	159
DpnI	GATC	2 cut(s)	87, 230
DpnII	GATC	2 cut(s)	85, 228
Eam1104I	CTCTTC	1 cut(s)	177
EarI	CTCTTC	1 cut(s)	177
Eco130I	CCWWGG	1 cut(s)	214
Eco57I	CTGAAG	1 cut(s)	243
EcoO109I	RGGNCCY	1 cut(s)	72
EcoRI	GAATTC	1 cut(s)	53
EcoRII	CCWGG	1 cut(s)	383
EcoT14I	CCWWGG	1 cut(s)	214
ErhI	CCWWGG	1 cut(s)	214
FaiI	YATR	6 cut(s)	123, 210, 274, 276, 322, 365
FblI	GTMKAC	1 cut(s)	202
FspBI	CTAG	1 cut(s)	249
HaeIII	GGCC	2 cut(s)	74, 253
Hpy166II	GTNNAC	1 cut(s)	203
Hpy188I	TCNGA	2 cut(s)	26, 118
Hpy8I	GTNNAC	1 cut(s)	203
Kzo9I	GATC	2 cut(s)	85, 228
LmnI	GCTCC	1 cut(s)	26
LpnPI	CCDG	4 cut(s)	141, 165, 267, 370
MaeI	CTAG	1 cut(s)	249
MaeIII	GTNAC	1 cut(s)	106
MalI	GATC	2 cut(s)	87, 230
MboI	GATC	2 cut(s)	85, 228
MboII	GAAGA	2 cut(s)	16, 194
MflI	RGATCY	1 cut(s)	228
MhlI	GDGCHC	2 cut(s)	31, 51
MluCI	AATT	3 cut(s)	37, 53, 359
MmeI	TCCRAC	1 cut(s)	4
MnlI	CCTC	2 cut(s)	85, 242
MseI	TTAA	2 cut(s)	243, 357
MslI	CAYNNNNRTG	1 cut(s)	319
MspR9I	CCNGG	1 cut(s)	385
MvaI	CCWGG	1 cut(s)	385
NdeII	GATC	2 cut(s)	85, 228
NlaIV	GGNNCC	1 cut(s)	73
Psp6I	CCWGG	1 cut(s)	383
PspGI	CCWGG	1 cut(s)	383
PspN4I	GGNNCC	1 cut(s)	73
PspPI	GGNCC	1 cut(s)	72
PsuI	RGATCY	1 cut(s)	228
RsaI	GTAC	1 cut(s)	160
RsaNI	GTAC	1 cut(s)	159
RseI	CAYNNNNRTG	1 cut(s)	319
SaqAI	TTAA	2 cut(s)	243, 357
Sau3AI	GATC	2 cut(s)	85, 228
Sau96I	GGNCC	1 cut(s)	72
ScrFI	CCNGG	1 cut(s)	385
SduI	GDGCHC	2 cut(s)	31, 51
SetI	ASST	4 cut(s)	129, 216, 259, 330
SmiMI	CAYNNNNRTG	1 cut(s)	319
Sse9I	AATT	3 cut(s)	37, 53, 359
SsiI	CCGC	1 cut(s)	278
SspI	AATATT	1 cut(s)	238
SspMI	CTAG	1 cut(s)	249
StyD4I	CCNGG	1 cut(s)	383
StyI	CCWWGG	1 cut(s)	214
TaqI	TCGA	1 cut(s)	51
TasI	AATT	3 cut(s)	37, 53, 359
Tru1I	TTAA	2 cut(s)	243, 357
Tru9I	TTAA	2 cut(s)	243, 357
TscAI	CASTG	1 cut(s)	267
TspDTI	ATGAA	3 cut(s)	17, 303, 352
TspRI	CASTG	1 cut(s)	267
XapI	RAATTY	2 cut(s)	53, 359
XmiI	GTMKAC	1 cut(s)	202
XspI	CTAG	1 cut(s)	249

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