Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1A

Orthogroup ID

OG0019856

Physical Location & Seq

Genomic Coordinates Forward (+)

6127609 .. 6130483

Gene Structure 2875 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1AG035000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 336 bp

ATGTCATCACGGACACACCCCTCATCCCCCAATTTCAAGTTTCAAGCAACGATAAACAAGATGAGCCAGATGGAAATTTTCCCTGCTGTTATTCCCCAAGCCACACAGATTTTTGTTAATGGCTGCTGGGTTGGCATACATTGTGATCCTGAAATTTTGGTGAGAACATTGAGGAAGCTAAGGTGGGTGGATGTCAATACTGAAGTTGGGGCCGTAAGAGATATCCATATGAAAGAATTGCAGATATATACCGATTATAGTCGTTGCAGTCATCCATTATTCATTGTGGACAAGCAAAGGCCGCTTATAAAGAACAAAGATATTCATGCATTGTAG

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:0005665 GO:0005737 GO:0005829 GO:0005911 GO:0006139 GO:0006396 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009506 GO:0009892 GO:0009987 GO:0010033 GO:0010467 GO:0010468 GO:0010605 GO:0010608 GO:0010629 GO:0014070 GO:0016070 GO:0016441 GO:0016458 GO:0016591 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019222 GO:0019438 GO:0030054 GO:0030880 GO:0031047 GO:0031050 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0034062 GO:0034641 GO:0034654 GO:0035194 GO:0035195 GO:0035196 GO:0040029 GO:0042221 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0043331 GO:0044237 GO:0044238 GO:0044249 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044451 GO:0044464 GO:0046483 GO:0048519 GO:0050789 GO:0050896 GO:0051716 GO:0055029 GO:0055044 GO:0060255 GO:0061695 GO:0065007 GO:0070013 GO:0070887 GO:0070918 GO:0071310 GO:0071359 GO:0071407 GO:0071704 GO:0090304 GO:0097747 GO:0140098 GO:1901360 GO:1901362 GO:1901576 GO:1901698 GO:1901699 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko05016 ko05169 map00230 map00240 map01100 map03020 map05016 map05169

Pfam Domains

Protein Families

RNA_pol_Rpb2_1 RNA_pol_Rpb2_2 RNA_pol_Rpb2_3 RNA_pol_Rpb2_4 RNA_pol_Rpb2_5 RNA_pol_Rpb2_6 RNA_pol_Rpb2_7

Protein Analysis

111

Amino Acids

12.86

Weight (kDa)

9.18

Isoelectric Point (pI)

58.34

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb2_4	PF04566	37 - 97	5.5e-17	RNA polymerase Rpb2, domain 4

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Orthologous Genes (Group: OG0019856)

Species	Orthologous Gene IDs
rosa_chinensis	RchiOBHm_Chr1g0318561
rosa_samantha	Rh1AG035000 Rh1CG328800 Rh1DG036300 Rh2CG296100 Rh2CG301100 Rh2DG333200

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	308
AciI	CCGC	1 cut(s)	302
AclWI	GGATC	1 cut(s)	140
AcsI	RAATTY	2 cut(s)	75, 153
AcuI	CTGAAG	1 cut(s)	222
AgsI	TTSAA	2 cut(s)	37, 44
AluBI	AGCT	1 cut(s)	178
AluI	AGCT	1 cut(s)	178
AlwI	GGATC	1 cut(s)	140
AoxI	GGCC	2 cut(s)	210, 299
ApeKI	GCWGC	1 cut(s)	123
ApoI	RAATTY	2 cut(s)	75, 153
AspS9I	GGNCC	1 cut(s)	210
AsuHPI	GGTGA	1 cut(s)	172
BbvI	GCAGC	1 cut(s)	110
BccI	CCATC	1 cut(s)	64
BceAI	ACGGC	1 cut(s)	197
BisI	GCNGC	2 cut(s)	124, 302
BlsI	GCNGC	2 cut(s)	125, 303
BmgT120I	GGNCC	1 cut(s)	210
BmiI	GGNNCC	1 cut(s)	211
Bpu10I	CCTNAGC	1 cut(s)	179
BseGI	GGATG	3 cut(s)	23, 196, 271
BseXI	GCAGC	1 cut(s)	110
BseYI	CCCAGC	1 cut(s)	126
BshFI	GGCC	2 cut(s)	212, 301
BsnI	GGCC	2 cut(s)	212, 301
Bsp143I	GATC	1 cut(s)	145
BspACI	CCGC	1 cut(s)	302
BspANI	GGCC	2 cut(s)	212, 301
BspLI	GGNNCC	1 cut(s)	211
BspPI	GGATC	1 cut(s)	140
BssMI	GATC	1 cut(s)	145
BstDEI	CTNAG	1 cut(s)	179
BstF5I	GGATG	3 cut(s)	23, 196, 271
BstKTI	GATC	1 cut(s)	148
BstMBI	GATC	1 cut(s)	145
BstMWI	GCNNNNNNNGC	2 cut(s)	132, 301
BstV1I	GCAGC	1 cut(s)	110
BsuRI	GGCC	2 cut(s)	212, 301
BtsCI	GGATG	3 cut(s)	23, 196, 271
Cfr13I	GGNCC	1 cut(s)	210
CviAII	CATG	1 cut(s)	326
CviJI	RGCY	6 cut(s)	66, 101, 123, 178, 212, 301
CviKI_1	RGCY	6 cut(s)	66, 101, 123, 178, 212, 301
DdeI	CTNAG	1 cut(s)	179
DpnI	GATC	1 cut(s)	147
DpnII	GATC	1 cut(s)	145
Eco32I	GATATC	1 cut(s)	223
Eco57I	CTGAAG	1 cut(s)	222
EcoRV	GATATC	1 cut(s)	223
EcoT22I	ATGCAT	1 cut(s)	331
FaeI	CATG	1 cut(s)	329
FaiI	YATR	8 cut(s)	137, 228, 230, 247, 249, 258, 308, 327
FatI	CATG	1 cut(s)	325
FauNDI	CATATG	1 cut(s)	228
Fnu4HI	GCNGC	2 cut(s)	124, 302
FokI	GGATG	3 cut(s)	10, 203, 258
Fsp4HI	GCNGC	2 cut(s)	124, 302
GluI	GCNGC	2 cut(s)	124, 302
GsaI	CCCAGC	1 cut(s)	130
HaeIII	GGCC	2 cut(s)	212, 301
Hin1II	CATG	1 cut(s)	329
HphI	GGTGA	1 cut(s)	172
Hpy166II	GTNNAC	1 cut(s)	289
Hpy188III	TCNNGA	1 cut(s)	149
Hpy8I	GTNNAC	1 cut(s)	289
HpyCH4V	TGCA	3 cut(s)	241, 267, 329
HpyF10VI	GCNNNNNNNGC	2 cut(s)	132, 301
HpyF3I	CTNAG	1 cut(s)	179
Hsp92II	CATG	1 cut(s)	329
Kzo9I	GATC	1 cut(s)	145
LpnPI	CCDG	4 cut(s)	80, 96, 112, 162
Lsp1109I	GCAGC	1 cut(s)	110
MalI	GATC	1 cut(s)	147
MboI	GATC	1 cut(s)	145
MluCI	AATT	4 cut(s)	31, 75, 153, 236
MnlI	CCTC	2 cut(s)	31, 165
Mph1103I	ATGCAT	1 cut(s)	331
MseI	TTAA	1 cut(s)	117
MwoI	GCNNNNNNNGC	2 cut(s)	132, 301
NdeI	CATATG	1 cut(s)	228
NdeII	GATC	1 cut(s)	145
NlaIII	CATG	1 cut(s)	329
NlaIV	GGNNCC	1 cut(s)	211
NsiI	ATGCAT	1 cut(s)	331
PkrI	GCNGC	2 cut(s)	125, 303
PsiI	TTATAA	1 cut(s)	308
PspFI	CCCAGC	1 cut(s)	126
PspN4I	GGNNCC	1 cut(s)	211
PspPI	GGNCC	1 cut(s)	210
SaqAI	TTAA	1 cut(s)	117
SatI	GCNGC	2 cut(s)	124, 302
Sau3AI	GATC	1 cut(s)	145
Sau96I	GGNCC	1 cut(s)	210
SetI	ASST	2 cut(s)	180, 185
Sse9I	AATT	4 cut(s)	31, 75, 153, 236
SsiI	CCGC	1 cut(s)	302
TasI	AATT	4 cut(s)	31, 75, 153, 236
TauI	GCSGC	1 cut(s)	304
Tru1I	TTAA	1 cut(s)	117
Tru9I	TTAA	1 cut(s)	117
TseI	GCWGC	1 cut(s)	123
TspDTI	ATGAA	3 cut(s)	245, 271, 314
TspGWI	ACGGA	1 cut(s)	25
XapI	RAATTY	2 cut(s)	75, 153
Zsp2I	ATGCAT	1 cut(s)	331

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