Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6A

Orthogroup ID

OG0009411

Physical Location & Seq

Genomic Coordinates Reverse (-)

17436398 .. 17437102

Gene Structure 705 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6AG115800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 351 bp

ATGAATGCCCCAGACCGATATGAGCGATTTGTTGTCCCTGAAGGGACAAAAAAGGTGTCGTATGAGAGGGATACGAAGATCATAAATGCTGCATCGTTTACAATTGAGAGAGAGGATCACACTATTGGCAACATCCTTCGCATGCAGCTGCACCGGGATGAAAGTGTTTTATTTGCTGGCTACAAGCTTCCTCACCCACTTCAGTACAAGATCATTGTCAGGATTCACACAACCAGCCAGTCATCACCAATGCAGGCATATAACCAGGCTATTAATGATCTTGACAAGGAACTTGACCTTTTGAAGAGTAATTTTGAGGTAATGTTATTTGATGTTCCTCCTTCAAATTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000418 GO:0000419 GO:0000428 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005665 GO:0016591 GO:0030880 GO:0031974 GO:0031981 GO:0032991 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044464 GO:0055029 GO:0061695 GO:0070013 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_L_2

Protein Analysis

116

Amino Acids

13.45

Weight (kDa)

6.05

Isoelectric Point (pI)

33.47

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_L_2	PF13656	31 - 103	1.7e-27	RNA polymerase Rpb3/Rpb11 dimerisation domain
RNA_pol_L	PF01193	33 - 97	1.8e-07	RNA polymerase Rpb3/Rpb11 dimerisation domain

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)

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Orthologous Genes (Group: OG0009411)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G52090 AT3G52090
fragaria_vesca	FvH4_2g07830
malus_domestica	MD05G1071600.v1.1 MD10G1083600.v1.1
prunus_persica	Prupe.8G106600_v2.0.a1 Prupe.8G106600_v2.0.a1
pyrus_communis	pycom05g06170 pycom10g06570
rosa_chinensis	RchiOBHm_Chr6g0262241
rosa_multiflora	Rmu_sc0002510.1_g000027 Rmu_sc0010083.1_g000004
rosa_roxburghii	Rroxscaffold_7G00207930
rosa_rugosa	Rorug05G0595600 Rorug05G0595700 Rorug05G0595700
rosa_samantha	Rh2AG296400 Rh2DG320300 Rh6AG115800 Rh6BG110100 Rh6DG098100
rosa_wichuraiana	Rw6G010080

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AclWI	GGATC	1 cut(s)	123
AcuI	CTGAAG	2 cut(s)	60, 185
AfaI	GTAC	1 cut(s)	206
AgsI	TTSAA	2 cut(s)	304, 345
AjnI	CCWGG	1 cut(s)	264
AluBI	AGCT	2 cut(s)	148, 187
AluI	AGCT	2 cut(s)	148, 187
AlwI	GGATC	1 cut(s)	123
ApeKI	GCWGC	3 cut(s)	89, 145, 148
ArsI	GACNNNNNNTTYG	2 cut(s)	41, 73
AseI	ATTAAT	1 cut(s)	273
AsuC2I	CCSGG	1 cut(s)	155
AsuHPI	GGTGA	2 cut(s)	185, 237
BbvI	GCAGC	3 cut(s)	76, 135, 157
BciT130I	CCWGG	1 cut(s)	266
BciVI	GTATCC	1 cut(s)	64
BcnI	CCSGG	1 cut(s)	155
BfuI	GTATCC	1 cut(s)	64
BisI	GCNGC	3 cut(s)	90, 146, 149
BlsI	GCNGC	3 cut(s)	91, 147, 150
Bme1390I	CCNGG	2 cut(s)	155, 266
BmrFI	CCNGG	2 cut(s)	155, 266
BmsI	GCATC	1 cut(s)	101
BpuMI	CCSGG	1 cut(s)	155
Bse1I	ACTGG	1 cut(s)	238
BseBI	CCWGG	1 cut(s)	266
BseGI	GGATG	2 cut(s)	132, 163
BseNI	ACTGG	1 cut(s)	238
BseXI	GCAGC	3 cut(s)	76, 135, 157
BsgI	GTGCAG	1 cut(s)	134
BsiSI	CCGG	1 cut(s)	154
BslFI	GGGAC	2 cut(s)	20, 58
BsmFI	GGGAC	2 cut(s)	20, 58
BsmI	GAATGC	1 cut(s)	10
Bsp143I	GATC	4 cut(s)	78, 115, 210, 277
BspPI	GGATC	1 cut(s)	123
BsrI	ACTGG	1 cut(s)	238
BssMI	GATC	4 cut(s)	78, 115, 210, 277
Bst2UI	CCWGG	1 cut(s)	266
Bst6I	CTCTTC	1 cut(s)	299
BstC8I	GCNNGC	3 cut(s)	143, 178, 255
BstF5I	GGATG	2 cut(s)	132, 163
BstKTI	GATC	4 cut(s)	81, 118, 213, 280
BstMBI	GATC	4 cut(s)	78, 115, 210, 277
BstNI	CCWGG	1 cut(s)	266
BstNSI	RCATGY	1 cut(s)	145
BstSCI	CCNGG	2 cut(s)	153, 264
BstV1I	GCAGC	3 cut(s)	76, 135, 157
BsuI	GTATCC	1 cut(s)	64
BtsCI	GGATG	2 cut(s)	132, 163
Cac8I	GCNNGC	3 cut(s)	143, 178, 255
Csp6I	GTAC	1 cut(s)	205
CviAII	CATG	1 cut(s)	142
CviJI	RGCY	5 cut(s)	148, 180, 187, 237, 269
CviKI_1	RGCY	5 cut(s)	148, 180, 187, 237, 269
CviQI	GTAC	1 cut(s)	205
DpnI	GATC	4 cut(s)	80, 117, 212, 279
DpnII	GATC	4 cut(s)	78, 115, 210, 277
Eam1104I	CTCTTC	1 cut(s)	299
EarI	CTCTTC	1 cut(s)	299
Eco57I	CTGAAG	2 cut(s)	60, 185
EcoRII	CCWGG	1 cut(s)	264
FaeI	CATG	1 cut(s)	145
FaiI	YATR	6 cut(s)	21, 63, 83, 143, 259, 261
FaqI	GGGAC	2 cut(s)	20, 58
FatI	CATG	1 cut(s)	141
Fnu4HI	GCNGC	3 cut(s)	90, 146, 149
FokI	GGATG	2 cut(s)	119, 170
Fsp4HI	GCNGC	3 cut(s)	90, 146, 149
GluI	GCNGC	3 cut(s)	90, 146, 149
HapII	CCGG	1 cut(s)	154
Hin1II	CATG	1 cut(s)	145
HindIII	AAGCTT	1 cut(s)	185
HinfI	GANTC	1 cut(s)	223
HpaII	CCGG	1 cut(s)	154
HphI	GGTGA	2 cut(s)	185, 237
Hpy166II	GTNNAC	1 cut(s)	99
Hpy188III	TCNNGA	2 cut(s)	220, 281
Hpy8I	GTNNAC	1 cut(s)	99
HpyAV	CCTTC	3 cut(s)	35, 146, 351
HpyCH4V	TGCA	4 cut(s)	92, 145, 151, 253
Hsp92II	CATG	1 cut(s)	145
Kzo9I	GATC	4 cut(s)	78, 115, 210, 277
Lsp1109I	GCAGC	3 cut(s)	76, 135, 157
LweI	GCATC	1 cut(s)	101
MalI	GATC	4 cut(s)	80, 117, 212, 279
MboI	GATC	4 cut(s)	78, 115, 210, 277
MboII	GAAGA	2 cut(s)	88, 316
MfeI	CAATTG	1 cut(s)	102
MluCI	AATT	3 cut(s)	102, 310, 346
MnlI	CCTC	5 cut(s)	60, 106, 201, 310, 348
MseI	TTAA	1 cut(s)	273
MslI	CAYNNNNRTG	1 cut(s)	156
MspA1I	CMGCKG	1 cut(s)	148
MspI	CCGG	1 cut(s)	154
MspR9I	CCNGG	2 cut(s)	155, 266
MunI	CAATTG	1 cut(s)	102
Mva1269I	GAATGC	1 cut(s)	10
MvaI	CCWGG	1 cut(s)	266
NciI	CCSGG	1 cut(s)	155
NdeII	GATC	4 cut(s)	78, 115, 210, 277
NlaIII	CATG	1 cut(s)	145
NspI	RCATGY	1 cut(s)	145
PaeI	GCATGC	1 cut(s)	145
PctI	GAATGC	1 cut(s)	10
PfeI	GAWTC	1 cut(s)	223
PkrI	GCNGC	3 cut(s)	91, 147, 150
PshBI	ATTAAT	1 cut(s)	273
Psp6I	CCWGG	1 cut(s)	264
PspGI	CCWGG	1 cut(s)	264
PvuII	CAGCTG	1 cut(s)	148
RsaI	GTAC	1 cut(s)	206
RsaNI	GTAC	1 cut(s)	205
RseI	CAYNNNNRTG	1 cut(s)	156
SaqAI	TTAA	1 cut(s)	273
SatI	GCNGC	3 cut(s)	90, 146, 149
Sau3AI	GATC	4 cut(s)	78, 115, 210, 277
ScrFI	CCNGG	2 cut(s)	155, 266
SetI	ASST	5 cut(s)	57, 150, 189, 300, 321
SfaNI	GCATC	1 cut(s)	101
SmiMI	CAYNNNNRTG	1 cut(s)	156
SphI	GCATGC	1 cut(s)	145
Sse9I	AATT	3 cut(s)	102, 310, 346
StyD4I	CCNGG	2 cut(s)	153, 264
TaqII	GACCGA	1 cut(s)	30
TasI	AATT	3 cut(s)	102, 310, 346
TatI	WGTACW	1 cut(s)	204
TfiI	GAWTC	1 cut(s)	223
Tru1I	TTAA	1 cut(s)	273
Tru9I	TTAA	1 cut(s)	273
TseI	GCWGC	3 cut(s)	89, 145, 148
TspDTI	ATGAA	2 cut(s)	17, 174
VspI	ATTAAT	1 cut(s)	273
XceI	RCATGY	1 cut(s)	145

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