Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1B

Orthogroup ID

OG0005329

Physical Location & Seq

Genomic Coordinates Reverse (-)

3463872 .. 3464939

Gene Structure 1068 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1BG026000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 462 bp

ATGGCAAAAATCAAAAAAGCTAAAAATTCCTTCAACCAAAGATTTCACAGGCTGCCTAGTCACGAAGAAATTGCTGAAATGGTAAATATGCAAGCCTCAACTGTAAGACTTGTTTGTGAGAGGAGCAGACTCCCTCTTTCATTGGATCGAGTGGTGACTGATCAAGGTTGCATGGCACTCCAGGATATCCTAAGAGGGCCGGATGAGATGATGCCAGAAACGATGCTTGGAAAACAGCTAATGAAGCAAGAGCTGGAGAAGCTTCTAAAGACGTTGAGTGATAGAGAAGCAAATGTATTGAGATTACACTTTGGACTAAATGGAGAGACCCCTCAGTCCTTTGAGGAGATAGGAAGATTGTTAGAACTTTCAAGGGAGAGGGTTCGACAGATCAACGGCATTGCATTATCAAAATTAAAGCAGACAAGTACTATGGACAATCTAAAATTGTATATTGTATAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000988 GO:0000990 GO:0003674 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0006139 GO:0006351 GO:0006352 GO:0006355 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009314 GO:0009416 GO:0009507 GO:0009536 GO:0009628 GO:0009889 GO:0009987 GO:0010467 GO:0010468 GO:0010556 GO:0016070 GO:0016987 GO:0018130 GO:0019219 GO:0019222 GO:0019438 GO:0031323 GO:0031326 GO:0032774 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043254 GO:0044087 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044424 GO:0044444 GO:0044464 GO:0046483 GO:0050789 GO:0050794 GO:0050896 GO:0051128 GO:0051171 GO:0051252 GO:0051716 GO:0060255 GO:0065007 GO:0071214 GO:0071478 GO:0071482 GO:0071704 GO:0080090 GO:0090304 GO:0097659 GO:0104004 GO:0140110 GO:1901360 GO:1901362 GO:1901576 GO:1903506 GO:2000112 GO:2000142 GO:2001141

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

Sigma70_r2 Sigma70_r3 Sigma70_r4

Protein Analysis

153

Amino Acids

17.61

Weight (kDa)

9.23

Isoelectric Point (pI)

39.08

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Sigma70_r3	PF04539	3 - 74	5.8e-13	Sigma-70 region 3
Sigma70_r4	PF04545	88 - 141	9.8e-14	Sigma-70, region 4

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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Orthologous Genes (Group: OG0005329)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G13730
fragaria_vesca	FvH4_7g01630
malus_domestica	MD02G1302300.v1.1 MD07G1021800.v1.1
prunus_persica	Prupe.2G021900_v2.0.a1 Prupe.2G021900_v2.0.a1 Prupe.2G021900_v2.0.a1 Prupe.2G021900_v2.0.a1 Prupe.2G021900_v2.0.a1 Prupe.2G021900_v2.0.a1 Prupe.2G021900_v2.0.a1 Prupe.2G021900_v2.0.a1 Prupe.2G021900_v2.0.a1 Prupe.2G021900_v2.0.a1
pyrus_communis	pycom02g25460 pycom07g01650
rosa_chinensis	RchiOBHm_Chr1g0317901
rosa_laevigata	RLG00000029590 RLG00000030578
rosa_multiflora	Rmu_sc0000654.1_g000054 Rmu_ssc0000008.1_g000049
rosa_roxburghii	Rroxscaffold_4G00330140
rosa_rugosa	Rorug01G0018500
rosa_samantha	Rh1AG030000 Rh1BG026000 Rh1BG026100 Rh1CG028600 Rh1DG041500
rosa_wichuraiana	Rw1G002260

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AasI	GACNNNNNNGTC	1 cut(s)	334
AclWI	GGATC	1 cut(s)	153
AcsI	RAATTY	1 cut(s)	25
AfaI	GTAC	1 cut(s)	430
AgsI	TTSAA	2 cut(s)	34, 372
AjnI	CCWGG	1 cut(s)	180
AjuI	GAANNNNNNNTTGG	2 cut(s)	210, 242
AluBI	AGCT	4 cut(s)	20, 238, 253, 262
AluI	AGCT	4 cut(s)	20, 238, 253, 262
Alw26I	GTCTC	1 cut(s)	320
AlwI	GGATC	1 cut(s)	153
AoxI	GGCC	1 cut(s)	197
ApeKI	GCWGC	1 cut(s)	52
ApoI	RAATTY	1 cut(s)	25
AspS9I	GGNCC	1 cut(s)	197
AsuHPI	GGTGA	1 cut(s)	166
BbvI	GCAGC	1 cut(s)	39
BceAI	ACGGC	1 cut(s)	412
BcgI	CGANNNNNNTGC	2 cut(s)	53, 87
BciT130I	CCWGG	1 cut(s)	182
BclI	TGATCA	1 cut(s)	160
BcoDI	GTCTC	1 cut(s)	320
BfaI	CTAG	1 cut(s)	57
BisI	GCNGC	1 cut(s)	53
BlsI	GCNGC	1 cut(s)	54
BmcAI	AGTACT	1 cut(s)	430
Bme1390I	CCNGG	1 cut(s)	182
BmgT120I	GGNCC	1 cut(s)	197
BmrFI	CCNGG	1 cut(s)	182
BmsI	GCATC	2 cut(s)	201, 213
BpmI	CTGGAG	2 cut(s)	164, 275
BsaI	GGTCTC	1 cut(s)	320
Bse3DI	GCAATG	1 cut(s)	399
BseBI	CCWGG	1 cut(s)	182
BseGI	GGATG	1 cut(s)	208
BseMI	GCAATG	1 cut(s)	399
BseMII	CTCAG	1 cut(s)	347
BseRI	GAGGAG	2 cut(s)	136, 359
BseXI	GCAGC	1 cut(s)	39
BshFI	GGCC	1 cut(s)	199
BsiSI	CCGG	1 cut(s)	200
BsmAI	GTCTC	1 cut(s)	320
BsnI	GGCC	1 cut(s)	199
Bso31I	GGTCTC	1 cut(s)	320
Bsp143I	GATC	3 cut(s)	145, 160, 390
BspANI	GGCC	1 cut(s)	199
BspCNI	CTCAG	1 cut(s)	346
BspPI	GGATC	1 cut(s)	153
BspTNI	GGTCTC	1 cut(s)	320
BsrDI	GCAATG	1 cut(s)	399
BssMI	GATC	3 cut(s)	145, 160, 390
Bst2UI	CCWGG	1 cut(s)	182
Bst4CI	ACNGT	1 cut(s)	103
BstC8I	GCNNGC	1 cut(s)	93
BstDEI	CTNAG	2 cut(s)	191, 333
BstF5I	GGATG	1 cut(s)	208
BstKTI	GATC	3 cut(s)	148, 163, 393
BstMAI	GTCTC	1 cut(s)	320
BstMBI	GATC	3 cut(s)	145, 160, 390
BstMWI	GCNNNNNNNGC	2 cut(s)	244, 259
BstNI	CCWGG	1 cut(s)	182
BstSCI	CCNGG	1 cut(s)	180
BstV1I	GCAGC	1 cut(s)	39
BsuRI	GGCC	1 cut(s)	199
BtsCI	GGATG	1 cut(s)	208
Cac8I	GCNNGC	1 cut(s)	93
Cfr13I	GGNCC	1 cut(s)	197
Csp6I	GTAC	1 cut(s)	429
CviAII	CATG	1 cut(s)	172
CviJI	RGCY	7 cut(s)	20, 52, 95, 199, 238, 253, 262
CviKI_1	RGCY	7 cut(s)	20, 52, 95, 199, 238, 253, 262
CviQI	GTAC	1 cut(s)	429
DdeI	CTNAG	2 cut(s)	191, 333
DpnI	GATC	3 cut(s)	147, 162, 392
DpnII	GATC	3 cut(s)	145, 160, 390
DrdI	GACNNNNNNGTC	1 cut(s)	334
DseDI	GACNNNNNNGTC	1 cut(s)	334
Eco31I	GGTCTC	1 cut(s)	320
Eco32I	GATATC	1 cut(s)	187
EcoRII	CCWGG	1 cut(s)	180
EcoRV	GATATC	1 cut(s)	187
FaeI	CATG	1 cut(s)	175
FaiI	YATR	5 cut(s)	89, 173, 434, 453, 460
FatI	CATG	1 cut(s)	171
FbaI	TGATCA	1 cut(s)	160
Fnu4HI	GCNGC	1 cut(s)	53
FokI	GGATG	1 cut(s)	215
Fsp4HI	GCNGC	1 cut(s)	53
FspBI	CTAG	1 cut(s)	57
GluI	GCNGC	1 cut(s)	53
GsuI	CTGGAG	2 cut(s)	164, 275
HaeIII	GGCC	1 cut(s)	199
HapII	CCGG	1 cut(s)	200
Hin1II	CATG	1 cut(s)	175
HindIII	AAGCTT	1 cut(s)	260
HinfI	GANTC	1 cut(s)	129
HpaII	CCGG	1 cut(s)	200
HphI	GGTGA	1 cut(s)	166
Hpy188III	TCNNGA	1 cut(s)	62
HpyAV	CCTTC	1 cut(s)	40
HpyCH4III	ACNGT	1 cut(s)	103
HpyCH4IV	ACGT	1 cut(s)	272
HpyCH4V	TGCA	3 cut(s)	91, 171, 404
HpyF10VI	GCNNNNNNNGC	2 cut(s)	244, 259
HpyF3I	CTNAG	2 cut(s)	191, 333
HpySE526I	ACGT	1 cut(s)	272
Hsp92II	CATG	1 cut(s)	175
Ksp22I	TGATCA	1 cut(s)	160
Kzo9I	GATC	3 cut(s)	145, 160, 390
LmnI	GCTCC	1 cut(s)	123
LpnPI	CCDG	6 cut(s)	34, 167, 194, 213, 228, 239
Lsp1109I	GCAGC	1 cut(s)	39
LweI	GCATC	2 cut(s)	201, 213
MaeI	CTAG	1 cut(s)	57
MaeII	ACGT	1 cut(s)	272
MaeIII	GTNAC	2 cut(s)	59, 154
MalI	GATC	3 cut(s)	147, 162, 392
MboI	GATC	3 cut(s)	145, 160, 390
MboII	GAAGA	2 cut(s)	77, 366
MluCI	AATT	4 cut(s)	25, 69, 413, 446
MlyI	GAGTC	1 cut(s)	123
MnlI	CCTC	7 cut(s)	106, 114, 144, 188, 337, 342, 372
MseI	TTAA	1 cut(s)	416
MspI	CCGG	1 cut(s)	200
MspR9I	CCNGG	1 cut(s)	182
MvaI	CCWGG	1 cut(s)	182
MwoI	GCNNNNNNNGC	2 cut(s)	244, 259
NdeII	GATC	3 cut(s)	145, 160, 390
NlaIII	CATG	1 cut(s)	175
NmuCI	GTSAC	2 cut(s)	59, 154
PfoI	TCCNGGA	1 cut(s)	180
PkrI	GCNGC	1 cut(s)	54
PleI	GAGTC	1 cut(s)	123
PpsI	GAGTC	1 cut(s)	123
Psp6I	CCWGG	1 cut(s)	180
PspGI	CCWGG	1 cut(s)	180
PspPI	GGNCC	1 cut(s)	197
RsaI	GTAC	1 cut(s)	430
RsaNI	GTAC	1 cut(s)	429
SaqAI	TTAA	1 cut(s)	416
SatI	GCNGC	1 cut(s)	53
Sau3AI	GATC	3 cut(s)	145, 160, 390
Sau96I	GGNCC	1 cut(s)	197
ScaI	AGTACT	1 cut(s)	430
SchI	GAGTC	1 cut(s)	123
ScrFI	CCNGG	1 cut(s)	182
SetI	ASST	6 cut(s)	22, 169, 240, 255, 264, 275
SfaNI	GCATC	2 cut(s)	201, 213
Sse9I	AATT	4 cut(s)	25, 69, 413, 446
SspMI	CTAG	1 cut(s)	57
StyD4I	CCNGG	1 cut(s)	180
TaaI	ACNGT	1 cut(s)	103
TaiI	ACGT	1 cut(s)	275
TaqI	TCGA	2 cut(s)	148, 385
TasI	AATT	4 cut(s)	25, 69, 413, 446
TatI	WGTACW	1 cut(s)	428
Tru1I	TTAA	1 cut(s)	416
Tru9I	TTAA	1 cut(s)	416
TseFI	GTSAC	2 cut(s)	59, 154
TseI	GCWGC	1 cut(s)	52
Tsp45I	GTSAC	2 cut(s)	59, 154
TspDTI	ATGAA	2 cut(s)	129, 257
XapI	RAATTY	1 cut(s)	25
XspI	CTAG	1 cut(s)	57
ZrmI	AGTACT	1 cut(s)	430

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