Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5B

Orthogroup ID

OG0003104

Physical Location & Seq

Genomic Coordinates Reverse (-)

5273268 .. 5275481

Gene Structure 2214 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5BG063700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 336 bp

ATGGATCTCAAATCCTGCCTTGTTGTGCTCCTCGTGGCCTTAGCCATGGTGGCCGCAGTAGAGTCCTCAAAGATCCAAGATGCCGCCTGGGGTCTCAAACACCGCTACAACAATGTGGGTGACATGATCGGAGAAGAAACTGAGATGTTACTGGACTCCGAGGCCGGCCGGCGTCAACTTTACCAAGGCCGTTACATTAGCTACGAGGCCCTTAAGAAAAACAACATACCGTGTGGCCAGCGCGGCAGATCCTACTATGACTGCAATAACAGACAGCAGATGAATTCTTACCGCCGAGGTTGTTCTTACATTACTCGATGCGCCCGCGGTGATTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0001558 GO:0003674 GO:0005102 GO:0005179 GO:0005488 GO:0005515 GO:0005575 GO:0005576 GO:0005623 GO:0005911 GO:0007154 GO:0007165 GO:0007267 GO:0008150 GO:0009506 GO:0009966 GO:0009987 GO:0010469 GO:0010646 GO:0010769 GO:0019722 GO:0019932 GO:0022603 GO:0022604 GO:0023051 GO:0023052 GO:0030054 GO:0030545 GO:0035556 GO:0040008 GO:0042995 GO:0043900 GO:0044464 GO:0045595 GO:0048018 GO:0048046 GO:0048583 GO:0048638 GO:0050789 GO:0050793 GO:0050794 GO:0050896 GO:0051128 GO:0051239 GO:0051510 GO:0051716 GO:0055044 GO:0060284 GO:0065007 GO:0065009 GO:0080092 GO:0090406 GO:0098772 GO:0120025 GO:2000241

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

RALF

Protein Analysis

111

Amino Acids

12.65

Weight (kDa)

8.87

Isoelectric Point (pI)

42.39

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RALF	PF05498	48 - 109	7.8e-24	Rapid ALkalinization Factor (RALF)

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)

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Publication-ready

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Orthologous Genes (Group: OG0003104)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G28270 AT2G33775 AT3G05490
fragaria_vesca	FvH4_3g09010 FvH4_3g09020
malus_domestica	MD00G1116200.v1.1 MD10G1292800.v1.1 MD10G1292900.v1.1
prunus_persica	Prupe.4G049000_v2.0.a1
pyrus_communis	pycom05g28940 pycom10g24490
rosa_chinensis	RchiOBHm_Chr5g0008651 RchiOBHm_Chr5g0008661 RchiOBHm_Chr5g0008671
rosa_laevigata	RLG00000031590 RLG00000031591 RLG00000031592
rosa_multiflora	Rmu_sc0001665.1_g000030 Rmu_sc0001665.1_g000031 Rmu_sc0001665.1_g000040
rosa_roxburghii	Rroxscaffold_1G00067890 Rroxscaffold_1G00067900 Rroxscaffold_1G00067910
rosa_rugosa	Rorug04G0437700 Rorug04G0437700 Rorug04G0437700
rosa_samantha	Rh5AG066300 Rh5BG063600 Rh5BG063700 Rh5CG073800 Rh5CG073900 Rh5CG074100 Rh5DG062500 Rh5DG062600
rosa_wichuraiana	Rw5G006230 Rw5G006260 Rw5G006270

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccII	CGCG	2 cut(s)	243, 327
AciI	CCGC	7 cut(s)	54, 84, 103, 243, 292, 325, 327
AclWI	GGATC	3 cut(s)	12, 67, 243
AcoI	YGGCCR	3 cut(s)	51, 166, 235
AcsI	RAATTY	1 cut(s)	283
AcyI	GRCGYC	1 cut(s)	172
AflII	CTTAAG	1 cut(s)	212
AjnI	CCWGG	1 cut(s)	86
AluBI	AGCT	1 cut(s)	201
AluI	AGCT	1 cut(s)	201
Alw21I	GWGCWC	1 cut(s)	30
Alw26I	GTCTC	1 cut(s)	98
AlwI	GGATC	3 cut(s)	12, 67, 243
AoxI	GGCC	7 cut(s)	36, 51, 162, 166, 187, 207, 235
ApoI	RAATTY	1 cut(s)	283
AspLEI	GCGC	2 cut(s)	243, 323
AspS9I	GGNCC	1 cut(s)	208
AsuHPI	GGTGA	1 cut(s)	131
BalI	TGGCCA	1 cut(s)	237
BauI	CACGAG	1 cut(s)	32
Bbv12I	GWGCWC	1 cut(s)	30
BceAI	ACGGC	1 cut(s)	174
BciT130I	CCWGG	1 cut(s)	88
BcoDI	GTCTC	1 cut(s)	98
BfrI	CTTAAG	1 cut(s)	212
BglI	GCCNNNNNGGC	2 cut(s)	50, 243
BisI	GCNGC	3 cut(s)	54, 84, 244
BlsI	GCNGC	3 cut(s)	55, 85, 245
Bme1390I	CCNGG	1 cut(s)	88
BmgT120I	GGNCC	1 cut(s)	208
BmrFI	CCNGG	1 cut(s)	88
BmsI	GCATC	2 cut(s)	70, 308
Bpu10I	CCTNAGC	1 cut(s)	40
BsaHI	GRCGYC	1 cut(s)	172
BsaI	GGTCTC	1 cut(s)	98
BsaJI	CCNNGG	6 cut(s)	45, 87, 159, 184, 295, 325
Bse118I	RCCGGY	2 cut(s)	164, 168
Bse1I	ACTGG	1 cut(s)	156
BseBI	CCWGG	1 cut(s)	88
BseDI	CCNNGG	6 cut(s)	45, 87, 159, 184, 295, 325
BseMII	CTCAG	1 cut(s)	132
BseNI	ACTGG	1 cut(s)	156
BseRI	GAGGAG	1 cut(s)	20
BseX3I	CGGCCG	1 cut(s)	166
Bsh1236I	CGCG	2 cut(s)	243, 327
Bsh1285I	CGRYCG	1 cut(s)	169
BshFI	GGCC	7 cut(s)	38, 53, 164, 168, 189, 209, 237
BsiEI	CGRYCG	1 cut(s)	169
BsiHKAI	GWGCWC	1 cut(s)	30
BsiSI	CCGG	2 cut(s)	165, 169
BsmAI	GTCTC	1 cut(s)	98
BsnI	GGCC	7 cut(s)	38, 53, 164, 168, 189, 209, 237
Bso31I	GGTCTC	1 cut(s)	98
Bsp1286I	GDGCHC	1 cut(s)	30
Bsp143I	GATC	4 cut(s)	4, 72, 126, 248
Bsp19I	CCATGG	1 cut(s)	45
BspACI	CCGC	7 cut(s)	54, 84, 103, 243, 292, 325, 327
BspANI	GGCC	7 cut(s)	38, 53, 164, 168, 189, 209, 237
BspCNI	CTCAG	1 cut(s)	133
BspFNI	CGCG	2 cut(s)	243, 327
BspPI	GGATC	3 cut(s)	12, 67, 243
BspTI	CTTAAG	1 cut(s)	212
BspTNI	GGTCTC	1 cut(s)	98
BsrFI	RCCGGY	2 cut(s)	164, 168
BsrI	ACTGG	1 cut(s)	156
BssAI	RCCGGY	2 cut(s)	164, 168
BssECI	CCNNGG	6 cut(s)	45, 87, 159, 184, 295, 325
BssMI	GATC	4 cut(s)	4, 72, 126, 248
BssNI	GRCGYC	1 cut(s)	172
BssSI	CACGAG	1 cut(s)	32
BssT1I	CCWWGG	2 cut(s)	45, 184
Bst2BI	CACGAG	1 cut(s)	32
Bst2UI	CCWGG	1 cut(s)	88
Bst4CI	ACNGT	1 cut(s)	231
BstACI	GRCGYC	1 cut(s)	172
BstAFI	CTTAAG	1 cut(s)	212
BstC8I	GCNNGC	4 cut(s)	166, 170, 239, 325
BstDEI	CTNAG	2 cut(s)	40, 141
BstDSI	CCRYGG	2 cut(s)	45, 325
BstFNI	CGCG	2 cut(s)	243, 327
BstHHI	GCGC	2 cut(s)	243, 323
BstKTI	GATC	4 cut(s)	7, 75, 129, 251
BstMAI	GTCTC	1 cut(s)	98
BstMBI	GATC	4 cut(s)	4, 72, 126, 248
BstMCI	CGRYCG	1 cut(s)	169
BstMWI	GCNNNNNNNGC	2 cut(s)	50, 243
BstNI	CCWGG	1 cut(s)	88
BstSCI	CCNGG	1 cut(s)	86
BstUI	CGCG	2 cut(s)	243, 327
BstX2I	RGATCY	3 cut(s)	4, 72, 248
BstYI	RGATCY	3 cut(s)	4, 72, 248
BstZI	CGGCCG	1 cut(s)	166
BsuRI	GGCC	7 cut(s)	38, 53, 164, 168, 189, 209, 237
BtgI	CCRYGG	2 cut(s)	45, 325
Cac8I	GCNNGC	4 cut(s)	166, 170, 239, 325
CfoI	GCGC	2 cut(s)	243, 323
Cfr10I	RCCGGY	2 cut(s)	164, 168
Cfr13I	GGNCC	1 cut(s)	208
Cfr42I	CCGCGG	1 cut(s)	328
CseI	GACGC	1 cut(s)	161
CviAII	CATG	2 cut(s)	46, 124
CviJI	RGCY	9 cut(s)	38, 44, 53, 164, 168, 189, 201, 209, 237
CviKI_1	RGCY	9 cut(s)	38, 44, 53, 164, 168, 189, 201, 209, 237
DdeI	CTNAG	2 cut(s)	40, 141
DpnI	GATC	4 cut(s)	6, 74, 128, 250
DpnII	GATC	4 cut(s)	4, 72, 126, 248
EaeI	YGGCCR	3 cut(s)	51, 166, 235
EagI	CGGCCG	1 cut(s)	166
EclXI	CGGCCG	1 cut(s)	166
Eco130I	CCWWGG	2 cut(s)	45, 184
Eco31I	GGTCTC	1 cut(s)	98
Eco52I	CGGCCG	1 cut(s)	166
EcoO109I	RGGNCCY	1 cut(s)	208
EcoRI	GAATTC	1 cut(s)	283
EcoRII	CCWGG	1 cut(s)	86
EcoT14I	CCWWGG	2 cut(s)	45, 184
ErhI	CCWWGG	2 cut(s)	45, 184
FaeI	CATG	2 cut(s)	49, 127
FaiI	YATR	4 cut(s)	47, 125, 227, 258
FatI	CATG	2 cut(s)	45, 123
FauI	CCCGC	1 cut(s)	332
Fnu4HI	GCNGC	3 cut(s)	54, 84, 244
FseI	GGCCGGCC	1 cut(s)	168
Fsp4HI	GCNGC	3 cut(s)	54, 84, 244
GlaI	GCGC	2 cut(s)	242, 322
GluI	GCNGC	3 cut(s)	54, 84, 244
HaeIII	GGCC	7 cut(s)	38, 53, 164, 168, 189, 209, 237
HapII	CCGG	2 cut(s)	165, 169
HgaI	GACGC	1 cut(s)	161
HhaI	GCGC	2 cut(s)	243, 323
Hin1I	GRCGYC	1 cut(s)	172
Hin1II	CATG	2 cut(s)	49, 127
Hin6I	GCGC	2 cut(s)	241, 321
HinP1I	GCGC	2 cut(s)	241, 321
HincII	GTYRAC	1 cut(s)	176
HindII	GTYRAC	1 cut(s)	176
HinfI	GANTC	2 cut(s)	62, 155
HpaII	CCGG	2 cut(s)	165, 169
HphI	GGTGA	1 cut(s)	131
Hpy166II	GTNNAC	1 cut(s)	176
Hpy188I	TCNGA	2 cut(s)	131, 160
Hpy8I	GTNNAC	1 cut(s)	176
HpyCH4III	ACNGT	1 cut(s)	231
HpyCH4V	TGCA	1 cut(s)	264
HpyF10VI	GCNNNNNNNGC	2 cut(s)	50, 243
HpyF3I	CTNAG	2 cut(s)	40, 141
Hsp92I	GRCGYC	1 cut(s)	172
Hsp92II	CATG	2 cut(s)	49, 127
HspAI	GCGC	2 cut(s)	241, 321
KroI	GCCGGC	2 cut(s)	164, 168
KroNI	GCCGGC	2 cut(s)	166, 170
KspI	CCGCGG	1 cut(s)	328
Kzo9I	GATC	4 cut(s)	4, 72, 126, 248
LmnI	GCTCC	1 cut(s)	33
LpnPI	CCDG	7 cut(s)	28, 73, 100, 137, 178, 182, 251
LweI	GCATC	2 cut(s)	70, 308
MaeIII	GTNAC	3 cut(s)	119, 147, 191
MalI	GATC	4 cut(s)	6, 74, 128, 250
MboI	GATC	4 cut(s)	4, 72, 126, 248
MboII	GAAGA	1 cut(s)	146
MflI	RGATCY	3 cut(s)	4, 72, 248
MhlI	GDGCHC	1 cut(s)	30
MlsI	TGGCCA	1 cut(s)	237
MluCI	AATT	1 cut(s)	283
MluNI	TGGCCA	1 cut(s)	237
MlyI	GAGTC	2 cut(s)	71, 149
MnlI	CCTC	5 cut(s)	41, 76, 154, 199, 290
Mox20I	TGGCCA	1 cut(s)	237
MroNI	GCCGGC	2 cut(s)	164, 168
MscI	TGGCCA	1 cut(s)	237
MseI	TTAA	1 cut(s)	213
Msp20I	TGGCCA	1 cut(s)	237
MspA1I	CMGCKG	1 cut(s)	327
MspCI	CTTAAG	1 cut(s)	212
MspI	CCGG	2 cut(s)	165, 169
MspR9I	CCNGG	1 cut(s)	88
MvaI	CCWGG	1 cut(s)	88
MvnI	CGCG	2 cut(s)	243, 327
MwoI	GCNNNNNNNGC	2 cut(s)	50, 243
NaeI	GCCGGC	2 cut(s)	166, 170
NcoI	CCATGG	1 cut(s)	45
NdeII	GATC	4 cut(s)	4, 72, 126, 248
NgoMIV	GCCGGC	2 cut(s)	164, 168
NlaIII	CATG	2 cut(s)	49, 127
NmeAIII	GCCGAG	1 cut(s)	320
NmuCI	GTSAC	1 cut(s)	119
PdiI	GCCGGC	2 cut(s)	166, 170
PkrI	GCNGC	3 cut(s)	55, 85, 245
PleI	GAGTC	2 cut(s)	70, 149
PpsI	GAGTC	2 cut(s)	70, 149
Psp6I	CCWGG	1 cut(s)	86
PspGI	CCWGG	1 cut(s)	86
PspPI	GGNCC	1 cut(s)	208
PsuI	RGATCY	3 cut(s)	4, 72, 248
RigI	GGCCGGCC	1 cut(s)	168
SacII	CCGCGG	1 cut(s)	328
SaqAI	TTAA	1 cut(s)	213
SatI	GCNGC	3 cut(s)	54, 84, 244
Sau3AI	GATC	4 cut(s)	4, 72, 126, 248
Sau96I	GGNCC	1 cut(s)	208
SchI	GAGTC	2 cut(s)	71, 149
ScrFI	CCNGG	1 cut(s)	88
SduI	GDGCHC	1 cut(s)	30
SetI	ASST	2 cut(s)	203, 301
SfaNI	GCATC	2 cut(s)	70, 308
Sfr303I	CCGCGG	1 cut(s)	328
SgrBI	CCGCGG	1 cut(s)	328
SmlI	CTYRAG	1 cut(s)	212
SmoI	CTYRAG	1 cut(s)	212
Sse9I	AATT	1 cut(s)	283
SsiI	CCGC	7 cut(s)	54, 84, 103, 243, 292, 325, 327
StyD4I	CCNGG	1 cut(s)	86
StyI	CCWWGG	2 cut(s)	45, 184
TaaI	ACNGT	1 cut(s)	231
TaqI	TCGA	1 cut(s)	316
TasI	AATT	1 cut(s)	283
TauI	GCSGC	3 cut(s)	56, 86, 246
Tru1I	TTAA	1 cut(s)	213
Tru9I	TTAA	1 cut(s)	213
TseFI	GTSAC	1 cut(s)	119
Tsp45I	GTSAC	1 cut(s)	119
TspDTI	ATGAA	1 cut(s)	296
Vha464I	CTTAAG	1 cut(s)	212
XapI	RAATTY	1 cut(s)	283

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