Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5B

Orthogroup ID

OG0004528

Physical Location & Seq

Genomic Coordinates Forward (+)

1280737 .. 1281087

Gene Structure 351 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5BG017400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 351 bp

ATGGAGAAGAAAATTATGACTTTCGCTGCGCTGGTGATTATGGTCGTCGTCCTCAATGCATGTCCTGCAATTGGAGGATGCGACGAAGCCTTAGTCGAGTTGTTGCCCTGTGCCACGTTCGTGATGGGTCCTGCAGAAGGAACTCCCCCTCCTGCGTGTTGTGAAGGTATGCAGCATGTCGTTGGTGGAGCAGATACCGCTGAGAAGCGCAGGAGTCTTTGCCAATGTTTGAAAGACACAGCTATTAAAAATGAGGTTAAAATCAAGCCTGAAAACATTAAGCATGCTGTTGATGCTTGTGGCGTTAAAATCCTTGTTCCTATTGATCCTAATATCGACTGCAGCAAGTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

No ontology terms assigned.

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

LTP_2 Tryp_alpha_amyl

Protein Analysis

116

Amino Acids

12.25

Weight (kDa)

5.63

Isoelectric Point (pI)

48.47

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
LTP_2	PF14368	12 - 103	3.3e-07	Probable lipid transfer
Tryp_alpha_amyl	PF00234	27 - 114	8.9e-09	Protease inhibitor/seed storage/LTP family

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: OG0004528)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_3g01200 FvH4_3g01230 FvH4_3g09850
rosa_chinensis	RchiOBHm_Chr5g0001761 RchiOBHm_Chr5g0015561
rosa_laevigata	RLG00000030969 RLG00000030970 RLG00000032208
rosa_multiflora	Rmu_sc0002886.1_g000025 Rmu_sc0008119.1_g000005 Rmu_sc0008119.1_g000007 Rmu_ssc0000237.1_g000015 Rmu_ssc0000237.1_g000017
rosa_roxburghii	Rroxscaffold_1G00071220 Rroxscaffold_1G00074560
rosa_rugosa	Rorug04G0392800 Rorug04G0392900 Rorug05G0028400
rosa_samantha	Rh5AG013900 Rh5AG014100 Rh5AG121700 Rh5BG017400 Rh5BG017500 Rh5BG120600 Rh5CG015000 Rh5CG015200 Rh5CG130900 Rh5DG015500 Rh5DG015600 Rh5DG119500
rosa_wichuraiana	Rw5G001360 Rw5G010510

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AciI	CCGC	1 cut(s)	198
AclWI	GGATC	1 cut(s)	320
AfiI	CCNNNNNNNGG	2 cut(s)	71, 137
AgsI	TTSAA	1 cut(s)	232
AleI	CACNNNNGTG	1 cut(s)	119
AloI	GAACNNNNNNTCC	2 cut(s)	133, 165
AluBI	AGCT	1 cut(s)	242
AluI	AGCT	1 cut(s)	242
AlwI	GGATC	1 cut(s)	320
ApeKI	GCWGC	3 cut(s)	26, 172, 342
ArsI	GACNNNNNNTTYG	2 cut(s)	78, 110
AspLEI	GCGC	2 cut(s)	31, 210
AspS9I	GGNCC	1 cut(s)	128
AsuHPI	GGTGA	1 cut(s)	46
AvaII	GGWCC	1 cut(s)	128
BbvI	GCAGC	2 cut(s)	13, 184
BccI	CCATC	1 cut(s)	118
BfmI	CTRYAG	2 cut(s)	132, 340
BisI	GCNGC	3 cut(s)	27, 173, 343
BlsI	GCNGC	3 cut(s)	28, 174, 344
Bme18I	GGWCC	1 cut(s)	128
BmgT120I	GGNCC	1 cut(s)	128
BmiI	GGNNCC	1 cut(s)	129
BmsI	GCATC	2 cut(s)	68, 283
BsaXI	ACNNNNNCTCC	2 cut(s)	133, 163
Bsc4I	CCNNNNNNNGG	2 cut(s)	71, 137
BseGI	GGATG	1 cut(s)	83
BseLI	CCNNNNNNNGG	2 cut(s)	71, 137
BseMII	CTCAG	1 cut(s)	192
BseXI	GCAGC	2 cut(s)	13, 184
BslI	CCNNNNNNNGG	2 cut(s)	71, 137
Bsp143I	GATC	1 cut(s)	325
BspACI	CCGC	1 cut(s)	198
BspCNI	CTCAG	1 cut(s)	193
BspLI	GGNNCC	1 cut(s)	129
BspMAI	CTGCAG	2 cut(s)	136, 344
BspPI	GGATC	1 cut(s)	320
BssMI	GATC	1 cut(s)	325
BstAPI	GCANNNNNTGC	1 cut(s)	65
BstC8I	GCNNGC	1 cut(s)	285
BstDEI	CTNAG	2 cut(s)	91, 201
BstENI	CCTNNNNNAGG	1 cut(s)	135
BstF5I	GGATG	1 cut(s)	83
BstHHI	GCGC	2 cut(s)	31, 210
BstKTI	GATC	1 cut(s)	328
BstMBI	GATC	1 cut(s)	325
BstMWI	GCNNNNNNNGC	3 cut(s)	65, 197, 293
BstNSI	RCATGY	3 cut(s)	63, 179, 287
BstSFI	CTRYAG	2 cut(s)	132, 340
BstV1I	GCAGC	2 cut(s)	13, 184
BtsCI	GGATG	1 cut(s)	83
Cac8I	GCNNGC	1 cut(s)	285
CfoI	GCGC	2 cut(s)	31, 210
Cfr13I	GGNCC	1 cut(s)	128
CviAII	CATG	3 cut(s)	60, 176, 284
CviJI	RGCY	3 cut(s)	89, 242, 268
CviKI_1	RGCY	3 cut(s)	89, 242, 268
DdeI	CTNAG	2 cut(s)	91, 201
DpnI	GATC	1 cut(s)	327
DpnII	GATC	1 cut(s)	325
Eco47I	GGWCC	1 cut(s)	128
EcoNI	CCTNNNNNAGG	1 cut(s)	135
EcoO109I	RGGNCCY	1 cut(s)	128
EcoT22I	ATGCAT	1 cut(s)	61
FaeI	CATG	3 cut(s)	63, 179, 287
FaiI	YATR	6 cut(s)	17, 41, 61, 170, 177, 285
FatI	CATG	3 cut(s)	59, 175, 283
Fnu4HI	GCNGC	3 cut(s)	27, 173, 343
FokI	GGATG	1 cut(s)	90
Fsp4HI	GCNGC	3 cut(s)	27, 173, 343
GlaI	GCGC	2 cut(s)	30, 209
GluI	GCNGC	3 cut(s)	27, 173, 343
HhaI	GCGC	2 cut(s)	31, 210
Hin1II	CATG	3 cut(s)	63, 179, 287
Hin6I	GCGC	2 cut(s)	29, 208
HinP1I	GCGC	2 cut(s)	29, 208
HinfI	GANTC	1 cut(s)	214
HphI	GGTGA	1 cut(s)	46
Hpy188III	TCNNGA	1 cut(s)	121
Hpy99I	CGWCG	2 cut(s)	50, 86
HpyAV	CCTTC	2 cut(s)	131, 158
HpyCH4IV	ACGT	1 cut(s)	116
HpyCH4V	TGCA	5 cut(s)	59, 68, 134, 172, 342
HpyF10VI	GCNNNNNNNGC	3 cut(s)	65, 197, 293
HpyF3I	CTNAG	2 cut(s)	91, 201
HpySE526I	ACGT	1 cut(s)	116
Hsp92II	CATG	3 cut(s)	63, 179, 287
HspAI	GCGC	2 cut(s)	29, 208
Kzo9I	GATC	1 cut(s)	325
LmnI	GCTCC	1 cut(s)	188
LpnPI	CCDG	7 cut(s)	17, 78, 121, 144, 165, 196, 282
Lsp1109I	GCAGC	2 cut(s)	13, 184
LweI	GCATC	2 cut(s)	68, 283
MaeII	ACGT	1 cut(s)	116
MalI	GATC	1 cut(s)	327
MboI	GATC	1 cut(s)	325
MboII	GAAGA	1 cut(s)	19
MfeI	CAATTG	1 cut(s)	69
MluCI	AATT	2 cut(s)	12, 69
MlyI	GAGTC	1 cut(s)	223
MnlI	CCTC	4 cut(s)	62, 68, 159, 247
Mph1103I	ATGCAT	1 cut(s)	61
MseI	TTAA	4 cut(s)	246, 258, 279, 306
MslI	CAYNNNNRTG	1 cut(s)	119
MspA1I	CMGCKG	1 cut(s)	200
MunI	CAATTG	1 cut(s)	69
MwoI	GCNNNNNNNGC	3 cut(s)	65, 197, 293
NdeII	GATC	1 cut(s)	325
NlaIII	CATG	3 cut(s)	63, 179, 287
NlaIV	GGNNCC	1 cut(s)	129
NsiI	ATGCAT	1 cut(s)	61
NspI	RCATGY	3 cut(s)	63, 179, 287
OliI	CACNNNNGTG	1 cut(s)	119
PaeI	GCATGC	1 cut(s)	287
PkrI	GCNGC	3 cut(s)	28, 174, 344
PleI	GAGTC	1 cut(s)	222
PpsI	GAGTC	1 cut(s)	222
PpuMI	RGGWCCY	1 cut(s)	128
Psp5II	RGGWCCY	1 cut(s)	128
PspN4I	GGNNCC	1 cut(s)	129
PspPI	GGNCC	1 cut(s)	128
PspPPI	RGGWCCY	1 cut(s)	128
PstI	CTGCAG	2 cut(s)	136, 344
RseI	CAYNNNNRTG	1 cut(s)	119
SaqAI	TTAA	4 cut(s)	246, 258, 279, 306
SatI	GCNGC	3 cut(s)	27, 173, 343
Sau3AI	GATC	1 cut(s)	325
Sau96I	GGNCC	1 cut(s)	128
SchI	GAGTC	1 cut(s)	223
SetI	ASST	4 cut(s)	119, 169, 244, 258
SfaNI	GCATC	2 cut(s)	68, 283
SfcI	CTRYAG	2 cut(s)	132, 340
SinI	GGWCC	1 cut(s)	128
SmiMI	CAYNNNNRTG	1 cut(s)	119
SphI	GCATGC	1 cut(s)	287
Sse9I	AATT	2 cut(s)	12, 69
SsiI	CCGC	1 cut(s)	198
TaiI	ACGT	1 cut(s)	119
TaqI	TCGA	2 cut(s)	96, 336
TasI	AATT	2 cut(s)	12, 69
Tru1I	TTAA	4 cut(s)	246, 258, 279, 306
Tru9I	TTAA	4 cut(s)	246, 258, 279, 306
TseI	GCWGC	3 cut(s)	26, 172, 342
VpaK11BI	GGWCC	1 cut(s)	128
XagI	CCTNNNNNAGG	1 cut(s)	135
XceI	RCATGY	3 cut(s)	63, 179, 287
XcmI	CCANNNNNNNNNTGG	1 cut(s)	121
Zsp2I	ATGCAT	1 cut(s)	61

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