Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1B

Orthogroup ID

OG0002279

Physical Location & Seq

Genomic Coordinates Reverse (-)

18074746 .. 18076141

Gene Structure 1396 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1BG103100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 261 bp

ATGGGCTGGTTCCTTCTTGCCTGTCTTGGCTGCAAAAATGAGTTCAGTAGCAGCGATCTTGAAGTTTATACATGTTTAAGTGCCTTTCATGCTCCACTTGATCCAAGCATTGCCTTGGGAGGATTCTCCGGAAACTACTACTATGAGGCTTCTGCATTCATAGTCACCTACTCAATTAATAATGCAGTTGATAATGTAGGAAATGAGAATGGGAATGCACTGGCTTGGGAGAAGGCTTTTATTCAGTTAGCAAAGGTTTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000323 GO:0003674 GO:0005488 GO:0005496 GO:0005575 GO:0005576 GO:0005622 GO:0005623 GO:0005634 GO:0005635 GO:0005737 GO:0005764 GO:0005773 GO:0005783 GO:0005886 GO:0005887 GO:0006082 GO:0006464 GO:0006486 GO:0006629 GO:0006807 GO:0006810 GO:0006869 GO:0007034 GO:0007041 GO:0008150 GO:0008152 GO:0008202 GO:0008206 GO:0008289 GO:0009058 GO:0009059 GO:0009100 GO:0009101 GO:0009987 GO:0010876 GO:0012505 GO:0015485 GO:0015850 GO:0015918 GO:0016020 GO:0016021 GO:0019538 GO:0019752 GO:0030301 GO:0031224 GO:0031226 GO:0031967 GO:0031975 GO:0032787 GO:0032934 GO:0033036 GO:0034645 GO:0036094 GO:0036211 GO:0042592 GO:0042632 GO:0043170 GO:0043178 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043412 GO:0043413 GO:0043436 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044267 GO:0044281 GO:0044422 GO:0044424 GO:0044425 GO:0044428 GO:0044444 GO:0044446 GO:0044459 GO:0044464 GO:0048471 GO:0048878 GO:0051179 GO:0051234 GO:0055088 GO:0055092 GO:0065007 GO:0065008 GO:0070085 GO:0071702 GO:0071704 GO:0071944 GO:0097159 GO:1901135 GO:1901137 GO:1901360 GO:1901564 GO:1901566 GO:1901576 GO:1901615

KEGG Pathways

Metabolic & Signaling

ko04142 ko04979 map04142 map04979

Pfam Domains

Protein Families

NPC1_N Patched

Protein Analysis

86

Amino Acids

9.32

Weight (kDa)

4.33

Isoelectric Point (pI)

21.02

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
NPC1_MLD	PF22314	6 - 83	1.3e-15	NPC1, middle luminal domain

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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Publication-ready

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Orthologous Genes (Group: OG0002279)

Species	Orthologous Gene IDs
malus_domestica	MD00G1080500.v1.1 MD16G1285200.v1.1
rosa_chinensis	RchiOBHm_Chr2g0175261 RchiOBHm_Chr6g0280801
rosa_laevigata	RLG00000013082 RLG00000019605 RLG00000033344 RLG00000034484 RLG00000036984
rosa_multiflora	Rmu_sc0000893.1_g000002 Rmu_sc0002494.1_g000006 Rmu_sc0007139.1_g000001
rosa_roxburghii	Rroxscaffold_4G00312410 Rroxscaffold_7G00187620
rosa_rugosa	Rorug01G0060900 Rorug02G0158200 Rorug02G0250000 Rorug06G0134700
rosa_samantha	Rh1AG184800 Rh1AG199900 Rh1AG262300 Rh1BG097700 Rh1BG103100 Rh2CG636900 Rh2DG687600 Rh3CG050700 Rh3DG112000 Rh4CG020800 Rh4CG194300 Rh4DG079900 Rh5AG202600 Rh5BG321300 Rh5CG365700 Rh6AG170000 Rh6CG250600 Rh6DG242200 Rh6DG280400 Rh7AG279500 Rh7CG298700 Rh7CG343600 Rh7DG079500
rosa_wichuraiana	Rw4G014860 Rw6G026540

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccIII	TCCGGA	1 cut(s)	128
AclWI	GGATC	1 cut(s)	95
AflIII	ACRYGT	1 cut(s)	71
AgsI	TTSAA	1 cut(s)	62
AlwI	GGATC	1 cut(s)	95
Aor13HI	TCCGGA	1 cut(s)	128
ApeKI	GCWGC	2 cut(s)	30, 51
AseI	ATTAAT	1 cut(s)	177
AsuHPI	GGTGA	1 cut(s)	157
BbvI	GCAGC	2 cut(s)	17, 63
BisI	GCNGC	2 cut(s)	31, 52
BlsI	GCNGC	2 cut(s)	32, 53
BmiI	GGNNCC	1 cut(s)	11
BsaJI	CCNNGG	1 cut(s)	114
BsaWI	WCCGGW	1 cut(s)	128
Bse1I	ACTGG	1 cut(s)	225
Bse3DI	GCAATG	1 cut(s)	108
BseAI	TCCGGA	1 cut(s)	128
BseDI	CCNNGG	1 cut(s)	114
BseMI	GCAATG	1 cut(s)	108
BseNI	ACTGG	1 cut(s)	225
BseXI	GCAGC	2 cut(s)	17, 63
BsiSI	CCGG	1 cut(s)	129
BsmI	GAATGC	2 cut(s)	155, 220
Bsp13I	TCCGGA	1 cut(s)	128
Bsp143I	GATC	2 cut(s)	55, 100
BspEI	TCCGGA	1 cut(s)	128
BspLI	GGNNCC	1 cut(s)	11
BspPI	GGATC	1 cut(s)	95
BsrDI	GCAATG	1 cut(s)	108
BsrI	ACTGG	1 cut(s)	225
BssECI	CCNNGG	1 cut(s)	114
BssMI	GATC	2 cut(s)	55, 100
BssT1I	CCWWGG	1 cut(s)	114
BstKTI	GATC	2 cut(s)	58, 103
BstMBI	GATC	2 cut(s)	55, 100
BstMWI	GCNNNNNNNGC	1 cut(s)	89
BstNSI	RCATGY	1 cut(s)	75
BstV1I	GCAGC	2 cut(s)	17, 63
BtsIMutI	CAGTG	1 cut(s)	218
CviAII	CATG	2 cut(s)	72, 89
CviJI	RGCY	5 cut(s)	6, 30, 149, 224, 236
CviKI_1	RGCY	5 cut(s)	6, 30, 149, 224, 236
DpnI	GATC	2 cut(s)	57, 102
DpnII	GATC	2 cut(s)	55, 100
Eco130I	CCWWGG	1 cut(s)	114
EcoT14I	CCWWGG	1 cut(s)	114
ErhI	CCWWGG	1 cut(s)	114
FaeI	CATG	2 cut(s)	75, 92
FaiI	YATR	5 cut(s)	69, 73, 90, 144, 161
FatI	CATG	2 cut(s)	71, 88
Fnu4HI	GCNGC	2 cut(s)	31, 52
Fsp4HI	GCNGC	2 cut(s)	31, 52
GluI	GCNGC	2 cut(s)	31, 52
HapII	CCGG	1 cut(s)	129
Hin1II	CATG	2 cut(s)	75, 92
HinfI	GANTC	1 cut(s)	123
HpaII	CCGG	1 cut(s)	129
HphI	GGTGA	1 cut(s)	157
Hpy188III	TCNNGA	2 cut(s)	59, 129
HpyAV	CCTTC	2 cut(s)	23, 226
HpyCH4V	TGCA	4 cut(s)	33, 155, 185, 218
HpyF10VI	GCNNNNNNNGC	1 cut(s)	89
Hsp92II	CATG	2 cut(s)	75, 92
Kpn2I	TCCGGA	1 cut(s)	128
Kzo9I	GATC	2 cut(s)	55, 100
LmnI	GCTCC	1 cut(s)	97
LpnPI	CCDG	3 cut(s)	34, 142, 206
Lsp1109I	GCAGC	2 cut(s)	17, 63
MaeIII	GTNAC	1 cut(s)	163
MalI	GATC	2 cut(s)	57, 102
MboI	GATC	2 cut(s)	55, 100
MluCI	AATT	1 cut(s)	174
MnlI	CCTC	2 cut(s)	113, 139
MroI	TCCGGA	1 cut(s)	128
MseI	TTAA	3 cut(s)	77, 177, 259
MspI	CCGG	1 cut(s)	129
Mva1269I	GAATGC	2 cut(s)	155, 220
MwoI	GCNNNNNNNGC	1 cut(s)	89
NdeII	GATC	2 cut(s)	55, 100
NlaIII	CATG	2 cut(s)	75, 92
NlaIV	GGNNCC	1 cut(s)	11
NmuCI	GTSAC	1 cut(s)	163
NspI	RCATGY	1 cut(s)	75
PciI	ACATGT	1 cut(s)	71
PctI	GAATGC	2 cut(s)	155, 220
PfeI	GAWTC	1 cut(s)	123
PkrI	GCNGC	2 cut(s)	32, 53
PscI	ACATGT	1 cut(s)	71
PshBI	ATTAAT	1 cut(s)	177
PspN4I	GGNNCC	1 cut(s)	11
SaqAI	TTAA	3 cut(s)	77, 177, 259
SatI	GCNGC	2 cut(s)	31, 52
Sau3AI	GATC	2 cut(s)	55, 100
SetI	ASST	2 cut(s)	170, 258
Sse9I	AATT	1 cut(s)	174
StyI	CCWWGG	1 cut(s)	114
TasI	AATT	1 cut(s)	174
TfiI	GAWTC	1 cut(s)	123
Tru1I	TTAA	3 cut(s)	77, 177, 259
Tru9I	TTAA	3 cut(s)	77, 177, 259
TscAI	CASTG	1 cut(s)	225
TseFI	GTSAC	1 cut(s)	163
TseI	GCWGC	2 cut(s)	30, 51
Tsp45I	GTSAC	1 cut(s)	163
TspDTI	ATGAA	2 cut(s)	77, 148
TspRI	CASTG	1 cut(s)	225
VspI	ATTAAT	1 cut(s)	177
XceI	RCATGY	1 cut(s)	75

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