Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr2C

Orthogroup ID

OG0002279

Physical Location & Seq

Genomic Coordinates Reverse (-)

80813007 .. 80814058

Gene Structure 1052 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh2CG636900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 351 bp

ATGTTTTTTGCTATCAGTTGTGGTTTCTGTGGAAAAAACTATTCCGAGGCATCAGCATTTATAATAACTTATCCTGTAAACAATGCTATTAATAAAGAGGGGAATGAAATTGAAAGAGCAGTGGCATGGGAGAAGGCCTTCATTGAGCTGGCAAAGGATGAGCTGTTGCAAATGGTGCAATCTAAAAACTTAACACTATCTTTCTCATCGGAGAGTTCCATTGAAGAAGAACTTAAGAGTGAAAGCACTGCAGATGCTATTACAATATTAGTCCATGAAGGTGCATTTGGTTCTATTGGTGATGATCAGTCACTTCTTAAATACTTGGAATCTCTGGGACAACATCAGTAA

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

116

Amino Acids

12.79

Weight (kDa)

4.47

Isoelectric Point (pI)

57.07

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
NPC1_MLD	PF22314	7 - 71	9.7e-11	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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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)
AanI	TTATAA	1 cut(s)	62
AflII	CTTAAG	1 cut(s)	233
AgsI	TTSAA	2 cut(s)	113, 224
AjuI	GAANNNNNNNTTGG	2 cut(s)	270, 302
AluBI	AGCT	2 cut(s)	148, 163
AluI	AGCT	2 cut(s)	148, 163
AoxI	GGCC	1 cut(s)	135
AseI	ATTAAT	1 cut(s)	90
Asp700I	GAANNNNTTC	1 cut(s)	137
AsuHPI	GGTGA	1 cut(s)	311
BclI	TGATCA	1 cut(s)	304
BfmI	CTRYAG	1 cut(s)	249
BfrI	CTTAAG	1 cut(s)	233
BmsI	GCATC	2 cut(s)	59, 244
BsaJI	CCNNGG	1 cut(s)	45
BseDI	CCNNGG	1 cut(s)	45
BseGI	GGATG	1 cut(s)	163
BshFI	GGCC	1 cut(s)	137
BsnI	GGCC	1 cut(s)	137
Bsp143I	GATC	1 cut(s)	304
BspANI	GGCC	1 cut(s)	137
BspMAI	CTGCAG	1 cut(s)	253
BspTI	CTTAAG	1 cut(s)	233
BssECI	CCNNGG	1 cut(s)	45
BssMI	GATC	1 cut(s)	304
BstAFI	CTTAAG	1 cut(s)	233
BstAPI	GCANNNNNTGC	1 cut(s)	175
BstC8I	GCNNGC	1 cut(s)	150
BstF5I	GGATG	1 cut(s)	163
BstKTI	GATC	1 cut(s)	307
BstMBI	GATC	1 cut(s)	304
BstMWI	GCNNNNNNNGC	1 cut(s)	175
BstSFI	CTRYAG	1 cut(s)	249
BsuRI	GGCC	1 cut(s)	137
BtsCI	GGATG	1 cut(s)	163
BtsI	GCAGTG	2 cut(s)	126, 246
BtsIMutI	CAGTG	2 cut(s)	126, 246
Cac8I	GCNNGC	1 cut(s)	150
CviAII	CATG	2 cut(s)	126, 275
CviJI	RGCY	3 cut(s)	137, 148, 163
CviKI_1	RGCY	3 cut(s)	137, 148, 163
DpnI	GATC	1 cut(s)	306
DpnII	GATC	1 cut(s)	304
Eco147I	AGGCCT	1 cut(s)	137
FaeI	CATG	2 cut(s)	129, 278
FaiI	YATR	3 cut(s)	62, 127, 276
FalI	AAGNNNNNCTT	2 cut(s)	216, 248
FatI	CATG	2 cut(s)	125, 274
FbaI	TGATCA	1 cut(s)	304
FokI	GGATG	1 cut(s)	170
HaeIII	GGCC	1 cut(s)	137
Hin1II	CATG	2 cut(s)	129, 278
HinfI	GANTC	1 cut(s)	329
HphI	GGTGA	1 cut(s)	311
Hpy166II	GTNNAC	1 cut(s)	79
Hpy188I	TCNGA	2 cut(s)	46, 211
Hpy8I	GTNNAC	1 cut(s)	79
HpyAV	CCTTC	3 cut(s)	127, 148, 272
HpyCH4V	TGCA	4 cut(s)	169, 178, 251, 284
HpyF10VI	GCNNNNNNNGC	1 cut(s)	175
Hsp92II	CATG	2 cut(s)	129, 278
Ksp22I	TGATCA	1 cut(s)	304
Kzo9I	GATC	1 cut(s)	304
LpnPI	CCDG	3 cut(s)	87, 134, 320
LweI	GCATC	2 cut(s)	59, 244
MaeIII	GTNAC	1 cut(s)	309
MalI	GATC	1 cut(s)	306
MboI	GATC	1 cut(s)	304
MboII	GAAGA	2 cut(s)	236, 239
MluCI	AATT	1 cut(s)	108
MnlI	CCTC	2 cut(s)	40, 91
MroXI	GAANNNNTTC	1 cut(s)	137
MseI	TTAA	4 cut(s)	90, 191, 234, 318
MslI	CAYNNNNRTG	1 cut(s)	279
MspCI	CTTAAG	1 cut(s)	233
MwoI	GCNNNNNNNGC	1 cut(s)	175
NdeII	GATC	1 cut(s)	304
NlaIII	CATG	2 cut(s)	129, 278
NmuCI	GTSAC	1 cut(s)	309
PceI	AGGCCT	1 cut(s)	137
PdmI	GAANNNNTTC	1 cut(s)	137
PfeI	GAWTC	1 cut(s)	329
PshBI	ATTAAT	1 cut(s)	90
PsiI	TTATAA	1 cut(s)	62
PstI	CTGCAG	1 cut(s)	253
RseI	CAYNNNNRTG	1 cut(s)	279
SaqAI	TTAA	4 cut(s)	90, 191, 234, 318
Sau3AI	GATC	1 cut(s)	304
SetI	ASST	3 cut(s)	150, 165, 283
SfaNI	GCATC	2 cut(s)	59, 244
SfcI	CTRYAG	1 cut(s)	249
SgeI	CNNG	7 cut(s)	58, 86, 138, 161, 287, 337, 347
SmiMI	CAYNNNNRTG	1 cut(s)	279
SmlI	CTYRAG	1 cut(s)	233
SmoI	CTYRAG	1 cut(s)	233
Sse9I	AATT	1 cut(s)	108
SseBI	AGGCCT	1 cut(s)	137
SspI	AATATT	1 cut(s)	267
StuI	AGGCCT	1 cut(s)	137
TasI	AATT	1 cut(s)	108
TfiI	GAWTC	1 cut(s)	329
Tru1I	TTAA	4 cut(s)	90, 191, 234, 318
Tru9I	TTAA	4 cut(s)	90, 191, 234, 318
TscAI	CASTG	2 cut(s)	126, 253
TseFI	GTSAC	1 cut(s)	309
Tsp45I	GTSAC	1 cut(s)	309
TspDTI	ATGAA	3 cut(s)	120, 130, 291
TspRI	CASTG	2 cut(s)	126, 253
Vha464I	CTTAAG	1 cut(s)	233
VspI	ATTAAT	1 cut(s)	90
XmnI	GAANNNNTTC	1 cut(s)	137

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