Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1A

Orthogroup ID

OG0002279

Physical Location & Seq

Genomic Coordinates Forward (+)

35202686 .. 35225502

Gene Structure 22817 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1AG184800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 381 bp

ATGGCTTTCCTTGTCATAGTGTGGCTCTATTTTGGCCTAATTTACTTCTCTCCTTCTGTTCTACTTCATTTCCCTAAGGCATCAACATTTATAATAACTTATCCTGTAAACAATGCTATTAATAAAGAGGGGAAAGAAATTGAAAGAGCAGTGGCATGGGAGAAGGCCTTCATTGAGCTGGCAAAGGATGAGCTATTACAAATGGTGCAATCTAAAAACTTAACACTATCTTTCTCATCGGAGAGTTCCATTGAAGAAGAACTTAAGAGTGAAAGCACTGCAGATGCTATTACAACATTGGTCCATGAAGGTGCATTTGGTTCTATTGGTGATGATCAGTCACTTCTTAAATACTTGGAATCTTTGGGACAACATCAGTAA

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

126

Amino Acids

14.12

Weight (kDa)

4.74

Isoelectric Point (pI)

56.35

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
NPC1_MLD	PF22314	24 - 81	7.1e-08	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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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)
AanI	TTATAA	1 cut(s)	92
AflII	CTTAAG	1 cut(s)	263
AgsI	TTSAA	2 cut(s)	143, 254
AjuI	GAANNNNNNNTTGG	2 cut(s)	300, 332
AluBI	AGCT	2 cut(s)	178, 193
AluI	AGCT	2 cut(s)	178, 193
AoxI	GGCC	2 cut(s)	34, 165
AseI	ATTAAT	1 cut(s)	120
Asp700I	GAANNNNTTC	1 cut(s)	167
AspS9I	GGNCC	1 cut(s)	301
AsuHPI	GGTGA	1 cut(s)	341
AvaII	GGWCC	1 cut(s)	301
AxyI	CCTNAGG	1 cut(s)	75
BclI	TGATCA	1 cut(s)	334
BfmI	CTRYAG	1 cut(s)	279
BfrI	CTTAAG	1 cut(s)	263
Bme18I	GGWCC	1 cut(s)	301
BmgT120I	GGNCC	1 cut(s)	301
BmsI	GCATC	2 cut(s)	89, 274
Bse21I	CCTNAGG	1 cut(s)	75
BseGI	GGATG	1 cut(s)	193
BshFI	GGCC	2 cut(s)	36, 167
BsnI	GGCC	2 cut(s)	36, 167
Bsp143I	GATC	1 cut(s)	334
BspANI	GGCC	2 cut(s)	36, 167
BspMAI	CTGCAG	1 cut(s)	283
BspTI	CTTAAG	1 cut(s)	263
BssMI	GATC	1 cut(s)	334
BstAFI	CTTAAG	1 cut(s)	263
BstC8I	GCNNGC	1 cut(s)	180
BstDEI	CTNAG	1 cut(s)	75
BstF5I	GGATG	1 cut(s)	193
BstKTI	GATC	1 cut(s)	337
BstMBI	GATC	1 cut(s)	334
BstSFI	CTRYAG	1 cut(s)	279
Bsu36I	CCTNAGG	1 cut(s)	75
BsuRI	GGCC	2 cut(s)	36, 167
BtsCI	GGATG	1 cut(s)	193
BtsI	GCAGTG	2 cut(s)	156, 276
BtsIMutI	CAGTG	2 cut(s)	156, 276
Cac8I	GCNNGC	1 cut(s)	180
Cfr13I	GGNCC	1 cut(s)	301
CviAII	CATG	2 cut(s)	156, 305
CviJI	RGCY	6 cut(s)	5, 25, 36, 167, 178, 193
CviKI_1	RGCY	6 cut(s)	5, 25, 36, 167, 178, 193
DdeI	CTNAG	1 cut(s)	75
DpnI	GATC	1 cut(s)	336
DpnII	GATC	1 cut(s)	334
Eco147I	AGGCCT	1 cut(s)	167
Eco47I	GGWCC	1 cut(s)	301
Eco81I	CCTNAGG	1 cut(s)	75
FaeI	CATG	2 cut(s)	159, 308
FaiI	YATR	4 cut(s)	17, 92, 157, 306
FalI	AAGNNNNNCTT	2 cut(s)	246, 278
FatI	CATG	2 cut(s)	155, 304
FbaI	TGATCA	1 cut(s)	334
FokI	GGATG	1 cut(s)	200
HaeIII	GGCC	2 cut(s)	36, 167
Hin1II	CATG	2 cut(s)	159, 308
HinfI	GANTC	1 cut(s)	359
HphI	GGTGA	1 cut(s)	341
Hpy166II	GTNNAC	1 cut(s)	109
Hpy188I	TCNGA	1 cut(s)	241
Hpy8I	GTNNAC	1 cut(s)	109
HpyAV	CCTTC	4 cut(s)	63, 157, 178, 302
HpyCH4V	TGCA	3 cut(s)	208, 281, 314
HpyF3I	CTNAG	1 cut(s)	75
Hsp92II	CATG	2 cut(s)	159, 308
Ksp22I	TGATCA	1 cut(s)	334
Kzo9I	GATC	1 cut(s)	334
LpnPI	CCDG	2 cut(s)	117, 164
LweI	GCATC	2 cut(s)	89, 274
MaeIII	GTNAC	1 cut(s)	339
MalI	GATC	1 cut(s)	336
MboI	GATC	1 cut(s)	334
MboII	GAAGA	2 cut(s)	266, 269
MluCI	AATT	2 cut(s)	39, 138
MnlI	CCTC	1 cut(s)	121
MroXI	GAANNNNTTC	1 cut(s)	167
MseI	TTAA	4 cut(s)	120, 221, 264, 348
MslI	CAYNNNNRTG	1 cut(s)	309
MspCI	CTTAAG	1 cut(s)	263
NdeII	GATC	1 cut(s)	334
NlaIII	CATG	2 cut(s)	159, 308
NmuCI	GTSAC	1 cut(s)	339
PceI	AGGCCT	1 cut(s)	167
PdmI	GAANNNNTTC	1 cut(s)	167
PfeI	GAWTC	1 cut(s)	359
PshBI	ATTAAT	1 cut(s)	120
PsiI	TTATAA	1 cut(s)	92
PspPI	GGNCC	1 cut(s)	301
PstI	CTGCAG	1 cut(s)	283
RseI	CAYNNNNRTG	1 cut(s)	309
SaqAI	TTAA	4 cut(s)	120, 221, 264, 348
Sau3AI	GATC	1 cut(s)	334
Sau96I	GGNCC	1 cut(s)	301
SetI	ASST	3 cut(s)	180, 195, 313
SfaNI	GCATC	2 cut(s)	89, 274
SfcI	CTRYAG	1 cut(s)	279
SgeI	CNNG	6 cut(s)	23, 116, 168, 191, 317, 367
SinI	GGWCC	1 cut(s)	301
SmiMI	CAYNNNNRTG	1 cut(s)	309
SmlI	CTYRAG	1 cut(s)	263
SmoI	CTYRAG	1 cut(s)	263
Sse9I	AATT	2 cut(s)	39, 138
SseBI	AGGCCT	1 cut(s)	167
StuI	AGGCCT	1 cut(s)	167
TasI	AATT	2 cut(s)	39, 138
TfiI	GAWTC	1 cut(s)	359
Tru1I	TTAA	4 cut(s)	120, 221, 264, 348
Tru9I	TTAA	4 cut(s)	120, 221, 264, 348
TscAI	CASTG	2 cut(s)	156, 283
TseFI	GTSAC	1 cut(s)	339
Tsp45I	GTSAC	1 cut(s)	339
TspDTI	ATGAA	3 cut(s)	56, 160, 321
TspRI	CASTG	2 cut(s)	156, 283
Vha464I	CTTAAG	1 cut(s)	263
VpaK11BI	GGWCC	1 cut(s)	301
VspI	ATTAAT	1 cut(s)	120
XmnI	GAANNNNTTC	1 cut(s)	167

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