Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1A

Orthogroup ID

OG0002279

Physical Location & Seq

Genomic Coordinates Reverse (-)

48514321 .. 48520225

Gene Structure 5905 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1AG262300.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 414 bp

ATGACCGTGGAATCCACCATTAGCGTCTTCACCGTCCACTTCACTGCAACGCGTCATCACCAGGACGATCGACCACCACCATGCCAAAGCATAGATAAAGCTCCTCTTGATCGCAGCACTGCTTTAGGTGGTTTCTCTGGGAAAAACTATTCCGAGGCATCAGCATTTATAATAACTTATCATGTAAACAATGCTATTAATAAAGAGGGGAATGAAATTGAAAGAGCAGTGGCATGGGAGAAGGCCTTCATTGAGCTGGCAAAGGCATCAACATTTATAATAACTTATCCTGTAAACAATGCTATTAATAAAGAGGGGAATGAAATTGAAAGAGCAGTGGCATGGGAGAAGGCCTTCATTGAGCTGGCAAAGGTCAATGCATTCAGGTCTGATCCTACAGAAAAGATGGTATAG

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

137

Amino Acids

15.29

Weight (kDa)

5.8

Isoelectric Point (pI)

52.42

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
NPC1_MLD	PF22314	25 - 87	9.9e-13	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	2 cut(s)	170, 278
AccII	CGCG	1 cut(s)	52
AclWI	GGATC	1 cut(s)	386
AflIII	ACRYGT	1 cut(s)	50
AgsI	TTSAA	2 cut(s)	221, 329
AjnI	CCWGG	1 cut(s)	60
AluBI	AGCT	3 cut(s)	101, 256, 364
AluI	AGCT	3 cut(s)	101, 256, 364
AlwI	GGATC	1 cut(s)	386
AoxI	GGCC	2 cut(s)	243, 351
ApeKI	GCWGC	1 cut(s)	114
AseI	ATTAAT	2 cut(s)	198, 306
Asp700I	GAANNNNTTC	2 cut(s)	245, 353
AsuHPI	GGTGA	2 cut(s)	22, 50
BbsI	GAAGAC	1 cut(s)	19
BbvI	GCAGC	1 cut(s)	126
BccI	CCATC	1 cut(s)	400
BciT130I	CCWGG	1 cut(s)	62
BfmI	CTRYAG	1 cut(s)	396
BisI	GCNGC	1 cut(s)	115
BlsI	GCNGC	1 cut(s)	116
Bme1390I	CCNGG	1 cut(s)	62
BmrFI	CCNGG	1 cut(s)	62
BmsI	GCATC	2 cut(s)	167, 275
BpiI	GAAGAC	1 cut(s)	19
BsaJI	CCNNGG	2 cut(s)	6, 153
BseBI	CCWGG	1 cut(s)	62
BseDI	CCNNGG	2 cut(s)	6, 153
BseRI	GAGGAG	1 cut(s)	93
BseXI	GCAGC	1 cut(s)	126
Bsh1236I	CGCG	1 cut(s)	52
Bsh1285I	CGRYCG	1 cut(s)	70
BshFI	GGCC	2 cut(s)	245, 353
BsiEI	CGRYCG	1 cut(s)	70
BsmI	GAATGC	1 cut(s)	380
BsnI	GGCC	2 cut(s)	245, 353
Bsp143I	GATC	3 cut(s)	67, 109, 391
BspANI	GGCC	2 cut(s)	245, 353
BspFNI	CGCG	1 cut(s)	52
BspPI	GGATC	1 cut(s)	386
BssECI	CCNNGG	2 cut(s)	6, 153
BssMI	GATC	3 cut(s)	67, 109, 391
Bst2UI	CCWGG	1 cut(s)	62
Bst4CI	ACNGT	2 cut(s)	7, 34
BstC8I	GCNNGC	2 cut(s)	258, 366
BstDSI	CCRYGG	1 cut(s)	6
BstFNI	CGCG	1 cut(s)	52
BstKTI	GATC	3 cut(s)	70, 112, 394
BstMBI	GATC	3 cut(s)	67, 109, 391
BstMCI	CGRYCG	1 cut(s)	70
BstNI	CCWGG	1 cut(s)	62
BstSCI	CCNGG	1 cut(s)	60
BstSFI	CTRYAG	1 cut(s)	396
BstUI	CGCG	1 cut(s)	52
BstV1I	GCAGC	1 cut(s)	126
BstV2I	GAAGAC	1 cut(s)	19
BsuRI	GGCC	2 cut(s)	245, 353
BtgI	CCRYGG	1 cut(s)	6
BtsI	GCAGTG	4 cut(s)	42, 117, 234, 342
BtsIMutI	CAGTG	4 cut(s)	42, 117, 234, 342
Cac8I	GCNNGC	2 cut(s)	258, 366
CseI	GACGC	2 cut(s)	13, 41
CviAII	CATG	4 cut(s)	81, 182, 234, 342
CviJI	RGCY	5 cut(s)	101, 245, 256, 353, 364
CviKI_1	RGCY	5 cut(s)	101, 245, 256, 353, 364
DpnI	GATC	3 cut(s)	69, 111, 393
DpnII	GATC	3 cut(s)	67, 109, 391
Eco147I	AGGCCT	2 cut(s)	245, 353
EcoRII	CCWGG	1 cut(s)	60
EcoT22I	ATGCAT	1 cut(s)	382
FaeI	CATG	4 cut(s)	84, 185, 237, 345
FaiI	YATR	8 cut(s)	82, 92, 170, 183, 235, 278, 343, 412
FalI	AAGNNNNNCTT	2 cut(s)	90, 122
FatI	CATG	4 cut(s)	80, 181, 233, 341
Fnu4HI	GCNGC	1 cut(s)	115
Fsp4HI	GCNGC	1 cut(s)	115
GluI	GCNGC	1 cut(s)	115
HaeIII	GGCC	2 cut(s)	245, 353
HgaI	GACGC	2 cut(s)	13, 41
Hin1II	CATG	4 cut(s)	84, 185, 237, 345
HinfI	GANTC	1 cut(s)	11
HphI	GGTGA	2 cut(s)	22, 50
Hpy166II	GTNNAC	3 cut(s)	37, 187, 295
Hpy188I	TCNGA	2 cut(s)	154, 391
Hpy188III	TCNNGA	1 cut(s)	107
Hpy8I	GTNNAC	3 cut(s)	37, 187, 295
HpyAV	CCTTC	4 cut(s)	235, 256, 343, 364
HpyCH4III	ACNGT	2 cut(s)	7, 34
HpyCH4V	TGCA	2 cut(s)	47, 380
Hsp92II	CATG	4 cut(s)	84, 185, 237, 345
Kzo9I	GATC	3 cut(s)	67, 109, 391
LmnI	GCTCC	1 cut(s)	106
LpnPI	CCDG	7 cut(s)	47, 74, 123, 242, 303, 350, 370
Lsp1109I	GCAGC	1 cut(s)	126
LweI	GCATC	2 cut(s)	167, 275
MalI	GATC	3 cut(s)	69, 111, 393
MboI	GATC	3 cut(s)	67, 109, 391
MboII	GAAGA	1 cut(s)	19
MluCI	AATT	2 cut(s)	216, 324
MluI	ACGCGT	1 cut(s)	50
MnlI	CCTC	4 cut(s)	114, 148, 199, 307
Mph1103I	ATGCAT	1 cut(s)	382
MroXI	GAANNNNTTC	2 cut(s)	245, 353
MseI	TTAA	2 cut(s)	198, 306
MslI	CAYNNNNRTG	1 cut(s)	79
MspR9I	CCNGG	1 cut(s)	62
Mva1269I	GAATGC	1 cut(s)	380
MvaI	CCWGG	1 cut(s)	62
MvnI	CGCG	1 cut(s)	52
NdeII	GATC	3 cut(s)	67, 109, 391
NlaIII	CATG	4 cut(s)	84, 185, 237, 345
NsiI	ATGCAT	1 cut(s)	382
PceI	AGGCCT	2 cut(s)	245, 353
PctI	GAATGC	1 cut(s)	380
PdmI	GAANNNNTTC	2 cut(s)	245, 353
PfeI	GAWTC	1 cut(s)	11
PkrI	GCNGC	1 cut(s)	116
Ple19I	CGATCG	1 cut(s)	70
PshBI	ATTAAT	2 cut(s)	198, 306
PsiI	TTATAA	2 cut(s)	170, 278
Psp6I	CCWGG	1 cut(s)	60
PspGI	CCWGG	1 cut(s)	60
PvuI	CGATCG	1 cut(s)	70
RseI	CAYNNNNRTG	1 cut(s)	79
SaqAI	TTAA	2 cut(s)	198, 306
SatI	GCNGC	1 cut(s)	115
Sau3AI	GATC	3 cut(s)	67, 109, 391
ScrFI	CCNGG	1 cut(s)	62
SetI	ASST	6 cut(s)	103, 130, 258, 366, 375, 389
SfaNI	GCATC	2 cut(s)	167, 275
SfcI	CTRYAG	1 cut(s)	396
SmiMI	CAYNNNNRTG	1 cut(s)	79
Sse9I	AATT	2 cut(s)	216, 324
SseBI	AGGCCT	2 cut(s)	245, 353
StuI	AGGCCT	2 cut(s)	245, 353
StyD4I	CCNGG	1 cut(s)	60
TaaI	ACNGT	2 cut(s)	7, 34
TaqI	TCGA	1 cut(s)	70
TasI	AATT	2 cut(s)	216, 324
TfiI	GAWTC	1 cut(s)	11
Tru1I	TTAA	2 cut(s)	198, 306
Tru9I	TTAA	2 cut(s)	198, 306
TscAI	CASTG	4 cut(s)	49, 124, 234, 342
TseI	GCWGC	1 cut(s)	114
TspDTI	ATGAA	4 cut(s)	228, 238, 336, 346
TspRI	CASTG	4 cut(s)	49, 124, 234, 342
VspI	ATTAAT	2 cut(s)	198, 306
XmnI	GAANNNNTTC	2 cut(s)	245, 353
Zsp2I	ATGCAT	1 cut(s)	382

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