Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6D

Orthogroup ID

OG0002279

Physical Location & Seq

Genomic Coordinates Forward (+)

47448660 .. 47460758

Gene Structure 12099 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6DG280400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 645 bp

ATGTCGCCACCTTTTCTAGCGAGCTGCTTCACAGCTCTGACGACAGAGATAGGCTCTGATTGCAGATCATTGTCGGTGCAATCTCTCTCGCATAGCCGCCTTCTCCTCCGGCGAGGATTTCCCGATAACCACAACTTCTTCATCGAATTCACCCTCATTCTCCGGCCACACTATCCGATCGAGCTAGAATCACAGACTGATCGGTGTTTGGTGCTTTCGAATTTGGATTTTCCAGCTTGCGTTGGGTTGCTTGCTTTTGGCCAGGCAAGCACTGCTTTAGGTGGTTTCTCTGGGAAAAACTGTTCCGAGGCATCAGCATTTATAATAACTTATCCTGTAAACAATGCTATTAATAAAGAGGGGAATGAAATTGAAAGAGCAGTGGCATGGGGGAAGGCCTTTATTGAGCTGGCAAAGGATGAGCTATTGCAAATGGTGCAATCTAAAAACTTAACACTATCTTTCTCATCGGAGAGTTCCATTGAAGAAGAACTTAAGAGTGAAAGCACTGCAGATGCTATTACAATATTGGGTATCATTCTCTTTGCATCTGTTGCTGCAACTCTTGGACTACAAATATTGCTGAGAGTCTGCTTGAGAACTGATCTCAAAGAGCAAATGAAACCTCAATGGGAAAAAGACTAG

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

214

Amino Acids

23.57

Weight (kDa)

5.06

Isoelectric Point (pI)

70.98

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
NPC1_MLD	PF22314	89 - 158	1.5e-10	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)
AanI	TTATAA	1 cut(s)	323
AciI	CCGC	1 cut(s)	97
AcoI	YGGCCR	2 cut(s)	164, 259
AcsI	RAATTY	2 cut(s)	146, 220
AflII	CTTAAG	1 cut(s)	494
AgsI	TTSAA	2 cut(s)	374, 485
AjnI	CCWGG	1 cut(s)	261
AloI	GAACNNNNNNTCC	2 cut(s)	286, 318
AluBI	AGCT	6 cut(s)	24, 35, 184, 236, 409, 424
AluI	AGCT	6 cut(s)	24, 35, 184, 236, 409, 424
AoxI	GGCC	3 cut(s)	164, 259, 396
ApeKI	GCWGC	2 cut(s)	24, 557
ApoI	RAATTY	2 cut(s)	146, 220
AseI	ATTAAT	1 cut(s)	351
AsuHPI	GGTGA	1 cut(s)	142
AsuII	TTCGAA	1 cut(s)	218
BalI	TGGCCA	1 cut(s)	261
BbvI	GCAGC	2 cut(s)	11, 544
BciT130I	CCWGG	1 cut(s)	263
BfaI	CTAG	3 cut(s)	17, 185, 643
BfmI	CTRYAG	1 cut(s)	510
BfrI	CTTAAG	1 cut(s)	494
BisI	GCNGC	3 cut(s)	25, 97, 558
BlsI	GCNGC	3 cut(s)	26, 98, 559
Bme1390I	CCNGG	1 cut(s)	263
BmrFI	CCNGG	1 cut(s)	263
BmsI	GCATC	3 cut(s)	320, 505, 557
BplI	GAGNNNNNCTC	2 cut(s)	38, 70
Bpu14I	TTCGAA	1 cut(s)	218
BpuEI	CTTGAG	1 cut(s)	616
BsaJI	CCNNGG	1 cut(s)	306
BseBI	CCWGG	1 cut(s)	263
BseDI	CCNNGG	1 cut(s)	306
BseGI	GGATG	1 cut(s)	424
BseMII	CTCAG	1 cut(s)	575
BseRI	GAGGAG	1 cut(s)	95
BseXI	GCAGC	2 cut(s)	11, 544
Bsh1285I	CGRYCG	1 cut(s)	180
BshFI	GGCC	3 cut(s)	166, 261, 398
BsiEI	CGRYCG	1 cut(s)	180
BsiSI	CCGG	2 cut(s)	109, 163
BsnI	GGCC	3 cut(s)	166, 261, 398
Bsp119I	TTCGAA	1 cut(s)	218
Bsp143I	GATC	4 cut(s)	65, 177, 199, 604
BspACI	CCGC	1 cut(s)	97
BspANI	GGCC	3 cut(s)	166, 261, 398
BspCNI	CTCAG	1 cut(s)	576
BspMAI	CTGCAG	1 cut(s)	514
BspT104I	TTCGAA	1 cut(s)	218
BspTI	CTTAAG	1 cut(s)	494
BssECI	CCNNGG	1 cut(s)	306
BssMI	GATC	4 cut(s)	65, 177, 199, 604
Bst2UI	CCWGG	1 cut(s)	263
Bst4CI	ACNGT	1 cut(s)	302
BstAFI	CTTAAG	1 cut(s)	494
BstAPI	GCANNNNNTGC	3 cut(s)	272, 436, 554
BstBI	TTCGAA	1 cut(s)	218
BstC8I	GCNNGC	5 cut(s)	22, 238, 252, 268, 411
BstDEI	CTNAG	1 cut(s)	584
BstF5I	GGATG	1 cut(s)	424
BstKTI	GATC	4 cut(s)	68, 180, 202, 607
BstMBI	GATC	4 cut(s)	65, 177, 199, 604
BstMCI	CGRYCG	1 cut(s)	180
BstMWI	GCNNNNNNNGC	5 cut(s)	60, 267, 272, 436, 554
BstNI	CCWGG	1 cut(s)	263
BstSCI	CCNGG	1 cut(s)	261
BstSFI	CTRYAG	1 cut(s)	510
BstV1I	GCAGC	2 cut(s)	11, 544
BsuRI	GGCC	3 cut(s)	166, 261, 398
BtsCI	GGATG	1 cut(s)	424
BtsI	GCAGTG	3 cut(s)	270, 387, 507
BtsIMutI	CAGTG	3 cut(s)	270, 387, 507
Cac8I	GCNNGC	5 cut(s)	22, 238, 252, 268, 411
CviAII	CATG	1 cut(s)	387
DdeI	CTNAG	1 cut(s)	584
DpnI	GATC	4 cut(s)	67, 179, 201, 606
DpnII	GATC	4 cut(s)	65, 177, 199, 604
EaeI	YGGCCR	2 cut(s)	164, 259
Eco147I	AGGCCT	1 cut(s)	398
EcoRI	GAATTC	1 cut(s)	146
EcoRII	CCWGG	1 cut(s)	261
FaeI	CATG	1 cut(s)	390
FaiI	YATR	3 cut(s)	93, 323, 388
FalI	AAGNNNNNCTT	4 cut(s)	259, 291, 477, 509
FatI	CATG	1 cut(s)	386
Fnu4HI	GCNGC	3 cut(s)	25, 97, 558
FokI	GGATG	1 cut(s)	431
Fsp4HI	GCNGC	3 cut(s)	25, 97, 558
FspBI	CTAG	3 cut(s)	17, 185, 643
GluI	GCNGC	3 cut(s)	25, 97, 558
HaeIII	GGCC	3 cut(s)	166, 261, 398
HapII	CCGG	2 cut(s)	109, 163
Hin1II	CATG	1 cut(s)	390
HinfI	GANTC	2 cut(s)	188, 588
HpaII	CCGG	2 cut(s)	109, 163
HphI	GGTGA	1 cut(s)	142
Hpy166II	GTNNAC	1 cut(s)	340
Hpy188I	TCNGA	5 cut(s)	39, 58, 177, 307, 472
Hpy188III	TCNNGA	1 cut(s)	122
Hpy8I	GTNNAC	1 cut(s)	340
HpyAV	CCTTC	2 cut(s)	110, 388
HpyCH4III	ACNGT	1 cut(s)	302
HpyCH4V	TGCA	7 cut(s)	63, 79, 430, 439, 512, 548, 560
HpyF10VI	GCNNNNNNNGC	5 cut(s)	60, 267, 272, 436, 554
HpyF3I	CTNAG	1 cut(s)	584
Hsp92II	CATG	1 cut(s)	390
Kzo9I	GATC	4 cut(s)	65, 177, 199, 604
LpnPI	CCDG	8 cut(s)	122, 176, 246, 248, 275, 276, 348, 395
Lsp1109I	GCAGC	2 cut(s)	11, 544
LweI	GCATC	3 cut(s)	320, 505, 557
MaeI	CTAG	3 cut(s)	17, 185, 643
MalI	GATC	4 cut(s)	67, 179, 201, 606
MboI	GATC	4 cut(s)	65, 177, 199, 604
MboII	GAAGA	3 cut(s)	130, 497, 500
MlsI	TGGCCA	1 cut(s)	261
MluCI	AATT	3 cut(s)	146, 220, 369
MluNI	TGGCCA	1 cut(s)	261
MlyI	GAGTC	1 cut(s)	597
MnlI	CCTC	6 cut(s)	107, 116, 164, 301, 352, 636
Mox20I	TGGCCA	1 cut(s)	261
MscI	TGGCCA	1 cut(s)	261
MseI	TTAA	3 cut(s)	351, 452, 495
Msp20I	TGGCCA	1 cut(s)	261
MspCI	CTTAAG	1 cut(s)	494
MspI	CCGG	2 cut(s)	109, 163
MspR9I	CCNGG	1 cut(s)	263
MvaI	CCWGG	1 cut(s)	263
MwoI	GCNNNNNNNGC	5 cut(s)	60, 267, 272, 436, 554
NdeII	GATC	4 cut(s)	65, 177, 199, 604
NlaIII	CATG	1 cut(s)	390
NspV	TTCGAA	1 cut(s)	218
PceI	AGGCCT	1 cut(s)	398
PfeI	GAWTC	1 cut(s)	188
PkrI	GCNGC	3 cut(s)	26, 98, 559
Ple19I	CGATCG	1 cut(s)	180
PleI	GAGTC	1 cut(s)	596
PpsI	GAGTC	1 cut(s)	596
PshBI	ATTAAT	1 cut(s)	351
PsiI	TTATAA	1 cut(s)	323
Psp6I	CCWGG	1 cut(s)	261
PspGI	CCWGG	1 cut(s)	261
PstI	CTGCAG	1 cut(s)	514
PvuI	CGATCG	1 cut(s)	180
SaqAI	TTAA	3 cut(s)	351, 452, 495
SatI	GCNGC	3 cut(s)	25, 97, 558
Sau3AI	GATC	4 cut(s)	65, 177, 199, 604
SchI	GAGTC	1 cut(s)	597
ScrFI	CCNGG	1 cut(s)	263
SetI	ASST	9 cut(s)	13, 26, 37, 186, 238, 283, 411, 426, 628
SfaNI	GCATC	3 cut(s)	320, 505, 557
SfcI	CTRYAG	1 cut(s)	510
SfuI	TTCGAA	1 cut(s)	218
SmlI	CTYRAG	2 cut(s)	494, 595
SmoI	CTYRAG	2 cut(s)	494, 595
Sse9I	AATT	3 cut(s)	146, 220, 369
SseBI	AGGCCT	1 cut(s)	398
SsiI	CCGC	1 cut(s)	97
SspI	AATATT	2 cut(s)	528, 579
SspMI	CTAG	3 cut(s)	17, 185, 643
StuI	AGGCCT	1 cut(s)	398
StyD4I	CCNGG	1 cut(s)	261
TaaI	ACNGT	1 cut(s)	302
TaqI	TCGA	3 cut(s)	144, 180, 218
TasI	AATT	3 cut(s)	146, 220, 369
TauI	GCSGC	1 cut(s)	99
TfiI	GAWTC	1 cut(s)	188
Tru1I	TTAA	3 cut(s)	351, 452, 495
Tru9I	TTAA	3 cut(s)	351, 452, 495
TscAI	CASTG	3 cut(s)	277, 387, 514
TseI	GCWGC	2 cut(s)	24, 557
TspDTI	ATGAA	3 cut(s)	130, 381, 635
TspRI	CASTG	3 cut(s)	277, 387, 514
Vha464I	CTTAAG	1 cut(s)	494
VspI	ATTAAT	1 cut(s)	351
XapI	RAATTY	2 cut(s)	146, 220
XspI	CTAG	3 cut(s)	17, 185, 643

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