Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6C

Orthogroup ID

OG0002279

Physical Location & Seq

Genomic Coordinates Reverse (-)

42112305 .. 42121450

Gene Structure 9146 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6CG250600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 747 bp

ATGCATATATACTCATATGTATCAGTGTGTGACTTCCCATGTGACATTGCCAGTGAGATTTCTCAGAGTTTTGCTTCCAAGGCTTTGATTAATGAGGTCAATGGCAAGCCAGATTTGGAGGCCGATCCTATAGAGTGTTGGTCCAAAGCAAGAGCTTTTCTTTTGTCACTACCTCAGGTTATATCACCAAATATGTTCAATATGCAACTTTGGGAAAAATGTGGTCATGCCGGAAAATACAAAAAGATTATGTTTGCTCTCGAGGTCCTGCTTGGTTTGTCAGGAGTATTGCTTGTAATGCTTTCTGTTCTTGGATCTGTTGGATTTTTCAGTGCTGTGAGAGTTAAATCTACATTAATCATAATGGAAGTCATTCCTTGCCTTGTTTTGGCTGTTGGTGTAGATAACATGTGTATATTGGTACATGCAATCACCGGAGTTACCTTTAGAATGACGATGGGAAGCTTCATGCCTATGCCAGCATGCCGAGTCTTCTCCATGTTTGCAGCCCTTGCTGTTTTGATGGACTTCTTTCTGCAAGTCACTGCATTTGTTGCGTTGATATACTCTGACCTTTTGAGAGCTGAGGATGGCAGGGTTGATTGTTTTCCTTGCATAAAAGTCTCGTCATCTTTTGTGGAATCCACGGAAGATGATGAAGAGAGGTCTGATGTAGACACACTAGGCACATTGAATGGAGTGGAAGATCTTAAGGTCTTAGACTGCTCAGTTCTTTATGATATTTAG

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

248

Amino Acids

27.26

Weight (kDa)

4.59

Isoelectric Point (pI)

37.62

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Patched	PF02460	85 - 147	3.2e-06	Patched SSD
Sterol-sensing	PF12349	87 - 145	1.8e-12	Sterol-sensing domain of SREBP cleavage-activation
Sterol-sensing	PF12349	151 - 207	7.6e-13	Sterol-sensing domain of SREBP cleavage-activation

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Align Labels (Cladogram)

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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)
AccI	GTMKAC	1 cut(s)	675
AclWI	GGATC	2 cut(s)	119, 322
AfaI	GTAC	1 cut(s)	423
AfiI	CCNNNNNNNGG	1 cut(s)	388
AflII	CTTAAG	1 cut(s)	710
AflIII	ACRYGT	1 cut(s)	408
AgsI	TTSAA	2 cut(s)	199, 694
AluBI	AGCT	3 cut(s)	155, 465, 584
AluI	AGCT	3 cut(s)	155, 465, 584
Alw26I	GTCTC	1 cut(s)	628
AlwI	GGATC	2 cut(s)	119, 322
Ama87I	CYCGRG	1 cut(s)	260
AoxI	GGCC	1 cut(s)	120
ApeKI	GCWGC	1 cut(s)	506
AseI	ATTAAT	2 cut(s)	90, 356
Asp700I	GAANNNNTTC	1 cut(s)	372
AspS9I	GGNCC	2 cut(s)	141, 265
AsuHPI	GGTGA	2 cut(s)	177, 424
AvaI	CYCGRG	1 cut(s)	260
AvaII	GGWCC	2 cut(s)	141, 265
AxyI	CCTNAGG	1 cut(s)	174
BbsI	GAAGAC	1 cut(s)	484
BbvCI	CCTCAGC	1 cut(s)	585
BbvI	GCAGC	1 cut(s)	518
BccI	CCATC	3 cut(s)	451, 517, 584
BcoDI	GTCTC	1 cut(s)	628
BfaI	CTAG	1 cut(s)	683
BfmI	CTRYAG	1 cut(s)	129
BfrI	CTTAAG	1 cut(s)	710
BglII	AGATCT	1 cut(s)	706
BisI	GCNGC	1 cut(s)	507
BlsI	GCNGC	1 cut(s)	508
Bme18I	GGWCC	2 cut(s)	141, 265
BmeT110I	CYCGRG	1 cut(s)	260
BmgT120I	GGNCC	2 cut(s)	141, 265
BpiI	GAAGAC	1 cut(s)	484
Bpu10I	CCTNAGC	1 cut(s)	585
BsaJI	CCNNGG	2 cut(s)	78, 645
BsaWI	WCCGGW	1 cut(s)	434
Bsc4I	CCNNNNNNNGG	1 cut(s)	388
Bse1I	ACTGG	1 cut(s)	51
Bse21I	CCTNAGG	1 cut(s)	174
Bse3DI	GCAATG	1 cut(s)	45
BseDI	CCNNGG	2 cut(s)	78, 645
BseGI	GGATG	1 cut(s)	595
BseLI	CCNNNNNNNGG	1 cut(s)	388
BseMI	GCAATG	1 cut(s)	45
BseMII	CTCAG	4 cut(s)	77, 188, 576, 741
BseNI	ACTGG	1 cut(s)	51
BseXI	GCAGC	1 cut(s)	518
BshFI	GGCC	1 cut(s)	122
BsiHKCI	CYCGRG	1 cut(s)	260
BsiSI	CCGG	2 cut(s)	231, 435
BslI	CCNNNNNNNGG	1 cut(s)	388
BsmAI	GTCTC	1 cut(s)	628
BsnI	GGCC	1 cut(s)	122
BsoBI	CYCGRG	1 cut(s)	260
Bsp143I	GATC	3 cut(s)	124, 314, 706
BspANI	GGCC	1 cut(s)	122
BspCNI	CTCAG	4 cut(s)	76, 187, 577, 740
BspPI	GGATC	2 cut(s)	119, 322
BspTI	CTTAAG	1 cut(s)	710
BsrDI	GCAATG	1 cut(s)	45
BsrI	ACTGG	1 cut(s)	51
BssECI	CCNNGG	2 cut(s)	78, 645
BssMI	GATC	3 cut(s)	124, 314, 706
BssT1I	CCWWGG	1 cut(s)	78
Bst6I	CTCTTC	1 cut(s)	654
BstAFI	CTTAAG	1 cut(s)	710
BstAPI	GCANNNNNTGC	2 cut(s)	512, 554
BstC8I	GCNNGC	3 cut(s)	107, 480, 484
BstDEI	CTNAG	5 cut(s)	63, 174, 585, 718, 727
BstDSI	CCRYGG	1 cut(s)	645
BstF5I	GGATG	1 cut(s)	595
BstKTI	GATC	3 cut(s)	127, 317, 709
BstMAI	GTCTC	1 cut(s)	628
BstMBI	GATC	3 cut(s)	124, 314, 706
BstMWI	GCNNNNNNNGC	4 cut(s)	80, 298, 512, 554
BstNSI	RCATGY	3 cut(s)	412, 428, 486
BstSFI	CTRYAG	1 cut(s)	129
BstV1I	GCAGC	1 cut(s)	518
BstV2I	GAAGAC	1 cut(s)	484
BstX2I	RGATCY	2 cut(s)	314, 706
BstYI	RGATCY	2 cut(s)	314, 706
Bsu36I	CCTNAGG	1 cut(s)	174
BsuRI	GGCC	1 cut(s)	122
BtgI	CCRYGG	1 cut(s)	645
BtsCI	GGATG	1 cut(s)	595
BtsI	GCAGTG	1 cut(s)	543
BtsIMutI	CAGTG	4 cut(s)	30, 58, 337, 543
Cac8I	GCNNGC	3 cut(s)	107, 480, 484
Cfr13I	GGNCC	2 cut(s)	141, 265
Csp6I	GTAC	1 cut(s)	422
CviAII	CATG	7 cut(s)	39, 227, 409, 425, 469, 483, 499
CviJI	RGCY	8 cut(s)	83, 109, 122, 155, 392, 465, 509, 584
CviKI_1	RGCY	8 cut(s)	83, 109, 122, 155, 392, 465, 509, 584
CviQI	GTAC	1 cut(s)	422
DdeI	CTNAG	5 cut(s)	63, 174, 585, 718, 727
DpnI	GATC	3 cut(s)	126, 316, 708
DpnII	GATC	3 cut(s)	124, 314, 706
Eam1104I	CTCTTC	1 cut(s)	654
EarI	CTCTTC	1 cut(s)	654
Eco130I	CCWWGG	1 cut(s)	78
Eco47I	GGWCC	2 cut(s)	141, 265
Eco81I	CCTNAGG	1 cut(s)	174
Eco88I	CYCGRG	1 cut(s)	260
EcoO109I	RGGNCCY	1 cut(s)	265
EcoT14I	CCWWGG	1 cut(s)	78
EcoT22I	ATGCAT	1 cut(s)	6
ErhI	CCWWGG	1 cut(s)	78
FaeI	CATG	7 cut(s)	42, 230, 412, 428, 472, 486, 502
FatI	CATG	7 cut(s)	38, 226, 408, 424, 468, 482, 498
FauNDI	CATATG	1 cut(s)	16
FblI	GTMKAC	1 cut(s)	675
Fnu4HI	GCNGC	1 cut(s)	507
FokI	GGATG	1 cut(s)	602
Fsp4HI	GCNGC	1 cut(s)	507
FspBI	CTAG	1 cut(s)	683
GluI	GCNGC	1 cut(s)	507
HaeIII	GGCC	1 cut(s)	122
HapII	CCGG	2 cut(s)	231, 435
Hin1II	CATG	7 cut(s)	42, 230, 412, 428, 472, 486, 502
HindIII	AAGCTT	1 cut(s)	463
HinfI	GANTC	2 cut(s)	489, 641
HpaII	CCGG	2 cut(s)	231, 435
HphI	GGTGA	2 cut(s)	177, 424
Hpy166II	GTNNAC	1 cut(s)	676
Hpy188I	TCNGA	3 cut(s)	66, 571, 670
Hpy188III	TCNNGA	2 cut(s)	260, 282
Hpy8I	GTNNAC	1 cut(s)	676
HpyCH4V	TGCA	7 cut(s)	4, 205, 428, 506, 538, 548, 615
HpyF10VI	GCNNNNNNNGC	4 cut(s)	80, 298, 512, 554
HpyF3I	CTNAG	5 cut(s)	63, 174, 585, 718, 727
Hsp92II	CATG	7 cut(s)	42, 230, 412, 428, 472, 486, 502
Kzo9I	GATC	3 cut(s)	124, 314, 706
LpnPI	CCDG	9 cut(s)	64, 123, 161, 244, 267, 281, 448, 492, 580
Lsp1109I	GCAGC	1 cut(s)	518
MaeI	CTAG	1 cut(s)	683
MaeIII	GTNAC	5 cut(s)	29, 41, 165, 439, 541
MalI	GATC	3 cut(s)	126, 316, 708
MboI	GATC	3 cut(s)	124, 314, 706
MboII	GAAGA	4 cut(s)	484, 662, 671, 716
MflI	RGATCY	2 cut(s)	314, 706
MlyI	GAGTC	1 cut(s)	498
MmeI	TCCRAC	1 cut(s)	301
MnlI	CCTC	6 cut(s)	88, 112, 183, 256, 580, 657
Mph1103I	ATGCAT	1 cut(s)	6
MroXI	GAANNNNTTC	1 cut(s)	372
MseI	TTAA	4 cut(s)	90, 345, 356, 711
MslI	CAYNNNNRTG	1 cut(s)	473
MspCI	CTTAAG	1 cut(s)	710
MspI	CCGG	2 cut(s)	231, 435
MwoI	GCNNNNNNNGC	4 cut(s)	80, 298, 512, 554
NdeI	CATATG	1 cut(s)	16
NdeII	GATC	3 cut(s)	124, 314, 706
NlaIII	CATG	7 cut(s)	42, 230, 412, 428, 472, 486, 502
NmeAIII	GCCGAG	1 cut(s)	512
NmuCI	GTSAC	4 cut(s)	29, 41, 165, 541
NsiI	ATGCAT	1 cut(s)	6
NspI	RCATGY	3 cut(s)	412, 428, 486
PaeI	GCATGC	1 cut(s)	486
PaeR7I	CTCGAG	1 cut(s)	260
PciI	ACATGT	1 cut(s)	408
PdmI	GAANNNNTTC	1 cut(s)	372
PfeI	GAWTC	1 cut(s)	641
PkrI	GCNGC	1 cut(s)	508
PleI	GAGTC	1 cut(s)	497
PpsI	GAGTC	1 cut(s)	497
PpuMI	RGGWCCY	1 cut(s)	265
PscI	ACATGT	1 cut(s)	408
PshBI	ATTAAT	2 cut(s)	90, 356
Psp5II	RGGWCCY	1 cut(s)	265
PspPI	GGNCC	2 cut(s)	141, 265
PspPPI	RGGWCCY	1 cut(s)	265
PsuI	RGATCY	2 cut(s)	314, 706
RsaI	GTAC	1 cut(s)	423
RsaNI	GTAC	1 cut(s)	422
RseI	CAYNNNNRTG	1 cut(s)	473
SaqAI	TTAA	4 cut(s)	90, 345, 356, 711
SatI	GCNGC	1 cut(s)	507
Sau3AI	GATC	3 cut(s)	124, 314, 706
Sau96I	GGNCC	2 cut(s)	141, 265
SchI	GAGTC	1 cut(s)	498
SfcI	CTRYAG	1 cut(s)	129
Sfr274I	CTCGAG	1 cut(s)	260
SinI	GGWCC	2 cut(s)	141, 265
SlaI	CTCGAG	1 cut(s)	260
SmiMI	CAYNNNNRTG	1 cut(s)	473
SmlI	CTYRAG	2 cut(s)	260, 710
SmoI	CTYRAG	2 cut(s)	260, 710
SphI	GCATGC	1 cut(s)	486
SspMI	CTAG	1 cut(s)	683
StyI	CCWWGG	1 cut(s)	78
TaqI	TCGA	1 cut(s)	261
TfiI	GAWTC	1 cut(s)	641
Tru1I	TTAA	4 cut(s)	90, 345, 356, 711
Tru9I	TTAA	4 cut(s)	90, 345, 356, 711
TscAI	CASTG	4 cut(s)	30, 58, 337, 550
TseFI	GTSAC	4 cut(s)	29, 41, 165, 541
TseI	GCWGC	1 cut(s)	506
Tsp45I	GTSAC	4 cut(s)	29, 41, 165, 541
TspDTI	ATGAA	2 cut(s)	457, 672
TspGWI	ACGGA	1 cut(s)	662
TspRI	CASTG	4 cut(s)	30, 58, 337, 550
Vha464I	CTTAAG	1 cut(s)	710
VpaK11BI	GGWCC	2 cut(s)	141, 265
VspI	ATTAAT	2 cut(s)	90, 356
XceI	RCATGY	3 cut(s)	412, 428, 486
XhoI	CTCGAG	1 cut(s)	260
XmiI	GTMKAC	1 cut(s)	675
XmnI	GAANNNNTTC	1 cut(s)	372
XspI	CTAG	1 cut(s)	683
Zsp2I	ATGCAT	1 cut(s)	6

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