Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6D

Orthogroup ID

OG0002279

Physical Location & Seq

Genomic Coordinates Reverse (-)

42961449 .. 42969373

Gene Structure 7925 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6DG242200.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 894 bp

ATGGGAAGTGCACAGAAGTCGTTTGTGAAATGTCTGAGAGACATGTTATCTCTGGGAGGTCAGGTGCATTGTGAGGAAGCTCAAATTGGCAATAAGATGTTCCAAAACACGGTATGTAAGCTTGACATAGAAACATTGGTTATATCACCAAATATGTTCAATATGCAACTTTGGGAAAAATGTGGTCATGCCGGAAAATACAAAAAGATTATGTTTGCTCTCGAGGCTTCAGCATTCGTAGTCACCTACCCAGTTAATAATGCAGTTGATGATGTAGGAAATGAGAATGGGAAGGCACTGGCTTGGGAGAAGGCTTTTATTCAGTTAGAAAAGGATGAACTGCTGCCAATGGTGCTGTCTCGGAATCTGAGTCTCTCATTTTCGGCCGAAAGCTCAACTGAGGAAGAATTAAAAAGAGAAAGTACTGCAGATGTTATGACCATAATAGTAAGCTATCTGGTCCTGCTTGGTTTGTCAGGAGTATTGCTTGTAATGCTTTCTGTTCTTGGATCTGTTGGATTTTTCAGTGCTGTGAGAGTTAAATCTACATTAATCATAATGGAAGTCATTCCTTGCCTTGTTTTGGCTGTTGGTGTAGATAACATGTGTATATTGGTACATGCAATCACCGGAGTTACCTTTAGAATGACGATGGGAAGCTTCATTCCTATGCCAGCATGCCGAGTCTTCTCCATGATTGCAGCCCTTGCTGTTTTGATGGACTTCTTTCTGCAAGTCACTGCATTTGTTGCGTTGATATACTTTGACCTTTTGAGAGCTGAGGATGGCAGGTTTGATTGTTTTCCATGCATAAAAGTCTCGTCATCTTTTGTGGAATCCACTGAAGGTATATTTGTGTGCTATGATAGTGTGTTGAGGTTGCTTTGCCTTTAG

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

297

Amino Acids

32.72

Weight (kDa)

5.09

Isoelectric Point (pI)

31.77

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Patched	PF02460	146 - 212	3.4e-06	Patched SSD
Sterol-sensing	PF12349	154 - 211	6.6e-12	Sterol-sensing domain of SREBP cleavage-activation
Sterol-sensing	PF12349	216 - 272	7.6e-12	Sterol-sensing domain of SREBP cleavage-activation

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

Tree File

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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)
Acc36I	ACCTGC	1 cut(s)	780
AclWI	GGATC	1 cut(s)	517
AcoI	YGGCCR	1 cut(s)	384
AcuI	CTGAAG	2 cut(s)	213, 864
AfaI	GTAC	2 cut(s)	424, 618
AfiI	CCNNNNNNNGG	2 cut(s)	109, 583
AflIII	ACRYGT	2 cut(s)	42, 603
AgsI	TTSAA	1 cut(s)	160
AjuI	GAANNNNNNNTTGG	2 cut(s)	69, 101
AluBI	AGCT	6 cut(s)	80, 121, 393, 453, 660, 779
AluI	AGCT	6 cut(s)	80, 121, 393, 453, 660, 779
Alw21I	GWGCWC	1 cut(s)	13
Alw26I	GTCTC	4 cut(s)	33, 363, 377, 823
Alw44I	GTGCAC	1 cut(s)	9
AlwI	GGATC	1 cut(s)	517
Ama87I	CYCGRG	1 cut(s)	221
AoxI	GGCC	1 cut(s)	384
ApaLI	GTGCAC	1 cut(s)	9
ApeKI	GCWGC	2 cut(s)	343, 701
AseI	ATTAAT	1 cut(s)	551
Asp700I	GAANNNNTTC	1 cut(s)	567
AspS9I	GGNCC	1 cut(s)	460
AsuHPI	GGTGA	3 cut(s)	138, 235, 619
AvaI	CYCGRG	1 cut(s)	221
AvaII	GGWCC	1 cut(s)	460
BaeGI	GKGCMC	1 cut(s)	13
BbsI	GAAGAC	1 cut(s)	679
Bbv12I	GWGCWC	1 cut(s)	13
BbvCI	CCTCAGC	1 cut(s)	780
BbvI	GCAGC	2 cut(s)	330, 713
BccI	CCATC	3 cut(s)	646, 712, 779
BcgI	CGANNNNNNTGC	1 cut(s)	34
BcoDI	GTCTC	4 cut(s)	33, 363, 377, 823
BfmI	CTRYAG	1 cut(s)	426
BfuAI	ACCTGC	1 cut(s)	780
BisI	GCNGC	2 cut(s)	344, 702
BlsI	GCNGC	2 cut(s)	345, 703
BmcAI	AGTACT	1 cut(s)	424
Bme18I	GGWCC	1 cut(s)	460
BmeT110I	CYCGRG	1 cut(s)	221
BmgT120I	GGNCC	1 cut(s)	460
BmrI	ACTGGG	1 cut(s)	245
BmuI	ACTGGG	1 cut(s)	245
BpiI	GAAGAC	1 cut(s)	679
Bpu10I	CCTNAGC	1 cut(s)	780
BsaWI	WCCGGW	1 cut(s)	629
BsaXI	ACNNNNNCTCC	2 cut(s)	48, 78
Bsc4I	CCNNNNNNNGG	2 cut(s)	109, 583
Bse1I	ACTGG	2 cut(s)	251, 303
BseGI	GGATG	2 cut(s)	340, 790
BseLI	CCNNNNNNNGG	2 cut(s)	109, 583
BseMII	CTCAG	4 cut(s)	26, 359, 390, 771
BseNI	ACTGG	2 cut(s)	251, 303
BseSI	GKGCMC	1 cut(s)	13
BseX3I	CGGCCG	1 cut(s)	384
BseXI	GCAGC	2 cut(s)	330, 713
Bsh1285I	CGRYCG	1 cut(s)	387
BshFI	GGCC	1 cut(s)	386
BsiEI	CGRYCG	1 cut(s)	387
BsiHKAI	GWGCWC	1 cut(s)	13
BsiHKCI	CYCGRG	1 cut(s)	221
BsiSI	CCGG	2 cut(s)	192, 630
BslI	CCNNNNNNNGG	2 cut(s)	109, 583
BsmAI	GTCTC	4 cut(s)	33, 363, 377, 823
BsmI	GAATGC	1 cut(s)	233
BsnI	GGCC	1 cut(s)	386
BsoBI	CYCGRG	1 cut(s)	221
Bsp1286I	GDGCHC	1 cut(s)	13
Bsp143I	GATC	1 cut(s)	509
BspANI	GGCC	1 cut(s)	386
BspCNI	CTCAG	4 cut(s)	27, 360, 391, 772
BspMAI	CTGCAG	1 cut(s)	430
BspMI	ACCTGC	1 cut(s)	780
BspPI	GGATC	1 cut(s)	517
BsrI	ACTGG	2 cut(s)	251, 303
BssMI	GATC	1 cut(s)	509
Bst4CI	ACNGT	1 cut(s)	112
BstAPI	GCANNNNNTGC	2 cut(s)	707, 749
BstC8I	GCNNGC	2 cut(s)	675, 679
BstDEI	CTNAG	4 cut(s)	35, 368, 399, 780
BstF5I	GGATG	2 cut(s)	340, 790
BstKTI	GATC	1 cut(s)	512
BstMAI	GTCTC	4 cut(s)	33, 363, 377, 823
BstMBI	GATC	1 cut(s)	509
BstMCI	CGRYCG	1 cut(s)	387
BstMWI	GCNNNNNNNGC	5 cut(s)	224, 352, 493, 707, 749
BstNSI	RCATGY	4 cut(s)	46, 607, 623, 681
BstSFI	CTRYAG	1 cut(s)	426
BstSLI	GKGCMC	1 cut(s)	13
BstV1I	GCAGC	2 cut(s)	330, 713
BstV2I	GAAGAC	1 cut(s)	679
BstX2I	RGATCY	1 cut(s)	509
BstYI	RGATCY	1 cut(s)	509
BstZI	CGGCCG	1 cut(s)	384
BsuRI	GGCC	1 cut(s)	386
BtsCI	GGATG	2 cut(s)	340, 790
BtsI	GCAGTG	1 cut(s)	738
BtsIMutI	CAGTG	4 cut(s)	296, 532, 738, 840
BveI	ACCTGC	1 cut(s)	780
Cac8I	GCNNGC	2 cut(s)	675, 679
Cfr13I	GGNCC	1 cut(s)	460
Csp6I	GTAC	2 cut(s)	423, 617
CviAII	CATG	7 cut(s)	43, 188, 604, 620, 678, 694, 807
CviQI	GTAC	2 cut(s)	423, 617
DdeI	CTNAG	4 cut(s)	35, 368, 399, 780
DpnI	GATC	1 cut(s)	511
DpnII	GATC	1 cut(s)	509
EaeI	YGGCCR	1 cut(s)	384
EagI	CGGCCG	1 cut(s)	384
EclXI	CGGCCG	1 cut(s)	384
Eco47I	GGWCC	1 cut(s)	460
Eco52I	CGGCCG	1 cut(s)	384
Eco57I	CTGAAG	2 cut(s)	213, 864
Eco88I	CYCGRG	1 cut(s)	221
EcoT22I	ATGCAT	1 cut(s)	812
FaeI	CATG	7 cut(s)	46, 191, 607, 623, 681, 697, 810
FatI	CATG	7 cut(s)	42, 187, 603, 619, 677, 693, 806
Fnu4HI	GCNGC	2 cut(s)	344, 702
FokI	GGATG	2 cut(s)	347, 797
Fsp4HI	GCNGC	2 cut(s)	344, 702
GluI	GCNGC	2 cut(s)	344, 702
HaeIII	GGCC	1 cut(s)	386
HapII	CCGG	2 cut(s)	192, 630
Hin1II	CATG	7 cut(s)	46, 191, 607, 623, 681, 697, 810
HindIII	AAGCTT	2 cut(s)	119, 658
HinfI	GANTC	4 cut(s)	364, 370, 684, 836
HpaII	CCGG	2 cut(s)	192, 630
HphI	GGTGA	3 cut(s)	138, 235, 619
Hpy166II	GTNNAC	1 cut(s)	11
Hpy188I	TCNGA	3 cut(s)	36, 363, 369
Hpy188III	TCNNGA	2 cut(s)	221, 477
Hpy8I	GTNNAC	1 cut(s)	11
HpyAV	CCTTC	3 cut(s)	286, 304, 839
HpyCH4III	ACNGT	1 cut(s)	112
HpyF10VI	GCNNNNNNNGC	5 cut(s)	224, 352, 493, 707, 749
HpyF3I	CTNAG	4 cut(s)	35, 368, 399, 780
Hsp92II	CATG	7 cut(s)	46, 191, 607, 623, 681, 697, 810
Kzo9I	GATC	1 cut(s)	509
Lsp1109I	GCAGC	2 cut(s)	330, 713
MaeIII	GTNAC	3 cut(s)	241, 634, 736
MalI	GATC	1 cut(s)	511
MboI	GATC	1 cut(s)	509
MboII	GAAGA	2 cut(s)	416, 679
MflI	RGATCY	1 cut(s)	509
MhlI	GDGCHC	1 cut(s)	13
MluCI	AATT	2 cut(s)	84, 407
MlyI	GAGTC	2 cut(s)	379, 693
MmeI	TCCRAC	1 cut(s)	496
MnlI	CCTC	6 cut(s)	50, 67, 217, 394, 775, 870
Mph1103I	ATGCAT	1 cut(s)	812
MroXI	GAANNNNTTC	1 cut(s)	567
MseI	TTAA	4 cut(s)	255, 410, 540, 551
MslI	CAYNNNNRTG	1 cut(s)	668
MspI	CCGG	2 cut(s)	192, 630
Mva1269I	GAATGC	1 cut(s)	233
MwoI	GCNNNNNNNGC	5 cut(s)	224, 352, 493, 707, 749
NdeII	GATC	1 cut(s)	509
NlaIII	CATG	7 cut(s)	46, 191, 607, 623, 681, 697, 810
NmeAIII	GCCGAG	1 cut(s)	707
NmuCI	GTSAC	2 cut(s)	241, 736
NsiI	ATGCAT	1 cut(s)	812
NspI	RCATGY	4 cut(s)	46, 607, 623, 681
PaeI	GCATGC	1 cut(s)	681
PaeR7I	CTCGAG	1 cut(s)	221
PciI	ACATGT	2 cut(s)	42, 603
PctI	GAATGC	1 cut(s)	233
PdmI	GAANNNNTTC	1 cut(s)	567
PfeI	GAWTC	2 cut(s)	364, 836
PkrI	GCNGC	2 cut(s)	345, 703
PleI	GAGTC	2 cut(s)	378, 692
PpsI	GAGTC	2 cut(s)	378, 692
PscI	ACATGT	2 cut(s)	42, 603
PshBI	ATTAAT	1 cut(s)	551
PspPI	GGNCC	1 cut(s)	460
PstI	CTGCAG	1 cut(s)	430
PsuI	RGATCY	1 cut(s)	509
RsaI	GTAC	2 cut(s)	424, 618
RsaNI	GTAC	2 cut(s)	423, 617
RseI	CAYNNNNRTG	1 cut(s)	668
SaqAI	TTAA	4 cut(s)	255, 410, 540, 551
SatI	GCNGC	2 cut(s)	344, 702
Sau3AI	GATC	1 cut(s)	509
Sau96I	GGNCC	1 cut(s)	460
ScaI	AGTACT	1 cut(s)	424
SchI	GAGTC	2 cut(s)	379, 693
SduI	GDGCHC	1 cut(s)	13
SfcI	CTRYAG	1 cut(s)	426
Sfr274I	CTCGAG	1 cut(s)	221
SinI	GGWCC	1 cut(s)	460
SlaI	CTCGAG	1 cut(s)	221
SmiMI	CAYNNNNRTG	1 cut(s)	668
SmlI	CTYRAG	1 cut(s)	221
SmoI	CTYRAG	1 cut(s)	221
SphI	GCATGC	1 cut(s)	681
Sse9I	AATT	2 cut(s)	84, 407
TaaI	ACNGT	1 cut(s)	112
TaqI	TCGA	1 cut(s)	222
TasI	AATT	2 cut(s)	84, 407
TatI	WGTACW	1 cut(s)	422
TfiI	GAWTC	2 cut(s)	364, 836
Tru1I	TTAA	4 cut(s)	255, 410, 540, 551
Tru9I	TTAA	4 cut(s)	255, 410, 540, 551
TscAI	CASTG	4 cut(s)	303, 532, 745, 847
TseFI	GTSAC	2 cut(s)	241, 736
TseI	GCWGC	2 cut(s)	343, 701
Tsp45I	GTSAC	2 cut(s)	241, 736
TspDTI	ATGAA	2 cut(s)	351, 652
TspRI	CASTG	4 cut(s)	303, 532, 745, 847
VneI	GTGCAC	1 cut(s)	9
VpaK11BI	GGWCC	1 cut(s)	460
VspI	ATTAAT	1 cut(s)	551
XceI	RCATGY	4 cut(s)	46, 607, 623, 681
XhoI	CTCGAG	1 cut(s)	221
XmnI	GAANNNNTTC	1 cut(s)	567
ZrmI	AGTACT	1 cut(s)	424
Zsp2I	ATGCAT	1 cut(s)	812

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