Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4D

Orthogroup ID

OG0000328

Physical Location & Seq

Genomic Coordinates Forward (+)

43857973 .. 43860023

Gene Structure 2051 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4DG231900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 555 bp

ATGATGCAGTCCATGCCGGAGCTCCGCCTTGTTCCCTCGTCGAGCCCACCATGGAAGATAAGACCTAACATTCAAGACAAGGCTCGCCGTCGATTCAGGAATACCTTGTTACAGCATCCAAGAACCAGATCTTGTATGTCTTCTTCAGTTCCCCTAGACTCCGGACTGCAGACATTGACAAAAAAAGCATCCGAAAGGAGAAACCGGAGGAGTTGGTTATGGTTCTTGCTCAGGCAAAGGCAGAAGCCATCCGGCCTAAGCTCCCAGTTGATGACTACGACAAATTATGCGGAAACTGTGCCGACTGCATGTTGGGAATACAGTACCCGCCCAATTTTTGGGTGGGGTGATGTTGGCTCCAAGCAGAAGCCTACTGCTGGATGGTTAGCAGCTTTTCCCGTATTTGAACCCCATTGGCAAATATGCATGGCTGGTGGATTGTCAACAAGCATTTGCTTATCTCTTGCATGCTTGCAAATAATTCTCTGGTTTATGTGGATTGATGACTTGTTGTTAACTTTGGAGATGAAACTTTACTTGCCAAATTATCTTTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003824 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0006082 GO:0006629 GO:0006631 GO:0006720 GO:0006721 GO:0006725 GO:0006766 GO:0006775 GO:0006778 GO:0006807 GO:0006810 GO:0006950 GO:0006970 GO:0006979 GO:0008150 GO:0008152 GO:0008643 GO:0009058 GO:0009110 GO:0009266 GO:0009314 GO:0009416 GO:0009507 GO:0009526 GO:0009528 GO:0009532 GO:0009534 GO:0009536 GO:0009570 GO:0009579 GO:0009628 GO:0009642 GO:0009644 GO:0009651 GO:0009706 GO:0009915 GO:0009941 GO:0009975 GO:0009976 GO:0009987 GO:0010189 GO:0010232 GO:0010233 GO:0010287 GO:0015766 GO:0015770 GO:0015772 GO:0015994 GO:0016020 GO:0016108 GO:0016116 GO:0016122 GO:0018130 GO:0019752 GO:0019866 GO:0031090 GO:0031347 GO:0031967 GO:0031969 GO:0031975 GO:0031976 GO:0031984 GO:0032501 GO:0032787 GO:0033013 GO:0042170 GO:0042360 GO:0042362 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043436 GO:0044237 GO:0044238 GO:0044249 GO:0044255 GO:0044281 GO:0044283 GO:0044422 GO:0044424 GO:0044434 GO:0044435 GO:0044444 GO:0044446 GO:0044464 GO:0046483 GO:0048583 GO:0050789 GO:0050896 GO:0051179 GO:0051186 GO:0051234 GO:0065007 GO:0071702 GO:0071704 GO:0080134 GO:1901360 GO:1901362 GO:1901564 GO:1901576 GO:1901615 GO:1901617

KEGG Pathways

Metabolic & Signaling

ko00130 ko01100 ko01110 map00130 map01100 map01110

Pfam Domains

Protein Families

Tocopherol_cycl

Protein Analysis

184

Amino Acids

21.29

Weight (kDa)

10.04

Isoelectric Point (pI)

90.46

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Tocopherol_cycl	PF14249	101 - 149	4e-19	Tocopherol cyclase

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Publication-ready

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Orthologous Genes (Group: OG0000328)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_2g13832 FvH4_3g26701 FvH4_4g14350 FvH4_7g17370
malus_domestica	MD12G1077900.v1.1 MD14G1070200.v1.1
prunus_persica	Prupe.2G073100_v2.0.a1 Prupe.2G186800_v2.0.a1 Prupe.2G186800_v2.0.a1 Prupe.2G186800_v2.0.a1
rosa_chinensis	RchiOBHm_Chr1g0365191 RchiOBHm_Chr2g0105141 RchiOBHm_Chr2g0120431 RchiOBHm_Chr2g0139381 RchiOBHm_Chr3g0494421 RchiOBHm_Chr6g0248181 RchiOBHm_Chr7g0235571
rosa_laevigata	RLG00000005158 RLG00000008937 RLG00000013742 RLG00000015899 RLG00000019885 RLG00000024515 RLG00000024516 RLG00000028740 RLG00000030656 RLG00000030662 RLG00000032758 RLG00000035668 RLG00000036717 RLG00000036718
rosa_multiflora	Rmu_sc0000252.1_g000016 Rmu_sc0001386.1_g000020 Rmu_sc0002271.1_g000010 Rmu_sc0003833.1_g000002 Rmu_sc0004718.1_g000004 Rmu_sc0006031.1_g000006 Rmu_sc0006598.1_g000013 Rmu_sc0007472.1_g000023 Rmu_sc0009313.1_g000012
rosa_roxburghii	Rroxscaffold_2G00103830 Rroxscaffold_2G00109880 Rroxscaffold_3G00225910 Rroxscaffold_3G00271600 Rroxscaffold_3G00274560 Rroxscaffold_4G00299580 Rroxscaffold_5G00352530 Rroxscaffold_5G00379280 Rroxscaffold_7G00177320
rosa_rugosa	Rorug01G0027200 Rorug01G0032100 Rorug02G0050600 Rorug02G0054800 Rorug04G0083300 Rorug05G0115200 Rorug07G0006800
rosa_samantha	Rh1CG086700 Rh1DG093300 Rh1DG217000 Rh2AG120200 Rh2AG227900 Rh2AG254000 Rh2AG434200 Rh2AG469200 Rh2BG159500 Rh2CG419900 Rh2CG455200 Rh2DG320100 Rh2DG603500 Rh3CG319900 Rh3DG300800 Rh3DG319200 Rh4AG199400 Rh4BG329100 Rh4BG329200 Rh4CG110800 Rh4DG042000 Rh4DG129400 Rh4DG187700 Rh4DG231900 Rh5AG038800 Rh5AG107300 Rh5AG303600 Rh5AG386500 Rh5AG454200 Rh5CG041800 Rh5CG534800 Rh5DG076400 Rh5DG109800 Rh5DG123600 Rh6AG164400 Rh6BG035100 Rh6BG036000 Rh6BG041000 Rh6BG215500 Rh6CG173900 Rh6CG174000 Rh6DG020300 Rh6DG166300 Rh6DG320000 Rh6DG509700 Rh7AG059500 Rh7AG291700 Rh7BG404300 Rh7DG402000
rosa_wichuraiana	Rw1G000890 Rw1G020020 Rw3G005730 Rw4G011330 Rw4G026960 Rw5G014010 Rw6G002230 Rw7G038480

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	338
AccIII	TCCGGA	1 cut(s)	161
AciI	CCGC	3 cut(s)	25, 290, 328
AcuI	CTGAAG	1 cut(s)	129
AfaI	GTAC	1 cut(s)	325
AfiI	CCNNNNNNNGG	2 cut(s)	338, 377
AgsI	TTSAA	2 cut(s)	74, 407
AluBI	AGCT	3 cut(s)	22, 261, 392
AluI	AGCT	3 cut(s)	22, 261, 392
Alw21I	GWGCWC	1 cut(s)	24
Aor13HI	TCCGGA	1 cut(s)	161
AoxI	GGCC	1 cut(s)	253
ApeKI	GCWGC	1 cut(s)	389
AsuHPI	GGTGA	1 cut(s)	359
BanII	GRGCYC	2 cut(s)	24, 47
BarI	GAAGNNNNNNTAC	2 cut(s)	127, 159
BbsI	GAAGAC	1 cut(s)	132
Bbv12I	GWGCWC	1 cut(s)	24
BbvI	GCAGC	1 cut(s)	401
BccI	CCATC	2 cut(s)	256, 375
BceAI	ACGGC	1 cut(s)	72
BfaI	CTAG	1 cut(s)	155
BfmI	CTRYAG	1 cut(s)	167
BglII	AGATCT	1 cut(s)	128
BisI	GCNGC	1 cut(s)	390
BlsI	GCNGC	1 cut(s)	391
BmiI	GGNNCC	1 cut(s)	358
BmrI	ACTGGG	1 cut(s)	259
BmsI	GCATC	2 cut(s)	124, 197
BmuI	ACTGGG	1 cut(s)	259
BpiI	GAAGAC	1 cut(s)	132
Bpu10I	CCTNAGC	2 cut(s)	230, 257
BsaJI	CCNNGG	1 cut(s)	50
BsaWI	WCCGGW	2 cut(s)	161, 204
Bsc4I	CCNNNNNNNGG	2 cut(s)	338, 377
Bse1I	ACTGG	1 cut(s)	265
BseAI	TCCGGA	1 cut(s)	161
BseDI	CCNNGG	1 cut(s)	50
BseGI	GGATG	4 cut(s)	115, 188, 248, 386
BseLI	CCNNNNNNNGG	2 cut(s)	338, 377
BseMII	CTCAG	1 cut(s)	244
BseNI	ACTGG	1 cut(s)	265
BseRI	GAGGAG	1 cut(s)	223
BseXI	GCAGC	1 cut(s)	401
BshFI	GGCC	1 cut(s)	255
BsiHKAI	GWGCWC	1 cut(s)	24
BsiSI	CCGG	4 cut(s)	17, 162, 205, 252
BslI	CCNNNNNNNGG	2 cut(s)	338, 377
BsnI	GGCC	1 cut(s)	255
Bsp1286I	GDGCHC	2 cut(s)	24, 47
Bsp13I	TCCGGA	1 cut(s)	161
Bsp143I	GATC	1 cut(s)	128
Bsp19I	CCATGG	1 cut(s)	50
BspACI	CCGC	3 cut(s)	25, 290, 328
BspANI	GGCC	1 cut(s)	255
BspCNI	CTCAG	1 cut(s)	243
BspEI	TCCGGA	1 cut(s)	161
BspLI	GGNNCC	1 cut(s)	358
BspMAI	CTGCAG	1 cut(s)	171
BsrI	ACTGG	1 cut(s)	265
BssECI	CCNNGG	1 cut(s)	50
BssMI	GATC	1 cut(s)	128
BssT1I	CCWWGG	1 cut(s)	50
Bst4CI	ACNGT	2 cut(s)	298, 323
BstAPI	GCANNNNNTGC	1 cut(s)	13
BstC8I	GCNNGC	3 cut(s)	85, 469, 473
BstDEI	CTNAG	2 cut(s)	230, 257
BstDSI	CCRYGG	1 cut(s)	50
BstF5I	GGATG	4 cut(s)	115, 188, 248, 386
BstKTI	GATC	1 cut(s)	131
BstMBI	GATC	1 cut(s)	128
BstMWI	GCNNNNNNNGC	1 cut(s)	13
BstNSI	RCATGY	2 cut(s)	312, 471
BstSFI	CTRYAG	1 cut(s)	167
BstV1I	GCAGC	1 cut(s)	401
BstV2I	GAAGAC	1 cut(s)	132
BstX2I	RGATCY	1 cut(s)	128
BstYI	RGATCY	1 cut(s)	128
BsuRI	GGCC	1 cut(s)	255
BtgI	CCRYGG	1 cut(s)	50
BtsCI	GGATG	4 cut(s)	115, 188, 248, 386
Cac8I	GCNNGC	3 cut(s)	85, 469, 473
Csp6I	GTAC	1 cut(s)	324
CviAII	CATG	5 cut(s)	13, 51, 309, 427, 468
CviQI	GTAC	1 cut(s)	324
DdeI	CTNAG	2 cut(s)	230, 257
DpnI	GATC	1 cut(s)	130
DpnII	GATC	1 cut(s)	128
EciI	GGCGGA	1 cut(s)	14
Ecl136II	GAGCTC	1 cut(s)	22
Eco130I	CCWWGG	1 cut(s)	50
Eco24I	GRGCYC	2 cut(s)	24, 47
Eco53kI	GAGCTC	1 cut(s)	22
Eco57I	CTGAAG	1 cut(s)	129
EcoICRI	GAGCTC	1 cut(s)	22
EcoT14I	CCWWGG	1 cut(s)	50
EcoT22I	ATGCAT	1 cut(s)	428
EcoT38I	GRGCYC	2 cut(s)	24, 47
ErhI	CCWWGG	1 cut(s)	50
FaeI	CATG	5 cut(s)	16, 54, 312, 430, 471
FatI	CATG	5 cut(s)	12, 50, 308, 426, 467
FauI	CCCGC	1 cut(s)	335
Fnu4HI	GCNGC	1 cut(s)	390
FokI	GGATG	4 cut(s)	102, 175, 235, 393
FriOI	GRGCYC	2 cut(s)	24, 47
Fsp4HI	GCNGC	1 cut(s)	390
FspBI	CTAG	1 cut(s)	155
GluI	GCNGC	1 cut(s)	390
HaeIII	GGCC	1 cut(s)	255
HapII	CCGG	4 cut(s)	17, 162, 205, 252
Hin1II	CATG	5 cut(s)	16, 54, 312, 430, 471
HincII	GTYRAC	2 cut(s)	444, 516
HindII	GTYRAC	2 cut(s)	444, 516
HinfI	GANTC	2 cut(s)	93, 158
HpaI	GTTAAC	1 cut(s)	516
HpaII	CCGG	4 cut(s)	17, 162, 205, 252
HphI	GGTGA	1 cut(s)	359
Hpy166II	GTNNAC	2 cut(s)	444, 516
Hpy188I	TCNGA	1 cut(s)	193
Hpy188III	TCNNGA	3 cut(s)	74, 97, 162
Hpy8I	GTNNAC	2 cut(s)	444, 516
Hpy99I	CGWCG	2 cut(s)	43, 93
HpyCH4III	ACNGT	2 cut(s)	298, 323
HpyCH4V	TGCA	6 cut(s)	7, 169, 308, 426, 467, 475
HpyF10VI	GCNNNNNNNGC	1 cut(s)	13
HpyF3I	CTNAG	2 cut(s)	230, 257
Hsp92II	CATG	5 cut(s)	16, 54, 312, 430, 471
Kpn2I	TCCGGA	1 cut(s)	161
KspAI	GTTAAC	1 cut(s)	516
Kzo9I	GATC	1 cut(s)	128
LmnI	GCTCC	4 cut(s)	19, 27, 266, 362
Lsp1109I	GCAGC	1 cut(s)	401
LweI	GCATC	2 cut(s)	124, 197
MaeI	CTAG	1 cut(s)	155
MaeIII	GTNAC	1 cut(s)	108
MalI	GATC	1 cut(s)	130
MboI	GATC	1 cut(s)	128
MboII	GAAGA	3 cut(s)	67, 132, 135
MflI	RGATCY	1 cut(s)	128
MhlI	GDGCHC	2 cut(s)	24, 47
MluCI	AATT	4 cut(s)	283, 333, 480, 544
MlyI	GAGTC	1 cut(s)	152
MnlI	CCTC	2 cut(s)	46, 201
Mph1103I	ATGCAT	1 cut(s)	428
MroI	TCCGGA	1 cut(s)	161
MseI	TTAA	1 cut(s)	515
MspI	CCGG	4 cut(s)	17, 162, 205, 252
MwoI	GCNNNNNNNGC	1 cut(s)	13
NcoI	CCATGG	1 cut(s)	50
NdeII	GATC	1 cut(s)	128
NlaIII	CATG	5 cut(s)	16, 54, 312, 430, 471
NlaIV	GGNNCC	1 cut(s)	358
NsiI	ATGCAT	1 cut(s)	428
NspI	RCATGY	2 cut(s)	312, 471
PaeI	GCATGC	1 cut(s)	471
PfeI	GAWTC	1 cut(s)	93
PflMI	CCANNNNNTGG	1 cut(s)	338
PkrI	GCNGC	1 cut(s)	391
PleI	GAGTC	1 cut(s)	152
PpsI	GAGTC	1 cut(s)	152
Psp124BI	GAGCTC	1 cut(s)	24
PspN4I	GGNNCC	1 cut(s)	358
PstI	CTGCAG	1 cut(s)	171
PsuI	RGATCY	1 cut(s)	128
RsaI	GTAC	1 cut(s)	325
RsaNI	GTAC	1 cut(s)	324
SacI	GAGCTC	1 cut(s)	24
SaqAI	TTAA	1 cut(s)	515
SatI	GCNGC	1 cut(s)	390
Sau3AI	GATC	1 cut(s)	128
SchI	GAGTC	1 cut(s)	152
SduI	GDGCHC	2 cut(s)	24, 47
SetI	ASST	5 cut(s)	24, 67, 107, 263, 394
SfaNI	GCATC	2 cut(s)	124, 197
SfcI	CTRYAG	1 cut(s)	167
SphI	GCATGC	1 cut(s)	471
Sse9I	AATT	4 cut(s)	283, 333, 480, 544
SsiI	CCGC	3 cut(s)	25, 290, 328
SspMI	CTAG	1 cut(s)	155
SstI	GAGCTC	1 cut(s)	24
StyI	CCWWGG	1 cut(s)	50
TaaI	ACNGT	2 cut(s)	298, 323
TaqI	TCGA	2 cut(s)	41, 91
TasI	AATT	4 cut(s)	283, 333, 480, 544
TfiI	GAWTC	1 cut(s)	93
Tru1I	TTAA	1 cut(s)	515
Tru9I	TTAA	1 cut(s)	515
TseI	GCWGC	1 cut(s)	389
TspDTI	ATGAA	1 cut(s)	542
Van91I	CCANNNNNTGG	1 cut(s)	338
XceI	RCATGY	2 cut(s)	312, 471
XcmI	CCANNNNNNNNNTGG	1 cut(s)	339
XspI	CTAG	1 cut(s)	155
Zsp2I	ATGCAT	1 cut(s)	428

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