Basic Information

Type: gene

Biological Identity

Species

arabidopsis_thaliana

Chromosome

Orthogroup ID

OG0006238

Physical Location & Seq

Genomic Coordinates Forward (+)

2563040 .. 2564835

Gene Structure 1796 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

AT4G05000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 633 bp

ATGATGGAGGTCAAATTATGGAACGACAAACGCGAAAGAGAGATGTATGAGAATTTTGCAGAGCTTTTTGCAATCATCAAAGCCACAGAGAAGCTAGAGAAAGCTTATATAAGAGACCTAATCAATCCTTCAGAGTACGAATCTGAATGCCAGAAACTCATTGTCCACTTCAAAACTTTATCCGCTACACTCAAAGACACGGTGCCAAACATTGAAAGATTTGCAGACACATACAAAATGGACTGTCCAGCTGCTCTATACCGCCTGGTGACATCAGGTCTTCCTGCCACAGTGGAACACCGAGCTACCGTTGCAGCATCTACGTCGAACTCTGCATCCATTGTTGCTGAATGTGTACAGAATTTCATCACTTCAATGGATTCTTTGAAACTAAACATGGTGGCTGTCGATCAGGTTTATCCTCTCTTGTCTGATCTATCTGCTTCTCTCAACAAACTGAGTATTCTACCGCCCGATTTCGAAGGGAAGACGAAGATGAAAGAATGGCTTTCGAGGTTGTCTAAGATGGGAGCAGCCGATGAGCTTACGGAACAACAGTCAAGGCAACTTCACTTTGATCTCGAGTCATCATACAACTCTTTCATGGCAGCTTTGCCTAAAGCTGGTAATTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000813 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005768 GO:0005794 GO:0005802 GO:0006508 GO:0006511 GO:0006807 GO:0006810 GO:0006886 GO:0007034 GO:0008104 GO:0008150 GO:0008152 GO:0009056 GO:0009057 GO:0009987 GO:0010008 GO:0012505 GO:0015031 GO:0015833 GO:0016020 GO:0016192 GO:0016197 GO:0019538 GO:0019941 GO:0030163 GO:0031090 GO:0031410 GO:0031982 GO:0031984 GO:0032509 GO:0032511 GO:0032991 GO:0033036 GO:0033365 GO:0034613 GO:0036452 GO:0042886 GO:0043162 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043328 GO:0043632 GO:0044237 GO:0044238 GO:0044248 GO:0044257 GO:0044260 GO:0044265 GO:0044267 GO:0044422 GO:0044424 GO:0044425 GO:0044431 GO:0044433 GO:0044440 GO:0044444 GO:0044446 GO:0044464 GO:0045184 GO:0045324 GO:0046907 GO:0051179 GO:0051234 GO:0051603 GO:0051641 GO:0051649 GO:0070727 GO:0071702 GO:0071704 GO:0071705 GO:0071985 GO:0072594 GO:0072665 GO:0072666 GO:0097708 GO:0098588 GO:0098791 GO:0098796 GO:0098805 GO:1901564 GO:1901565 GO:1901575

KEGG Pathways

Metabolic & Signaling

ko04144 map04144

Pfam Domains

Protein Families

VPS28

Protein Analysis

210

Amino Acids

23.69

Weight (kDa)

5.34

Isoelectric Point (pI)

36.72

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
VPS28	PF03997	19 - 205	5.3e-72	VPS28 protein

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: OG0006238)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT4G05000 AT4G05000 AT4G05000 AT4G21560 AT4G21560 AT4G21560
fragaria_vesca	FvH4_3g04140 FvH4_3g04140 FvH4_3g04140
malus_domestica	MD05G1324500.v1.1 MD10G1302300.v1.1
prunus_persica	Prupe.4G035900_v2.0.a1 Prupe.4G035900_v2.0.a1
pyrus_communis	pycom05g29870 pycom10g25480
rosa_chinensis	RchiOBHm_Chr5g0006591
rosa_laevigata	RLG00000031402
rosa_multiflora	Rmu_sc0001972.1_g000001 Rmu_sc0011154.1_g000006
rosa_roxburghii	Rroxscaffold_1G00069450
rosa_rugosa	Rorug04G0422800 Rorug04G0422800
rosa_samantha	Rh5AG050000 Rh5BG049300 Rh5CG057500 Rh5DG048700
rosa_wichuraiana	Rw5G005010

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	202
AccII	CGCG	1 cut(s)	33
AciI	CCGC	3 cut(s)	183, 262, 470
AcsI	RAATTY	2 cut(s)	52, 361
AcuI	CTGAAG	1 cut(s)	114
AfaI	GTAC	2 cut(s)	137, 357
AfiI	CCNNNNNNNGG	1 cut(s)	623
AgsI	TTSAA	4 cut(s)	172, 215, 375, 388
AhdI	GACNNNNNGTC	1 cut(s)	276
AjnI	CCWGG	1 cut(s)	264
AloI	GAACNNNNNNTCC	2 cut(s)	320, 352
AluBI	AGCT	8 cut(s)	64, 94, 104, 251, 305, 544, 611, 623
AluI	AGCT	8 cut(s)	64, 94, 104, 251, 305, 544, 611, 623
Alw26I	GTCTC	1 cut(s)	108
Ama87I	CYCGRG	1 cut(s)	581
ApeKI	GCWGC	4 cut(s)	251, 314, 533, 608
ApoI	RAATTY	2 cut(s)	52, 361
AsuHPI	GGTGA	1 cut(s)	280
AsuII	TTCGAA	1 cut(s)	480
AvaI	CYCGRG	1 cut(s)	581
BanI	GGYRCC	1 cut(s)	202
BbsI	GAAGAC	2 cut(s)	272, 494
BbvI	GCAGC	4 cut(s)	238, 326, 545, 620
BccI	CCATC	1 cut(s)	520
BcgI	CGANNNNNNTGC	2 cut(s)	306, 340
BciT130I	CCWGG	1 cut(s)	266
BcoDI	GTCTC	1 cut(s)	108
BfaI	CTAG	1 cut(s)	95
BisI	GCNGC	4 cut(s)	252, 315, 534, 609
BlsI	GCNGC	4 cut(s)	253, 316, 535, 610
Bme1390I	CCNGG	1 cut(s)	266
BmeRI	GACNNNNNGTC	1 cut(s)	276
BmeT110I	CYCGRG	1 cut(s)	581
BmiI	GGNNCC	1 cut(s)	204
BmrFI	CCNGG	1 cut(s)	266
BmsI	GCATC	2 cut(s)	326, 344
BpiI	GAAGAC	2 cut(s)	272, 494
Bpu14I	TTCGAA	1 cut(s)	480
BsaI	GGTCTC	1 cut(s)	108
Bsc4I	CCNNNNNNNGG	1 cut(s)	623
BseBI	CCWGG	1 cut(s)	266
BseGI	GGATG	1 cut(s)	335
BseLI	CCNNNNNNNGG	1 cut(s)	623
BseMII	CTCAG	1 cut(s)	449
BseXI	GCAGC	4 cut(s)	238, 326, 545, 620
Bsh1236I	CGCG	1 cut(s)	33
BshNI	GGYRCC	1 cut(s)	202
BsiHKCI	CYCGRG	1 cut(s)	581
BslI	CCNNNNNNNGG	1 cut(s)	623
BsmAI	GTCTC	1 cut(s)	108
BsmI	GAATGC	1 cut(s)	152
Bso31I	GGTCTC	1 cut(s)	108
BsoBI	CYCGRG	1 cut(s)	581
Bsp119I	TTCGAA	1 cut(s)	480
Bsp1407I	TGTACA	1 cut(s)	355
Bsp143I	GATC	3 cut(s)	409, 433, 577
BspACI	CCGC	3 cut(s)	183, 262, 470
BspCNI	CTCAG	1 cut(s)	450
BspFNI	CGCG	1 cut(s)	33
BspLI	GGNNCC	1 cut(s)	204
BspT104I	TTCGAA	1 cut(s)	480
BspT107I	GGYRCC	1 cut(s)	202
BspTNI	GGTCTC	1 cut(s)	108
BsrGI	TGTACA	1 cut(s)	355
BssMI	GATC	3 cut(s)	409, 433, 577
Bst2UI	CCWGG	1 cut(s)	266
Bst4CI	ACNGT	5 cut(s)	202, 245, 292, 310, 558
BstAUI	TGTACA	1 cut(s)	355
BstBI	TTCGAA	1 cut(s)	480
BstDEI	CTNAG	2 cut(s)	458, 522
BstF5I	GGATG	1 cut(s)	335
BstFNI	CGCG	1 cut(s)	33
BstKTI	GATC	3 cut(s)	412, 436, 580
BstMAI	GTCTC	1 cut(s)	108
BstMBI	GATC	3 cut(s)	409, 433, 577
BstMWI	GCNNNNNNNGC	1 cut(s)	311
BstNI	CCWGG	1 cut(s)	266
BstSCI	CCNGG	1 cut(s)	264
BstUI	CGCG	1 cut(s)	33
BstV1I	GCAGC	4 cut(s)	238, 326, 545, 620
BstV2I	GAAGAC	2 cut(s)	272, 494
BtsCI	GGATG	1 cut(s)	335
BtsIMutI	CAGTG	1 cut(s)	297
Csp6I	GTAC	2 cut(s)	136, 356
CviAII	CATG	2 cut(s)	397, 604
CviQI	GTAC	2 cut(s)	136, 356
DdeI	CTNAG	2 cut(s)	458, 522
DpnI	GATC	3 cut(s)	411, 435, 579
DpnII	GATC	3 cut(s)	409, 433, 577
DriI	GACNNNNNGTC	1 cut(s)	276
Eam1105I	GACNNNNNGTC	1 cut(s)	276
Eco31I	GGTCTC	1 cut(s)	108
Eco57I	CTGAAG	1 cut(s)	114
Eco88I	CYCGRG	1 cut(s)	581
EcoRII	CCWGG	1 cut(s)	264
FaeI	CATG	2 cut(s)	400, 607
FaiI	YATR	9 cut(s)	19, 48, 108, 110, 232, 259, 398, 592, 605
FalI	AAGNNNNNCTT	2 cut(s)	492, 524
FatI	CATG	2 cut(s)	396, 603
Fnu4HI	GCNGC	4 cut(s)	252, 315, 534, 609
FokI	GGATG	1 cut(s)	322
Fsp4HI	GCNGC	4 cut(s)	252, 315, 534, 609
FspBI	CTAG	1 cut(s)	95
GluI	GCNGC	4 cut(s)	252, 315, 534, 609
Hin1II	CATG	2 cut(s)	400, 607
HindIII	AAGCTT	1 cut(s)	102
HinfI	GANTC	3 cut(s)	140, 380, 584
HphI	GGTGA	1 cut(s)	280
Hpy166II	GTNNAC	2 cut(s)	166, 356
Hpy188I	TCNGA	3 cut(s)	133, 145, 433
Hpy188III	TCNNGA	1 cut(s)	581
Hpy8I	GTNNAC	2 cut(s)	166, 356
Hpy99I	CGWCG	1 cut(s)	328
HpyAV	CCTTC	2 cut(s)	138, 476
HpyCH4III	ACNGT	5 cut(s)	202, 245, 292, 310, 558
HpyCH4IV	ACGT	1 cut(s)	323
HpyCH4V	TGCA	5 cut(s)	59, 71, 224, 314, 335
HpyF10VI	GCNNNNNNNGC	1 cut(s)	311
HpyF3I	CTNAG	2 cut(s)	458, 522
HpySE526I	ACGT	1 cut(s)	323
Hsp92II	CATG	2 cut(s)	400, 607
Kzo9I	GATC	3 cut(s)	409, 433, 577
LmnI	GCTCC	1 cut(s)	530
LpnPI	CCDG	8 cut(s)	164, 251, 261, 261, 278, 297, 398, 609
Lsp1109I	GCAGC	4 cut(s)	238, 326, 545, 620
LweI	GCATC	2 cut(s)	326, 344
MaeI	CTAG	1 cut(s)	95
MaeII	ACGT	1 cut(s)	323
MaeIII	GTNAC	1 cut(s)	268
MalI	GATC	3 cut(s)	411, 435, 579
MboI	GATC	3 cut(s)	409, 433, 577
MboII	GAAGA	3 cut(s)	272, 499, 505
MluCI	AATT	4 cut(s)	14, 52, 361, 628
MlyI	GAGTC	1 cut(s)	593
MnlI	CCTC	2 cut(s)	432, 507
MseI	TTAA	1 cut(s)	631
MslI	CAYNNNNRTG	1 cut(s)	374
MspA1I	CMGCKG	1 cut(s)	251
MspR9I	CCNGG	1 cut(s)	266
Mva1269I	GAATGC	1 cut(s)	152
MvaI	CCWGG	1 cut(s)	266
MvnI	CGCG	1 cut(s)	33
MwoI	GCNNNNNNNGC	1 cut(s)	311
NdeII	GATC	3 cut(s)	409, 433, 577
NlaIII	CATG	2 cut(s)	400, 607
NlaIV	GGNNCC	1 cut(s)	204
NmuCI	GTSAC	1 cut(s)	268
NspV	TTCGAA	1 cut(s)	480
PaeR7I	CTCGAG	1 cut(s)	581
PcsI	WCGNNNNNNNCGW	1 cut(s)	30
PctI	GAATGC	1 cut(s)	152
PfeI	GAWTC	2 cut(s)	140, 380
PkrI	GCNGC	4 cut(s)	253, 316, 535, 610
PleI	GAGTC	1 cut(s)	592
PpsI	GAGTC	1 cut(s)	592
Psp6I	CCWGG	1 cut(s)	264
PspGI	CCWGG	1 cut(s)	264
PspN4I	GGNNCC	1 cut(s)	204
PvuII	CAGCTG	1 cut(s)	251
RsaI	GTAC	2 cut(s)	137, 357
RsaNI	GTAC	2 cut(s)	136, 356
RseI	CAYNNNNRTG	1 cut(s)	374
SaqAI	TTAA	1 cut(s)	631
SatI	GCNGC	4 cut(s)	252, 315, 534, 609
Sau3AI	GATC	3 cut(s)	409, 433, 577
SchI	GAGTC	1 cut(s)	593
ScrFI	CCNGG	1 cut(s)	266
SfaNI	GCATC	2 cut(s)	326, 344
Sfr274I	CTCGAG	1 cut(s)	581
SfuI	TTCGAA	1 cut(s)	480
SlaI	CTCGAG	1 cut(s)	581
SmiMI	CAYNNNNRTG	1 cut(s)	374
SmlI	CTYRAG	1 cut(s)	581
SmoI	CTYRAG	1 cut(s)	581
Sse9I	AATT	4 cut(s)	14, 52, 361, 628
SsiI	CCGC	3 cut(s)	183, 262, 470
SspMI	CTAG	1 cut(s)	95
StyD4I	CCNGG	1 cut(s)	264
TaaI	ACNGT	5 cut(s)	202, 245, 292, 310, 558
TaiI	ACGT	1 cut(s)	326
TaqI	TCGA	5 cut(s)	326, 408, 480, 512, 582
TasI	AATT	4 cut(s)	14, 52, 361, 628
TatI	WGTACW	1 cut(s)	355
TfiI	GAWTC	2 cut(s)	140, 380
Tru1I	TTAA	1 cut(s)	631
Tru9I	TTAA	1 cut(s)	631
TscAI	CASTG	1 cut(s)	297
TseFI	GTSAC	1 cut(s)	268
TseI	GCWGC	4 cut(s)	251, 314, 533, 608
Tsp45I	GTSAC	1 cut(s)	268
TspDTI	ATGAA	3 cut(s)	355, 512, 592
TspGWI	ACGGA	1 cut(s)	563
TspRI	CASTG	1 cut(s)	297
XapI	RAATTY	2 cut(s)	52, 361
XhoI	CTCGAG	1 cut(s)	581
XspI	CTAG	1 cut(s)	95

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