Basic Information

Type: gene

Biological Identity

Species

arabidopsis_thaliana

Chromosome

Orthogroup ID

OG0004315

Physical Location & Seq

Genomic Coordinates Forward (+)

18378225 .. 18380417

Gene Structure 2193 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

AT4G39540.3

Sequence Viewer

CDS Protein Promoter (2k)

Length: 903 bp

ATGGAAGCAGCTACTGTTCAGAGGTTTCAGTACTCATCATGGAATGATTTGAGAAATTTTGAAGGGAAGCCTCGTGGTTCTCTGAGGTATAATACACAGCGAATTAAGGAAGATAAAAGGTTTAGAGTTGTTGCTTTAACTCTTGACAAAAGAAGGGATCATCGACTTAGATCAGTTTCTGATAAGAACTCCTCAGCATTGTTGGAAACTGGAAGTCTTCTTCATTCTCCATTTGATGAAGAACAACAGATTTTGAAGAAAAAAGCTGAAGAGGTTAAACCGTATTTAAATGGACGATCGATGTATCTTGTTGGTATGATGGGTTCCGGGAAAACGACTGTAGGGAAGATTATGGCAAGATCGCTTGGTTATACATTCTTTGATTGTGACACTTTGATCGAGCAGGCTATGAAGGGAACTTCTGTAGCTGAGATATTTGAGCATTTCGGTGAGAGTGTCTTCAGAGAAAAAGAGACTGAAGCGTTAAAGAAACTCTCTTTGATGTACCACCAAGTTGTTGTTTCAACCGGGGGAGGGGCAGTTATAAGACCCATCAATTGGAAGTACATGCATAAAGGTATTAGTATTTGGCTTGATGTACCTCTAGAAGCCTTAGCGCATAGAATAGCTGCTGTAGGAACTGGTTCAAGACCATTGCTACATGATGATGAGTCAGGGGACACATACACAGCGGCTTTAAACCGTCTTTCAACGATTTGGGATGCACGTGGTGAAGCATACACTAAAGCCAGCGCAAGAGTTTCCTTGGAGAATATTACTTTGAAGCTCGGTTATAGAAGTGTCTCAGATCTTACACCAGCTGAAATCGCCATTGAGGCCTTTGAGCAAGTTCAGAGCTATTTAGAGAAAGAAGATGGTATGGCTAGACCAGATGGACTCTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000287 GO:0003674 GO:0003824 GO:0004765 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0006082 GO:0006520 GO:0006725 GO:0006793 GO:0006796 GO:0006807 GO:0008150 GO:0008152 GO:0008652 GO:0009058 GO:0009072 GO:0009073 GO:0009507 GO:0009536 GO:0009987 GO:0016053 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0016773 GO:0019438 GO:0019632 GO:0019752 GO:0032787 GO:0043167 GO:0043169 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043436 GO:0044237 GO:0044238 GO:0044249 GO:0044281 GO:0044283 GO:0044424 GO:0044444 GO:0044464 GO:0046394 GO:0046872 GO:0071704 GO:1901360 GO:1901362 GO:1901564 GO:1901566 GO:1901576 GO:1901615

KEGG Pathways

Metabolic & Signaling

ko00400 ko01100 ko01110 ko01130 ko01230 map00400 map01100 map01110 map01130 map01230

Pfam Domains

Protein Families

SKI

Protein Analysis

300

Amino Acids

33.78

Weight (kDa)

8.44

Isoelectric Point (pI)

39.63

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
AAA_18	PF13238	113 - 221	3.4e-07	AAA domain
SKI	PF01202	115 - 269	1.5e-42	Shikimate kinase

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: OG0004315)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT2G21940 AT2G21940 AT2G21940 AT2G21940 AT2G21940 AT2G21940 AT2G21940 AT4G39540 AT4G39540 AT4G39540
malus_domestica	MD01G1019500.v1.1 MD15G1332900.v1.1
prunus_persica	Prupe.6G172800_v2.0.a1 Prupe.6G172800_v2.0.a1
pyrus_communis	pycom01g04900 pycom15g29260
rosa_chinensis	RchiOBHm_Chr2g0116491 RchiOBHm_Chr2g0116501 RchiOBHm_Chr2g0116521 RchiOBHm_Chr6g0259311
rosa_laevigata	RLG00000018276 RLG00000018279
rosa_multiflora	Rmu_sc0004191.1_g000047 Rmu_sc0018630.1_g000001 Rmu_ssc0000050.1_g000062
rosa_roxburghii	Rroxscaffold_2G00127140 Rroxscaffold_2G00127150
rosa_rugosa	Rorug02G0207100 Rorug05G0587200
rosa_samantha	Rh2CG268700
rosa_wichuraiana	Rw2G020620 Rw2G020630

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	545
AccB7I	CCANNNNNTGG	1 cut(s)	558
AciI	CCGC	1 cut(s)	692
AclWI	GGATC	1 cut(s)	165
AcsI	RAATTY	1 cut(s)	55
AcuI	CTGAAG	3 cut(s)	288, 445, 498
AcvI	CACGTG	1 cut(s)	728
AdeI	CACNNNGTG	1 cut(s)	731
AfaI	GTAC	4 cut(s)	32, 506, 566, 600
AfiI	CCNNNNNNNGG	2 cut(s)	534, 558
AgsI	TTSAA	6 cut(s)	62, 256, 525, 648, 711, 784
AluBI	AGCT	7 cut(s)	11, 266, 428, 629, 787, 821, 858
AluI	AGCT	7 cut(s)	11, 266, 428, 629, 787, 821, 858
Alw26I	GTCTC	2 cut(s)	467, 808
AlwI	GGATC	1 cut(s)	165
AlwNI	CAGNNNCTG	2 cut(s)	14, 179
AoxI	GGCC	1 cut(s)	837
ApeKI	GCWGC	2 cut(s)	8, 629
ApoI	RAATTY	1 cut(s)	55
Asp700I	GAANNNNTTC	1 cut(s)	643
AspLEI	GCGC	2 cut(s)	619, 755
AsuC2I	CCSGG	2 cut(s)	328, 529
AsuHPI	GGTGA	2 cut(s)	461, 743
BauI	CACGAG	1 cut(s)	72
BbrPI	CACGTG	1 cut(s)	728
BbsI	GAAGAC	2 cut(s)	209, 451
BbvCI	CCTCAGC	1 cut(s)	193
BbvI	GCAGC	2 cut(s)	20, 616
BccI	CCATC	4 cut(s)	313, 560, 869, 887
BcnI	CCSGG	2 cut(s)	328, 529
BcoDI	GTCTC	2 cut(s)	467, 808
BfaI	CTAG	3 cut(s)	605, 885, 901
BfmI	CTRYAG	3 cut(s)	339, 423, 633
BglI	GCCNNNNNGGC	1 cut(s)	836
BglII	AGATCT	1 cut(s)	808
BisI	GCNGC	3 cut(s)	9, 630, 693
BlsI	GCNGC	3 cut(s)	10, 631, 694
BmcAI	AGTACT	1 cut(s)	32
Bme1390I	CCNGG	2 cut(s)	328, 529
BmiI	GGNNCC	1 cut(s)	325
BmrFI	CCNGG	2 cut(s)	328, 529
BmsI	GCATC	1 cut(s)	712
BpiI	GAAGAC	2 cut(s)	209, 451
Bpu10I	CCTNAGC	2 cut(s)	193, 613
BpuMI	CCSGG	2 cut(s)	328, 529
Bsa29I	ATCGAT	1 cut(s)	299
BsaAI	YACGTR	1 cut(s)	728
BsaJI	CCNNGG	2 cut(s)	528, 765
BsaXI	ACNNNNNCTCC	2 cut(s)	525, 555
Bsc4I	CCNNNNNNNGG	2 cut(s)	534, 558
Bse1I	ACTGG	2 cut(s)	214, 646
Bse3DI	GCAATG	1 cut(s)	653
BseCI	ATCGAT	1 cut(s)	299
BseDI	CCNNGG	2 cut(s)	528, 765
BseGI	GGATG	1 cut(s)	727
BseLI	CCNNNNNNNGG	2 cut(s)	534, 558
BseMI	GCAATG	1 cut(s)	653
BseMII	CTCAG	4 cut(s)	74, 207, 420, 819
BseNI	ACTGG	2 cut(s)	214, 646
BseRI	GAGGAG	1 cut(s)	181
BseXI	GCAGC	2 cut(s)	20, 616
Bsh1285I	CGRYCG	1 cut(s)	299
BshFI	GGCC	1 cut(s)	839
BshVI	ATCGAT	1 cut(s)	299
BsiEI	CGRYCG	1 cut(s)	299
BsiSI	CCGG	2 cut(s)	327, 528
BslFI	GGGAC	1 cut(s)	692
BslI	CCNNNNNNNGG	2 cut(s)	534, 558
BsmAI	GTCTC	2 cut(s)	467, 808
BsmFI	GGGAC	1 cut(s)	692
BsnI	GGCC	1 cut(s)	839
Bsp143I	GATC	6 cut(s)	157, 170, 296, 359, 396, 808
BspACI	CCGC	1 cut(s)	692
BspANI	GGCC	1 cut(s)	839
BspCNI	CTCAG	4 cut(s)	75, 206, 421, 818
BspDI	ATCGAT	1 cut(s)	299
BspLI	GGNNCC	1 cut(s)	325
BspPI	GGATC	1 cut(s)	165
BsrDI	GCAATG	1 cut(s)	653
BsrI	ACTGG	2 cut(s)	214, 646
BssECI	CCNNGG	2 cut(s)	528, 765
BssMI	GATC	6 cut(s)	157, 170, 296, 359, 396, 808
BssSI	CACGAG	1 cut(s)	72
BssT1I	CCWWGG	1 cut(s)	765
Bst2BI	CACGAG	1 cut(s)	72
Bst4CI	ACNGT	4 cut(s)	16, 282, 340, 704
Bst6I	CTCTTC	1 cut(s)	264
BstBAI	YACGTR	1 cut(s)	728
BstC8I	GCNNGC	2 cut(s)	405, 751
BstDEI	CTNAG	6 cut(s)	83, 167, 193, 429, 613, 805
BstF5I	GGATG	1 cut(s)	727
BstHHI	GCGC	2 cut(s)	619, 755
BstKTI	GATC	6 cut(s)	160, 173, 299, 362, 399, 811
BstMAI	GTCTC	2 cut(s)	467, 808
BstMBI	GATC	6 cut(s)	157, 170, 296, 359, 396, 808
BstMCI	CGRYCG	1 cut(s)	299
BstMWI	GCNNNNNNNGC	2 cut(s)	827, 836
BstNSI	RCATGY	1 cut(s)	571
BstSCI	CCNGG	2 cut(s)	326, 527
BstSFI	CTRYAG	3 cut(s)	339, 423, 633
BstV1I	GCAGC	2 cut(s)	20, 616
BstV2I	GAAGAC	2 cut(s)	209, 451
BstX2I	RGATCY	1 cut(s)	808
BstYI	RGATCY	1 cut(s)	808
Bsu15I	ATCGAT	1 cut(s)	299
BsuRI	GGCC	1 cut(s)	839
BsuTUI	ATCGAT	1 cut(s)	299
BtsCI	GGATG	1 cut(s)	727
Cac8I	GCNNGC	2 cut(s)	405, 751
CaiI	CAGNNNCTG	2 cut(s)	14, 179
CfoI	GCGC	2 cut(s)	619, 755
ClaI	ATCGAT	1 cut(s)	299
Csp6I	GTAC	4 cut(s)	31, 505, 565, 599
CviAII	CATG	3 cut(s)	39, 568, 662
CviQI	GTAC	4 cut(s)	31, 505, 565, 599
DdeI	CTNAG	6 cut(s)	83, 167, 193, 429, 613, 805
DpnI	GATC	6 cut(s)	159, 172, 298, 361, 398, 810
DpnII	GATC	6 cut(s)	157, 170, 296, 359, 396, 808
DraI	TTTAAA	2 cut(s)	288, 699
DraIII	CACNNNGTG	1 cut(s)	731
Eam1104I	CTCTTC	1 cut(s)	264
EarI	CTCTTC	1 cut(s)	264
Eco130I	CCWWGG	1 cut(s)	765
Eco147I	AGGCCT	1 cut(s)	839
Eco57I	CTGAAG	3 cut(s)	288, 445, 498
Eco72I	CACGTG	1 cut(s)	728
EcoT14I	CCWWGG	1 cut(s)	765
EcoT22I	ATGCAT	1 cut(s)	573
ErhI	CCWWGG	1 cut(s)	765
FaeI	CATG	3 cut(s)	42, 571, 665
FaqI	GGGAC	1 cut(s)	692
FatI	CATG	3 cut(s)	38, 567, 661
Fnu4HI	GCNGC	3 cut(s)	9, 630, 693
FokI	GGATG	1 cut(s)	734
Fsp4HI	GCNGC	3 cut(s)	9, 630, 693
FspBI	CTAG	3 cut(s)	605, 885, 901
GlaI	GCGC	2 cut(s)	618, 754
GluI	GCNGC	3 cut(s)	9, 630, 693
HaeIII	GGCC	1 cut(s)	839
HapII	CCGG	2 cut(s)	327, 528
HhaI	GCGC	2 cut(s)	619, 755
Hin1II	CATG	3 cut(s)	42, 571, 665
Hin6I	GCGC	2 cut(s)	617, 753
HinP1I	GCGC	2 cut(s)	617, 753
HinfI	GANTC	2 cut(s)	671, 897
HpaII	CCGG	2 cut(s)	327, 528
HphI	GGTGA	2 cut(s)	461, 743
Hpy188I	TCNGA	6 cut(s)	21, 84, 181, 464, 808, 855
Hpy188III	TCNNGA	3 cut(s)	143, 605, 648
HpyAV	CCTTC	3 cut(s)	56, 147, 406
HpyCH4III	ACNGT	4 cut(s)	16, 282, 340, 704
HpyCH4IV	ACGT	1 cut(s)	727
HpyCH4V	TGCA	2 cut(s)	571, 725
HpyF10VI	GCNNNNNNNGC	2 cut(s)	827, 836
HpyF3I	CTNAG	6 cut(s)	83, 167, 193, 429, 613, 805
HpySE526I	ACGT	1 cut(s)	727
Hsp92II	CATG	3 cut(s)	42, 571, 665
HspAI	GCGC	2 cut(s)	617, 753
Kzo9I	GATC	6 cut(s)	157, 170, 296, 359, 396, 808
LpnPI	CCDG	8 cut(s)	195, 340, 389, 541, 627, 660, 763, 831
Lsp1109I	GCAGC	2 cut(s)	20, 616
LweI	GCATC	1 cut(s)	712
MaeI	CTAG	3 cut(s)	605, 885, 901
MaeII	ACGT	1 cut(s)	727
MaeIII	GTNAC	1 cut(s)	386
MalI	GATC	6 cut(s)	159, 172, 298, 361, 398, 810
MboI	GATC	6 cut(s)	157, 170, 296, 359, 396, 808
MboII	GAAGA	9 cut(s)	122, 209, 212, 251, 268, 281, 358, 451, 884
MfeI	CAATTG	1 cut(s)	556
MflI	RGATCY	1 cut(s)	808
MluCI	AATT	3 cut(s)	55, 102, 556
MlyI	GAGTC	2 cut(s)	680, 891
MmeI	TCCRAC	1 cut(s)	183
MnlI	CCTC	8 cut(s)	15, 78, 81, 202, 265, 527, 612, 829
Mph1103I	ATGCAT	1 cut(s)	573
MroXI	GAANNNNTTC	1 cut(s)	643
MseI	TTAA	6 cut(s)	105, 137, 276, 287, 485, 698
MslI	CAYNNNNRTG	2 cut(s)	447, 666
MspA1I	CMGCKG	2 cut(s)	692, 821
MspI	CCGG	2 cut(s)	327, 528
MspR9I	CCNGG	2 cut(s)	328, 529
MunI	CAATTG	1 cut(s)	556
MwoI	GCNNNNNNNGC	2 cut(s)	827, 836
NciI	CCSGG	2 cut(s)	328, 529
NdeII	GATC	6 cut(s)	157, 170, 296, 359, 396, 808
NlaIII	CATG	3 cut(s)	42, 571, 665
NlaIV	GGNNCC	1 cut(s)	325
NmuCI	GTSAC	1 cut(s)	386
NsiI	ATGCAT	1 cut(s)	573
NspI	RCATGY	1 cut(s)	571
PceI	AGGCCT	1 cut(s)	839
PdmI	GAANNNNTTC	1 cut(s)	643
PflMI	CCANNNNNTGG	1 cut(s)	558
PfoI	TCCNGGA	1 cut(s)	326
PkrI	GCNGC	3 cut(s)	10, 631, 694
Ple19I	CGATCG	1 cut(s)	299
PleI	GAGTC	2 cut(s)	679, 891
PmaCI	CACGTG	1 cut(s)	728
PmlI	CACGTG	1 cut(s)	728
PpsI	GAGTC	2 cut(s)	679, 891
Ppu21I	YACGTR	1 cut(s)	728
PsiI	TTATAA	1 cut(s)	545
PspCI	CACGTG	1 cut(s)	728
PspN4I	GGNNCC	1 cut(s)	325
PsrI	GAACNNNNNNTAC	2 cut(s)	307, 339
PstNI	CAGNNNCTG	2 cut(s)	14, 179
PsuI	RGATCY	1 cut(s)	808
PvuI	CGATCG	1 cut(s)	299
PvuII	CAGCTG	1 cut(s)	821
RsaI	GTAC	4 cut(s)	32, 506, 566, 600
RsaNI	GTAC	4 cut(s)	31, 505, 565, 599
RseI	CAYNNNNRTG	2 cut(s)	447, 666
SaqAI	TTAA	6 cut(s)	105, 137, 276, 287, 485, 698
SatI	GCNGC	3 cut(s)	9, 630, 693
Sau3AI	GATC	6 cut(s)	157, 170, 296, 359, 396, 808
ScaI	AGTACT	1 cut(s)	32
SchI	GAGTC	2 cut(s)	680, 891
ScrFI	CCNGG	2 cut(s)	328, 529
SfaNI	GCATC	1 cut(s)	712
SfcI	CTRYAG	3 cut(s)	339, 423, 633
SmiI	ATTTAAAT	1 cut(s)	288
SmiMI	CAYNNNNRTG	2 cut(s)	447, 666
Sse9I	AATT	3 cut(s)	55, 102, 556
SseBI	AGGCCT	1 cut(s)	839
SsiI	CCGC	1 cut(s)	692
SspI	AATATT	1 cut(s)	775
SspMI	CTAG	3 cut(s)	605, 885, 901
StuI	AGGCCT	1 cut(s)	839
StyD4I	CCNGG	2 cut(s)	326, 527
StyI	CCWWGG	1 cut(s)	765
SwaI	ATTTAAAT	1 cut(s)	288
TaaI	ACNGT	4 cut(s)	16, 282, 340, 704
TaiI	ACGT	1 cut(s)	730
TaqI	TCGA	3 cut(s)	163, 299, 399
TasI	AATT	3 cut(s)	55, 102, 556
TatI	WGTACW	2 cut(s)	30, 564
TauI	GCSGC	1 cut(s)	695
Tru1I	TTAA	6 cut(s)	105, 137, 276, 287, 485, 698
Tru9I	TTAA	6 cut(s)	105, 137, 276, 287, 485, 698
TseFI	GTSAC	1 cut(s)	386
TseI	GCWGC	2 cut(s)	8, 629
Tsp45I	GTSAC	1 cut(s)	386
TspDTI	ATGAA	3 cut(s)	212, 252, 425
Van91I	CCANNNNNTGG	1 cut(s)	558
XapI	RAATTY	1 cut(s)	55
XbaI	TCTAGA	1 cut(s)	604
XceI	RCATGY	1 cut(s)	571
XmnI	GAANNNNTTC	1 cut(s)	643
XspI	CTAG	3 cut(s)	605, 885, 901
ZrmI	AGTACT	1 cut(s)	32
Zsp2I	ATGCAT	1 cut(s)	573

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