Basic Information

Type: gene

Biological Identity

Species

arabidopsis_thaliana

Chromosome

Orthogroup ID

OG0009952

Physical Location & Seq

Genomic Coordinates Forward (+)

16330129 .. 16333405

Gene Structure 3277 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

AT2G39140.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1233 bp

ATGGCGTCGGTGGCGGCATCATCGTCGATATCATTCGCTGCATCATTCCTCAAAATCAAAGCATTCCCTCTCTCCCCTCGCTTCTTCCCCATCCGTACACTCCGTTGCTCTGTCTCCTCCTCCTCCTCTGAGCCCATTGAATTCGACATCTCCTTCGCTCCTCCCAAACCCAAACCCTCCTCCACTCACGGCGGCGTCACCCCTCAACAACTCTTCATCCCTTGGATCGTCCGTAGTGATGACGGCACTCTCAAACTCCAATCTCAACCTCCTGCTCGTTTAATCCACAACCTCGCCATCGATGCCACTACTCAAAACCCTAAGAAGAAAGATAAATCTAAGAAGAAACAACCTCAAGCTACCTCCTCTTCCTCCGCCACCACCACCGCCTCATCTCCAGCTTCACACTCAGAGGTAAAGCCAAAGCTATCCAAAGCGGCGCGTAGGTTTTACAATGAGAATTTTAAAGAACAACCTCAACGTTTAAGCAAAGTTCTCGCTGCTGCTGGAGTGGCATCAAGAAGAACCTCTGAAGAACTTATTTTTGATGGCAAGGTTACTGTTAATGGTATTCTCTGCAACACTCCACAGACTCGAGTTGATCCATCAAGAGACATTATTTATGTTAATGGAAATCGTATTCCTAAGAAACTTCCTCCAAAGGTTTATTTTGCTCTGAACAAGCCTAAAGGATATATTTGTTCTTCCGGAGAGAAAGAGATCAAATCTGCTATTAGTTTGTTTGACGAGTACTTGTCCTCTTGGGATAAAAGGAATCCGGGGACTCCCAAACCTCGCCTTTTTACTGTTGGTCGTCTTGATGTTGCCACAACGGGATTGATAGTTGTTACAAATGATGGAGATTTCGCACAGAAACTTTCACATCCTTCATCTAGTTTACCGAAAGAATATATTACCACGGTTGTCGGTGATATACACAAACGACACTTAATGGCTATCAGTGAAGGCACAATGGTGGAAGGAGTCCACTGTGTCCCAGATTCAGTTGAGTTGATGCCAAAGCAGCATGATATACCAAGAGCAAGGCTGCGTATAGTGGTTCACGAAGGAAGAAATCATGAAGTCAGGGAATTAGTGAAAAATGCTGGGCTTGAGGTTCATTCATTGAAGCGTGTCCGTATAGGTGGATTCAGACTTCCTTCAGATCTTGGGCTAGGGAAGCATGTGGAATTGAAGCAGAGCGAGCTAAAGGCATTGGGTTGGAAGAATTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000154 GO:0000455 GO:0000470 GO:0000488 GO:0000489 GO:0001522 GO:0003674 GO:0003824 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005829 GO:0006139 GO:0006364 GO:0006396 GO:0006412 GO:0006518 GO:0006725 GO:0006807 GO:0006996 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009451 GO:0009501 GO:0009507 GO:0009536 GO:0009657 GO:0009982 GO:0009987 GO:0010467 GO:0016043 GO:0016070 GO:0016072 GO:0016853 GO:0016866 GO:0019538 GO:0022613 GO:0030490 GO:0031118 GO:0032544 GO:0034470 GO:0034641 GO:0034645 GO:0034660 GO:0042254 GO:0042273 GO:0042274 GO:0043043 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043412 GO:0043603 GO:0043604 GO:0044085 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044267 GO:0044271 GO:0044424 GO:0044444 GO:0044464 GO:0046483 GO:0071704 GO:0071840 GO:0090304 GO:1901360 GO:1901564 GO:1901566 GO:1901576

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PseudoU_synth_2 S4

Protein Analysis

410

Amino Acids

45.11

Weight (kDa)

9.95

Isoelectric Point (pI)

44.84

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
S4	PF01479	160 - 204	8.7e-11	S4 domain
PseudoU_synth_2	PF00849	223 - 365	7.9e-19	RNA pseudouridylate synthase

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

Font Size (px)

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0009952)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT2G39140 AT2G39140
fragaria_vesca	FvH4_7g18810 FvH4_7g18810 FvH4_7g18810 FvH4_7g18810 FvH4_7g18810 FvH4_7g18810
malus_domestica	MD07G1170000.v1.1
prunus_persica	Prupe.2G208900_v2.0.a1
pyrus_communis	pycom07g16390
rosa_chinensis	RchiOBHm_Chr1g0362601
rosa_laevigata	RLG00000027635
rosa_multiflora	Rmu_sc0005725.1_g000010
rosa_roxburghii	Rroxscaffold_4G00293910
rosa_rugosa	Rorug01G0300000.1
rosa_samantha	Rh1AG308600 Rh1BG272300 Rh1CG289500 Rh1DG302700
rosa_wichuraiana	Rw1G027410

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccII	CGCG	1 cut(s)	442
AccIII	TCCGGA	1 cut(s)	707
AciI	CCGC	5 cut(s)	14, 192, 375, 387, 437
AclI	AACGTT	1 cut(s)	481
AclWI	GGATC	2 cut(s)	233, 596
AcsI	RAATTY	2 cut(s)	140, 460
AcuI	CTGAAG	2 cut(s)	552, 1146
AcyI	GRCGYC	2 cut(s)	5, 195
AfaI	GTAC	2 cut(s)	97, 752
AgsI	TTSAA	3 cut(s)	140, 1129, 1195
AleI	CACNNNNGTG	1 cut(s)	974
AluBI	AGCT	4 cut(s)	359, 401, 427, 1207
AluI	AGCT	4 cut(s)	359, 401, 427, 1207
Alw26I	GTCTC	2 cut(s)	118, 606
AlwI	GGATC	2 cut(s)	233, 596
Ama87I	CYCGRG	1 cut(s)	594
Aor13HI	TCCGGA	1 cut(s)	707
ApeKI	GCWGC	5 cut(s)	38, 500, 503, 1024, 1048
ApoI	RAATTY	2 cut(s)	140, 460
ArsI	GACNNNNNNTTYG	2 cut(s)	137, 169
AspLEI	GCGC	1 cut(s)	442
AsuC2I	CCSGG	1 cut(s)	780
AsuHPI	GGTGA	2 cut(s)	190, 941
AvaI	CYCGRG	1 cut(s)	594
BanII	GRGCYC	1 cut(s)	135
BbvI	GCAGC	5 cut(s)	25, 487, 490, 1035, 1036
BccI	CCATC	5 cut(s)	98, 305, 542, 613, 851
BceAI	ACGGC	2 cut(s)	205, 259
BcgI	CGANNNNNNTGC	4 cut(s)	6, 40, 478, 512
BcnI	CCSGG	1 cut(s)	780
BcoDI	GTCTC	2 cut(s)	118, 606
BfaI	CTAG	2 cut(s)	894, 1175
BglII	AGATCT	1 cut(s)	1165
BisI	GCNGC	8 cut(s)	15, 39, 193, 438, 501, 504, 1025, 1049
BlsI	GCNGC	8 cut(s)	16, 40, 194, 439, 502, 505, 1026, 1050
BmcAI	AGTACT	1 cut(s)	752
Bme1390I	CCNGG	1 cut(s)	780
BmeT110I	CYCGRG	1 cut(s)	594
BmrFI	CCNGG	1 cut(s)	780
BmsI	GCATC	5 cut(s)	26, 50, 292, 524, 1005
BpmI	CTGGAG	2 cut(s)	381, 528
BpuEI	CTTGAG	2 cut(s)	339, 1133
BpuMI	CCSGG	1 cut(s)	780
Bsa29I	ATCGAT	1 cut(s)	300
BsaHI	GRCGYC	2 cut(s)	5, 195
BsaJI	CCNNGG	3 cut(s)	221, 779, 918
BsaWI	WCCGGW	1 cut(s)	707
BseAI	TCCGGA	1 cut(s)	707
BseCI	ATCGAT	1 cut(s)	300
BseDI	CCNNGG	3 cut(s)	221, 779, 918
BseGI	GGATG	3 cut(s)	90, 216, 883
BseMII	CTCAG	2 cut(s)	120, 423
BseRI	GAGGAG	7 cut(s)	106, 109, 112, 115, 150, 169, 355
BseXI	GCAGC	5 cut(s)	25, 487, 490, 1035, 1036
BseYI	CCCAGC	1 cut(s)	1106
Bsh1236I	CGCG	1 cut(s)	442
BshVI	ATCGAT	1 cut(s)	300
BsiHKCI	CYCGRG	1 cut(s)	594
BsiSI	CCGG	2 cut(s)	708, 779
BslFI	GGGAC	2 cut(s)	796, 980
BsmAI	GTCTC	2 cut(s)	118, 606
BsmFI	GGGAC	2 cut(s)	796, 980
BsmI	GAATGC	1 cut(s)	62
BsoBI	CYCGRG	1 cut(s)	594
Bsp1286I	GDGCHC	1 cut(s)	135
Bsp13I	TCCGGA	1 cut(s)	707
Bsp143I	GATC	4 cut(s)	225, 601, 720, 1165
BspACI	CCGC	5 cut(s)	14, 192, 375, 387, 437
BspCNI	CTCAG	2 cut(s)	121, 422
BspDI	ATCGAT	1 cut(s)	300
BspEI	TCCGGA	1 cut(s)	707
BspFNI	CGCG	1 cut(s)	442
BspHI	TCATGA	1 cut(s)	1078
BspPI	GGATC	2 cut(s)	233, 596
BssECI	CCNNGG	3 cut(s)	221, 779, 918
BssMI	GATC	4 cut(s)	225, 601, 720, 1165
BssNI	GRCGYC	2 cut(s)	5, 195
BssT1I	CCWWGG	1 cut(s)	221
Bst4CI	ACNGT	4 cut(s)	562, 808, 922, 992
Bst6I	CTCTTC	2 cut(s)	218, 373
BstACI	GRCGYC	2 cut(s)	5, 195
BstC8I	GCNNGC	1 cut(s)	1205
BstDEI	CTNAG	5 cut(s)	129, 321, 339, 409, 645
BstDSI	CCRYGG	1 cut(s)	918
BstF5I	GGATG	3 cut(s)	90, 216, 883
BstFNI	CGCG	1 cut(s)	442
BstHHI	GCGC	1 cut(s)	442
BstKTI	GATC	4 cut(s)	228, 604, 723, 1168
BstMAI	GTCTC	2 cut(s)	118, 606
BstMBI	GATC	4 cut(s)	225, 601, 720, 1165
BstMWI	GCNNNNNNNGC	6 cut(s)	11, 302, 512, 1024, 1180, 1204
BstNSI	RCATGY	1 cut(s)	1187
BstSCI	CCNGG	1 cut(s)	778
BstUI	CGCG	1 cut(s)	442
BstV1I	GCAGC	5 cut(s)	25, 487, 490, 1035, 1036
BstX2I	RGATCY	1 cut(s)	1165
BstYI	RGATCY	1 cut(s)	1165
Bsu15I	ATCGAT	1 cut(s)	300
BsuTUI	ATCGAT	1 cut(s)	300
BtgI	CCRYGG	1 cut(s)	918
BtsCI	GGATG	3 cut(s)	90, 216, 883
BtsIMutI	CAGTG	2 cut(s)	967, 988
Cac8I	GCNNGC	1 cut(s)	1205
CciI	TCATGA	1 cut(s)	1078
CfoI	GCGC	1 cut(s)	442
ClaI	ATCGAT	1 cut(s)	300
CseI	GACGC	1 cut(s)	184
Csp6I	GTAC	2 cut(s)	96, 751
CviAII	CATG	3 cut(s)	1028, 1079, 1184
CviQI	GTAC	2 cut(s)	96, 751
DdeI	CTNAG	5 cut(s)	129, 321, 339, 409, 645
DpnI	GATC	4 cut(s)	227, 603, 722, 1167
DpnII	GATC	4 cut(s)	225, 601, 720, 1165
DraI	TTTAAA	1 cut(s)	466
Eam1104I	CTCTTC	2 cut(s)	218, 373
EarI	CTCTTC	2 cut(s)	218, 373
EciI	GGCGGA	1 cut(s)	364
Eco130I	CCWWGG	1 cut(s)	221
Eco24I	GRGCYC	1 cut(s)	135
Eco32I	GATATC	1 cut(s)	30
Eco57I	CTGAAG	2 cut(s)	552, 1146
Eco88I	CYCGRG	1 cut(s)	594
EcoRI	GAATTC	1 cut(s)	140
EcoRV	GATATC	1 cut(s)	30
EcoT14I	CCWWGG	1 cut(s)	221
EcoT38I	GRGCYC	1 cut(s)	135
ErhI	CCWWGG	1 cut(s)	221
FaeI	CATG	3 cut(s)	1031, 1082, 1187
FaqI	GGGAC	2 cut(s)	796, 980
FatI	CATG	3 cut(s)	1027, 1078, 1183
Fnu4HI	GCNGC	8 cut(s)	15, 39, 193, 438, 501, 504, 1025, 1049
FokI	GGATG	3 cut(s)	77, 203, 870
FriOI	GRGCYC	1 cut(s)	135
Fsp4HI	GCNGC	8 cut(s)	15, 39, 193, 438, 501, 504, 1025, 1049
FspBI	CTAG	2 cut(s)	894, 1175
GlaI	GCGC	1 cut(s)	441
GluI	GCNGC	8 cut(s)	15, 39, 193, 438, 501, 504, 1025, 1049
GsaI	CCCAGC	1 cut(s)	1110
GsuI	CTGGAG	2 cut(s)	381, 528
HapII	CCGG	2 cut(s)	708, 779
HgaI	GACGC	1 cut(s)	184
HhaI	GCGC	1 cut(s)	442
Hin1I	GRCGYC	2 cut(s)	5, 195
Hin1II	CATG	3 cut(s)	1031, 1082, 1187
Hin6I	GCGC	1 cut(s)	440
HinP1I	GCGC	1 cut(s)	440
HinfI	GANTC	6 cut(s)	592, 775, 784, 984, 1001, 1149
HpaII	CCGG	2 cut(s)	708, 779
HphI	GGTGA	2 cut(s)	190, 941
Hpy166II	GTNNAC	4 cut(s)	98, 899, 988, 1063
Hpy188I	TCNGA	6 cut(s)	130, 412, 532, 678, 1154, 1165
Hpy188III	TCNNGA	6 cut(s)	519, 609, 708, 818, 1064, 1079
Hpy8I	GTNNAC	4 cut(s)	98, 899, 988, 1063
Hpy99I	CGWCG	2 cut(s)	10, 28
HpyAV	CCTTC	6 cut(s)	163, 897, 959, 974, 1061, 1170
HpyCH4III	ACNGT	4 cut(s)	562, 808, 922, 992
HpyCH4IV	ACGT	1 cut(s)	481
HpyCH4V	TGCA	2 cut(s)	41, 579
HpyF10VI	GCNNNNNNNGC	6 cut(s)	11, 302, 512, 1024, 1180, 1204
HpyF3I	CTNAG	5 cut(s)	129, 321, 339, 409, 645
HpySE526I	ACGT	1 cut(s)	481
Hsp92I	GRCGYC	2 cut(s)	5, 195
Hsp92II	CATG	3 cut(s)	1031, 1082, 1187
HspAI	GCGC	1 cut(s)	440
Kpn2I	TCCGGA	1 cut(s)	707
Kzo9I	GATC	4 cut(s)	225, 601, 720, 1165
LmnI	GCTCC	1 cut(s)	163
LpnPI	CCDG	8 cut(s)	285, 411, 492, 721, 792, 1011, 1072, 1092
Lsp1109I	GCAGC	5 cut(s)	25, 487, 490, 1035, 1036
LweI	GCATC	5 cut(s)	26, 50, 292, 524, 1005
MaeI	CTAG	2 cut(s)	894, 1175
MaeII	ACGT	1 cut(s)	481
MaeIII	GTNAC	3 cut(s)	196, 556, 847
MalI	GATC	4 cut(s)	227, 603, 722, 1167
MboI	GATC	4 cut(s)	225, 601, 720, 1165
MboII	GAAGA	9 cut(s)	76, 205, 337, 355, 360, 534, 545, 696, 1083
MflI	RGATCY	1 cut(s)	1165
MhlI	GDGCHC	1 cut(s)	135
MluCI	AATT	5 cut(s)	140, 460, 1091, 1190, 1228
MlyI	GAGTC	3 cut(s)	586, 778, 993
MmeI	TCCRAC	1 cut(s)	1202
MroI	TCCGGA	1 cut(s)	707
MseI	TTAA	6 cut(s)	281, 465, 485, 564, 627, 950
MslI	CAYNNNNRTG	1 cut(s)	974
MspI	CCGG	2 cut(s)	708, 779
MspR9I	CCNGG	1 cut(s)	780
Mva1269I	GAATGC	1 cut(s)	62
MvnI	CGCG	1 cut(s)	442
MwoI	GCNNNNNNNGC	6 cut(s)	11, 302, 512, 1024, 1180, 1204
NciI	CCSGG	1 cut(s)	780
NdeII	GATC	4 cut(s)	225, 601, 720, 1165
NlaIII	CATG	3 cut(s)	1031, 1082, 1187
NmuCI	GTSAC	1 cut(s)	196
NspI	RCATGY	1 cut(s)	1187
OliI	CACNNNNGTG	1 cut(s)	974
PaeR7I	CTCGAG	1 cut(s)	594
PagI	TCATGA	1 cut(s)	1078
PctI	GAATGC	1 cut(s)	62
PfeI	GAWTC	3 cut(s)	775, 1001, 1149
PkrI	GCNGC	8 cut(s)	16, 40, 194, 439, 502, 505, 1026, 1050
PleI	GAGTC	3 cut(s)	586, 778, 992
PpsI	GAGTC	3 cut(s)	586, 778, 992
Psp1406I	AACGTT	1 cut(s)	481
PspFI	CCCAGC	1 cut(s)	1106
PspXI	VCTCGAGB	1 cut(s)	594
PsuI	RGATCY	1 cut(s)	1165
RsaI	GTAC	2 cut(s)	97, 752
RsaNI	GTAC	2 cut(s)	96, 751
RseI	CAYNNNNRTG	1 cut(s)	974
SaqAI	TTAA	6 cut(s)	281, 465, 485, 564, 627, 950
SatI	GCNGC	8 cut(s)	15, 39, 193, 438, 501, 504, 1025, 1049
Sau3AI	GATC	4 cut(s)	225, 601, 720, 1165
ScaI	AGTACT	1 cut(s)	752
SchI	GAGTC	3 cut(s)	586, 778, 993
ScrFI	CCNGG	1 cut(s)	780
SduI	GDGCHC	1 cut(s)	135
SfaNI	GCATC	5 cut(s)	26, 50, 292, 524, 1005
Sfr274I	CTCGAG	1 cut(s)	594
SlaI	CTCGAG	1 cut(s)	594
SmiMI	CAYNNNNRTG	1 cut(s)	974
SmlI	CTYRAG	3 cut(s)	354, 594, 1112
SmoI	CTYRAG	3 cut(s)	354, 594, 1112
Sse9I	AATT	5 cut(s)	140, 460, 1091, 1190, 1228
SsiI	CCGC	5 cut(s)	14, 192, 375, 387, 437
SspMI	CTAG	2 cut(s)	894, 1175
StyD4I	CCNGG	1 cut(s)	778
StyI	CCWWGG	1 cut(s)	221
TaaI	ACNGT	4 cut(s)	562, 808, 922, 992
TaiI	ACGT	1 cut(s)	484
TaqI	TCGA	4 cut(s)	26, 144, 300, 595
TasI	AATT	5 cut(s)	140, 460, 1091, 1190, 1228
TatI	WGTACW	1 cut(s)	750
TauI	GCSGC	3 cut(s)	17, 195, 440
TfiI	GAWTC	3 cut(s)	775, 1001, 1149
Tru1I	TTAA	6 cut(s)	281, 465, 485, 564, 627, 950
Tru9I	TTAA	6 cut(s)	281, 465, 485, 564, 627, 950
TscAI	CASTG	2 cut(s)	967, 995
TseFI	GTSAC	1 cut(s)	196
TseI	GCWGC	5 cut(s)	38, 500, 503, 1024, 1048
Tsp45I	GTSAC	1 cut(s)	196
TspDTI	ATGAA	5 cut(s)	205, 879, 1095, 1109, 1113
TspGWI	ACGGA	4 cut(s)	83, 92, 221, 1127
TspRI	CASTG	2 cut(s)	967, 995
XapI	RAATTY	2 cut(s)	140, 460
XceI	RCATGY	1 cut(s)	1187
XhoI	CTCGAG	1 cut(s)	594
XspI	CTAG	2 cut(s)	894, 1175
ZrmI	AGTACT	1 cut(s)	752

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