Basic Information

Type: gene

Biological Identity

Species

arabidopsis_thaliana

Chromosome

Orthogroup ID

OG0004698

Physical Location & Seq

Genomic Coordinates Reverse (-)

19383266 .. 19386553

Gene Structure 3288 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

AT3G52260.4

Sequence Viewer

CDS Protein Promoter (2k)

Length: 885 bp

ATGTCGCCGCCGCCGCAACGTATCGGCTTGCCATGGCCTGAGCTTAACGATGGTTTGGCATACAAGGATGCCATCTCTTCTTCTGAATCAGAGTTAACGACGGTGTCAGAATTCTACTTCACCAAATACAAGAGTTCAGCTCCATTGCTAGGGTGGATTCAACGAATCCAAAACGGACAGATACAAATTGACGGTGAAGTTGTAAAAGATCCCAACACACTTCTTAGGAGTGGTTCGAAATTAGTTTACAGTAGGCTTCCTTGGAAGGAACCTGACACGCCATACTCGCTTGAAGTTTTGTATGAAGATGATGATTTGATCGCTTTAAACAAGCCTTCTGGACTTCAAGTATTGCCCGGAGGACTTTTCCAGCAACGGACTGTGTTGACGCAGCTGCAGTGGTGTTTTGGTAAAAATGACTCTTACATCGGATCGCGTGAATCACCACATCCTGTCCCTGTACATCGACTGGGTAGAGGAACTTCAGGTATACTTCTCTGTGCAAAGACCAAGCTGGCAAAAACGAAACTTGCAGCGTATTTTGCTGAGGGAACATCTCTTGTCGGCTCCGGCAACCTGGATCAAGAGTGTGGAACAGGAAGAAAACTATCAAAGATATATCGAGCACTAGCAGATGGTATAGTTGAAGAAGACGAGGTAGTAATCAAACAGCCTATAGGAGTGGTTCGATATCCTGGGGTCGCACAAGGATTATATGTTGCTTCTCCGGAAGGGAAACCTGCTTTCAGTAAAGTATTTGTTCTGGAGAGGGACAGGGAAAAAAATTGCTCGCTTGTTAAGGTAGAGATACAATCTGGAAGACCACATCAAATCCGGATTCATCTTGCATACATGGGACATCCCTTGGGGACCCTCTTTATGTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000154 GO:0000455 GO:0001522 GO:0003674 GO:0003824 GO:0006139 GO:0006364 GO:0006396 GO:0006399 GO:0006400 GO:0006725 GO:0006807 GO:0008033 GO:0008150 GO:0008152 GO:0009451 GO:0009982 GO:0009987 GO:0010467 GO:0016070 GO:0016072 GO:0016853 GO:0016866 GO:0022613 GO:0031118 GO:0031119 GO:0034470 GO:0034641 GO:0034660 GO:0042254 GO:0043170 GO:0043412 GO:0044085 GO:0044237 GO:0044238 GO:0046483 GO:0071704 GO:0071840 GO:0090304 GO:1901360

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PseudoU_synth_2

Protein Analysis

294

Amino Acids

32.5

Weight (kDa)

8.53

Isoelectric Point (pI)

40.96

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PseudoU_synth_2	PF00849	105 - 283	5.5e-24	RNA pseudouridylate synthase

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

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0004698)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G52260 AT3G52260 AT3G52260 AT3G52260
fragaria_vesca	FvH4_7g19860
malus_domestica	MD07G1176900.v1.1
prunus_persica	Prupe.2G215700_v2.0.a1 Prupe.2G215700_v2.0.a1
pyrus_communis	pycom07g17100
rosa_chinensis	RchiOBHm_Chr1g0363851 RchiOBHm_Chr2g0104231 RchiOBHm_Chr2g0110391 RchiOBHm_Chr5g0046841
rosa_laevigata	RLG00000027541 RLG00000030372
rosa_multiflora	Rmu_sc0002474.1_g000014
rosa_roxburghii	Rroxscaffold_4G00292920
rosa_rugosa	Rorug01G0309800 Rorug01G0309900
rosa_samantha	Rh1AG318300 Rh1BG281500 Rh1CG297900 Rh1DG312800 Rh3CG345100 Rh4AG103100 Rh4CG111400 Rh5AG515700 Rh5BG320500 Rh5DG331200
rosa_wichuraiana	Rw1G028250 Rw5G039760

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc36I	ACCTGC	1 cut(s)	748
AccI	GTMKAC	1 cut(s)	490
AccII	CGCG	1 cut(s)	436
AccIII	TCCGGA	2 cut(s)	727, 834
AciI	CCGC	3 cut(s)	8, 11, 14
AclWI	GGATC	3 cut(s)	203, 439, 588
AcsI	RAATTY	1 cut(s)	110
AcuI	CTGAAG	1 cut(s)	468
AfaI	GTAC	1 cut(s)	462
AfiI	CCNNNNNNNGG	1 cut(s)	149
AgsI	TTSAA	4 cut(s)	161, 293, 347, 647
AjnI	CCWGG	2 cut(s)	576, 694
AluBI	AGCT	4 cut(s)	43, 140, 394, 514
AluI	AGCT	4 cut(s)	43, 140, 394, 514
Alw21I	GWGCWC	1 cut(s)	628
AlwI	GGATC	3 cut(s)	203, 439, 588
Aor13HI	TCCGGA	2 cut(s)	727, 834
AoxI	GGCC	1 cut(s)	35
ApeKI	GCWGC	3 cut(s)	391, 394, 533
ApoI	RAATTY	1 cut(s)	110
AspS9I	GGNCC	1 cut(s)	870
AsuC2I	CCSGG	1 cut(s)	357
AsuHPI	GGTGA	3 cut(s)	112, 206, 435
AsuII	TTCGAA	1 cut(s)	236
AvaII	GGWCC	1 cut(s)	870
BarI	GAAGNNNNNNTAC	2 cut(s)	466, 498
BbsI	GAAGAC	2 cut(s)	657, 826
Bbv12I	GWGCWC	1 cut(s)	628
BbvCI	CCTCAGC	1 cut(s)	546
BbvI	GCAGC	3 cut(s)	381, 403, 545
BccI	CCATC	3 cut(s)	44, 80, 629
BciT130I	CCWGG	2 cut(s)	578, 696
BcnI	CCSGG	1 cut(s)	357
BfaI	CTAG	2 cut(s)	149, 629
BfmI	CTRYAG	2 cut(s)	395, 675
BfuAI	ACCTGC	1 cut(s)	748
BisI	GCNGC	6 cut(s)	8, 11, 14, 392, 395, 534
BlsI	GCNGC	6 cut(s)	9, 12, 15, 393, 396, 535
Bme1390I	CCNGG	3 cut(s)	357, 578, 696
Bme18I	GGWCC	1 cut(s)	870
BmgT120I	GGNCC	1 cut(s)	870
BmiI	GGNNCC	4 cut(s)	270, 568, 871, 872
BmrFI	CCNGG	3 cut(s)	357, 578, 696
BmrI	ACTGGG	1 cut(s)	479
BmsI	GCATC	1 cut(s)	58
BmuI	ACTGGG	1 cut(s)	479
BpiI	GAAGAC	2 cut(s)	657, 826
BplI	GAGNNNNNCTC	2 cut(s)	124, 156
BpmI	CTGGAG	1 cut(s)	785
Bpu10I	CCTNAGC	2 cut(s)	39, 546
Bpu14I	TTCGAA	1 cut(s)	236
BpuMI	CCSGG	1 cut(s)	357
BsaJI	CCNNGG	4 cut(s)	32, 260, 695, 864
BsaWI	WCCGGW	2 cut(s)	727, 834
Bsc4I	CCNNNNNNNGG	1 cut(s)	149
Bse1I	ACTGG	1 cut(s)	474
Bse3DI	GCAATG	1 cut(s)	143
BseAI	TCCGGA	2 cut(s)	727, 834
BseBI	CCWGG	2 cut(s)	578, 696
BseDI	CCNNGG	4 cut(s)	32, 260, 695, 864
BseGI	GGATG	3 cut(s)	73, 448, 859
BseLI	CCNNNNNNNGG	1 cut(s)	149
BseMI	GCAATG	1 cut(s)	143
BseMII	CTCAG	2 cut(s)	30, 537
BseNI	ACTGG	1 cut(s)	474
BseXI	GCAGC	3 cut(s)	381, 403, 545
Bsh1236I	CGCG	1 cut(s)	436
BshFI	GGCC	1 cut(s)	37
BsiHKAI	GWGCWC	1 cut(s)	628
BsiSI	CCGG	4 cut(s)	357, 570, 728, 835
BslFI	GGGAC	3 cut(s)	440, 785, 870
BslI	CCNNNNNNNGG	1 cut(s)	149
BsmFI	GGGAC	3 cut(s)	440, 785, 870
BsnI	GGCC	1 cut(s)	37
Bsp119I	TTCGAA	1 cut(s)	236
Bsp1286I	GDGCHC	1 cut(s)	628
Bsp13I	TCCGGA	2 cut(s)	727, 834
Bsp1407I	TGTACA	1 cut(s)	460
Bsp143I	GATC	4 cut(s)	208, 318, 431, 580
Bsp19I	CCATGG	1 cut(s)	32
BspACI	CCGC	3 cut(s)	8, 11, 14
BspANI	GGCC	1 cut(s)	37
BspCNI	CTCAG	2 cut(s)	31, 538
BspEI	TCCGGA	2 cut(s)	727, 834
BspFNI	CGCG	1 cut(s)	436
BspLI	GGNNCC	4 cut(s)	270, 568, 871, 872
BspMAI	CTGCAG	1 cut(s)	399
BspMI	ACCTGC	1 cut(s)	748
BspPI	GGATC	3 cut(s)	203, 439, 588
BspT104I	TTCGAA	1 cut(s)	236
BsrDI	GCAATG	1 cut(s)	143
BsrGI	TGTACA	1 cut(s)	460
BsrI	ACTGG	1 cut(s)	474
BssECI	CCNNGG	4 cut(s)	32, 260, 695, 864
BssMI	GATC	4 cut(s)	208, 318, 431, 580
BssNAI	GTATAC	1 cut(s)	491
BssT1I	CCWWGG	3 cut(s)	32, 260, 864
Bst1107I	GTATAC	1 cut(s)	491
Bst2UI	CCWGG	2 cut(s)	578, 696
Bst4CI	ACNGT	4 cut(s)	103, 194, 251, 382
Bst6I	CTCTTC	1 cut(s)	82
BstAUI	TGTACA	1 cut(s)	460
BstBI	TTCGAA	1 cut(s)	236
BstC8I	GCNNGC	3 cut(s)	29, 516, 791
BstDEI	CTNAG	3 cut(s)	39, 224, 546
BstDSI	CCRYGG	1 cut(s)	32
BstF5I	GGATG	3 cut(s)	73, 448, 859
BstFNI	CGCG	1 cut(s)	436
BstKTI	GATC	4 cut(s)	211, 321, 434, 583
BstMBI	GATC	4 cut(s)	208, 318, 431, 580
BstMWI	GCNNNNNNNGC	3 cut(s)	13, 286, 542
BstNI	CCWGG	2 cut(s)	578, 696
BstSCI	CCNGG	3 cut(s)	355, 576, 694
BstSFI	CTRYAG	2 cut(s)	395, 675
BstUI	CGCG	1 cut(s)	436
BstV1I	GCAGC	3 cut(s)	381, 403, 545
BstV2I	GAAGAC	2 cut(s)	657, 826
BstX2I	RGATCY	1 cut(s)	208
BstYI	RGATCY	1 cut(s)	208
BstZ17I	GTATAC	1 cut(s)	491
BsuRI	GGCC	1 cut(s)	37
BtgI	CCRYGG	1 cut(s)	32
BtsCI	GGATG	3 cut(s)	73, 448, 859
BtsI	GCAGTG	1 cut(s)	404
BtsIMutI	CAGTG	1 cut(s)	404
BveI	ACCTGC	1 cut(s)	748
Cac8I	GCNNGC	3 cut(s)	29, 516, 791
Cfr13I	GGNCC	1 cut(s)	870
CseI	GACGC	1 cut(s)	397
Csp6I	GTAC	1 cut(s)	461
CviAII	CATG	2 cut(s)	33, 853
CviQI	GTAC	1 cut(s)	461
DdeI	CTNAG	3 cut(s)	39, 224, 546
DpnI	GATC	4 cut(s)	210, 320, 433, 582
DpnII	GATC	4 cut(s)	208, 318, 431, 580
DraI	TTTAAA	1 cut(s)	327
Eam1104I	CTCTTC	1 cut(s)	82
EarI	CTCTTC	1 cut(s)	82
Eco130I	CCWWGG	3 cut(s)	32, 260, 864
Eco32I	GATATC	1 cut(s)	692
Eco47I	GGWCC	1 cut(s)	870
Eco57I	CTGAAG	1 cut(s)	468
EcoO109I	RGGNCCY	1 cut(s)	870
EcoRI	GAATTC	1 cut(s)	110
EcoRII	CCWGG	2 cut(s)	576, 694
EcoRV	GATATC	1 cut(s)	692
EcoT14I	CCWWGG	3 cut(s)	32, 260, 864
ErhI	CCWWGG	3 cut(s)	32, 260, 864
FaeI	CATG	2 cut(s)	36, 856
FaqI	GGGAC	3 cut(s)	440, 785, 870
FatI	CATG	2 cut(s)	32, 852
FblI	GTMKAC	1 cut(s)	490
Fnu4HI	GCNGC	6 cut(s)	8, 11, 14, 392, 395, 534
FokI	GGATG	3 cut(s)	80, 435, 846
Fsp4HI	GCNGC	6 cut(s)	8, 11, 14, 392, 395, 534
FspBI	CTAG	2 cut(s)	149, 629
GluI	GCNGC	6 cut(s)	8, 11, 14, 392, 395, 534
GsuI	CTGGAG	1 cut(s)	785
HaeIII	GGCC	1 cut(s)	37
HapII	CCGG	4 cut(s)	357, 570, 728, 835
HgaI	GACGC	1 cut(s)	397
Hin1II	CATG	2 cut(s)	36, 856
HincII	GTYRAC	2 cut(s)	96, 387
HindII	GTYRAC	2 cut(s)	96, 387
HinfI	GANTC	6 cut(s)	86, 157, 165, 419, 440, 838
HpaI	GTTAAC	1 cut(s)	96
HpaII	CCGG	4 cut(s)	357, 570, 728, 835
HphI	GGTGA	3 cut(s)	112, 206, 435
Hpy166II	GTNNAC	4 cut(s)	96, 247, 387, 491
Hpy188I	TCNGA	4 cut(s)	85, 91, 109, 431
Hpy188III	TCNNGA	6 cut(s)	339, 584, 728, 764, 816, 835
Hpy8I	GTNNAC	4 cut(s)	96, 247, 387, 491
Hpy99I	CGWCG	1 cut(s)	103
HpyAV	CCTTC	3 cut(s)	259, 345, 725
HpyCH4III	ACNGT	4 cut(s)	103, 194, 251, 382
HpyCH4IV	ACGT	1 cut(s)	19
HpyCH4V	TGCA	4 cut(s)	397, 503, 533, 848
HpyF10VI	GCNNNNNNNGC	3 cut(s)	13, 286, 542
HpyF3I	CTNAG	3 cut(s)	39, 224, 546
HpySE526I	ACGT	1 cut(s)	19
Hsp92II	CATG	2 cut(s)	36, 856
KflI	GGGWCCC	1 cut(s)	870
Kpn2I	TCCGGA	2 cut(s)	727, 834
KspAI	GTTAAC	1 cut(s)	96
Kzo9I	GATC	4 cut(s)	208, 318, 431, 580
LmnI	GCTCC	2 cut(s)	145, 572
Lsp1109I	GCAGC	3 cut(s)	381, 403, 545
LweI	GCATC	1 cut(s)	58
MaeI	CTAG	2 cut(s)	149, 629
MaeII	ACGT	1 cut(s)	19
MalI	GATC	4 cut(s)	210, 320, 433, 582
MboI	GATC	4 cut(s)	208, 318, 431, 580
MboII	GAAGA	7 cut(s)	69, 72, 317, 612, 659, 662, 831
MflI	RGATCY	1 cut(s)	208
MhlI	GDGCHC	1 cut(s)	628
MluCI	AATT	4 cut(s)	110, 186, 239, 784
MlyI	GAGTC	1 cut(s)	413
MnlI	CCTC	6 cut(s)	353, 470, 541, 649, 762, 884
MroI	TCCGGA	2 cut(s)	727, 834
MseI	TTAA	4 cut(s)	45, 95, 326, 798
MspA1I	CMGCKG	1 cut(s)	394
MspI	CCGG	4 cut(s)	357, 570, 728, 835
MspR9I	CCNGG	3 cut(s)	357, 578, 696
MvaI	CCWGG	2 cut(s)	578, 696
MvnI	CGCG	1 cut(s)	436
MwoI	GCNNNNNNNGC	3 cut(s)	13, 286, 542
NciI	CCSGG	1 cut(s)	357
NcoI	CCATGG	1 cut(s)	32
NdeII	GATC	4 cut(s)	208, 318, 431, 580
NlaIII	CATG	2 cut(s)	36, 856
NlaIV	GGNNCC	4 cut(s)	270, 568, 871, 872
NspV	TTCGAA	1 cut(s)	236
PfeI	GAWTC	5 cut(s)	86, 157, 165, 440, 838
PflFI	GACNNNGTC	1 cut(s)	103
PkrI	GCNGC	6 cut(s)	9, 12, 15, 393, 396, 535
PleI	GAGTC	1 cut(s)	413
PpsI	GAGTC	1 cut(s)	413
PpuMI	RGGWCCY	1 cut(s)	870
Psp5II	RGGWCCY	1 cut(s)	870
Psp6I	CCWGG	2 cut(s)	576, 694
PspGI	CCWGG	2 cut(s)	576, 694
PspN4I	GGNNCC	4 cut(s)	270, 568, 871, 872
PspPI	GGNCC	1 cut(s)	870
PspPPI	RGGWCCY	1 cut(s)	870
PstI	CTGCAG	1 cut(s)	399
PsuI	RGATCY	1 cut(s)	208
PsyI	GACNNNGTC	1 cut(s)	103
PvuII	CAGCTG	1 cut(s)	394
RsaI	GTAC	1 cut(s)	462
RsaNI	GTAC	1 cut(s)	461
SaqAI	TTAA	4 cut(s)	45, 95, 326, 798
SatI	GCNGC	6 cut(s)	8, 11, 14, 392, 395, 534
Sau3AI	GATC	4 cut(s)	208, 318, 431, 580
Sau96I	GGNCC	1 cut(s)	870
SchI	GAGTC	1 cut(s)	413
ScrFI	CCNGG	3 cut(s)	357, 578, 696
SduI	GDGCHC	1 cut(s)	628
SfaNI	GCATC	1 cut(s)	58
SfcI	CTRYAG	2 cut(s)	395, 675
SfuI	TTCGAA	1 cut(s)	236
SinI	GGWCC	1 cut(s)	870
Sse9I	AATT	4 cut(s)	110, 186, 239, 784
SsiI	CCGC	3 cut(s)	8, 11, 14
SspMI	CTAG	2 cut(s)	149, 629
StyD4I	CCNGG	3 cut(s)	355, 576, 694
StyI	CCWWGG	3 cut(s)	32, 260, 864
TaaI	ACNGT	4 cut(s)	103, 194, 251, 382
TaiI	ACGT	1 cut(s)	22
TaqI	TCGA	4 cut(s)	236, 466, 622, 688
TasI	AATT	4 cut(s)	110, 186, 239, 784
TatI	WGTACW	1 cut(s)	460
TauI	GCSGC	3 cut(s)	10, 13, 16
TfiI	GAWTC	5 cut(s)	86, 157, 165, 440, 838
Tru1I	TTAA	4 cut(s)	45, 95, 326, 798
Tru9I	TTAA	4 cut(s)	45, 95, 326, 798
TscAI	CASTG	1 cut(s)	404
TseI	GCWGC	3 cut(s)	391, 394, 533
TspDTI	ATGAA	2 cut(s)	318, 830
TspGWI	ACGGA	2 cut(s)	189, 391
TspRI	CASTG	1 cut(s)	404
Tth111I	GACNNNGTC	1 cut(s)	103
VpaK11BI	GGWCC	1 cut(s)	870
XapI	RAATTY	1 cut(s)	110
XcmI	CCANNNNNNNNNTGG	1 cut(s)	150
XmiI	GTMKAC	1 cut(s)	490
XspI	CTAG	2 cut(s)	149, 629

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