Basic Information

Type: gene

Biological Identity

Species

arabidopsis_thaliana

Chromosome

Orthogroup ID

OG0008030

Physical Location & Seq

Genomic Coordinates Forward (+)

20560802 .. 20563885

Gene Structure 3084 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

AT3G55460.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 789 bp

ATGAGGAGATACAGTCCGCCTTATTACAGTCCTCCGAGGAGAGGATACGGTGGTCGAGGTAGAAGTCCTCCTCCTCCTCCTCCTCGACGTGGATATGGTGGTGGTGGTGGTGGTGGTGGACGTAGAGGATCTAGCCATGGAAGTCTCTTGGTTCGTAACATTCCTCTTGATTGCAGACCAGAAGAGCTTCGTGAGCCCTTTGAGAGGTTTGGACCTGTGAGAGATGTCTATATCCCCAGAGACTATTACTCAGGGCAACCGCGGGGGTTTGCGTTTGTGGAGTTTGTTGATGCATATGATGCTGGGGAGGCTCAAAGAAGCATGAACAGGAGAAGCTTTGCTGGAAGAGAGATAACGGTGGTTGTTGCTTCAGAGTCTAGGAAAAGGCCTGAAGAGATGCGTGTGAAGACTAGGACTCGTAGTAGGGAACCTTCAGGCTCCAGGGATCGTTCTCATGGACGGTCTCGTTCACGTTCAATCTCTCGATCACGTTCTCCACGTCGTCCGTCAGATTCTAGAAGCAGATACCGATCAAGGTCTTACTCTCCTGCACCAAGACGAAGAGGAGGTCCTCCTCGTGGGGAAGAAGATGAAAATTACAGTCGTAGGTCCTACTCCCCTGGCTATGAAGGTGCTGCTGCTGCTGCTCCAGATCGGGACAGAAATGGAGACAATGAGATTAGAGAAAAACCGGGCTATGAAGCAGAGGATAGACGTCGTGGTGGAAGAGCAGTTTCAAGGTCGCCATCAGGATCCAGGTCCAGGTCTGTGGAGGTATCTCCAAGATGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000375 GO:0000377 GO:0000398 GO:0003674 GO:0003676 GO:0003723 GO:0003729 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0006139 GO:0006396 GO:0006397 GO:0006725 GO:0006807 GO:0006950 GO:0006979 GO:0008150 GO:0008152 GO:0008380 GO:0009987 GO:0010467 GO:0016070 GO:0016071 GO:0016604 GO:0016607 GO:0031974 GO:0031981 GO:0034641 GO:0042802 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044237 GO:0044238 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044464 GO:0046483 GO:0050896 GO:0070013 GO:0071704 GO:0090304 GO:0097159 GO:1901360 GO:1901363

KEGG Pathways

Metabolic & Signaling

ko03040 map03040

Pfam Domains

Protein Families

RRM_1

Protein Analysis

262

Amino Acids

29.57

Weight (kDa)

11.27

Isoelectric Point (pI)

110.1

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RRM_1	PF00076	49 - 119	3.9e-19	RNA recognition motif

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0008030)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G55460
fragaria_vesca	FvH4_7g22601 FvH4_7g22602
malus_domestica	MD01G1135000.v1.1 MD07G1199700.v1.1
prunus_persica	Prupe.2G236400_v2.0.a1 Prupe.2G236400_v2.0.a1 Prupe.2G236400_v2.0.a1 Prupe.2G236400_v2.0.a1
pyrus_communis	pycom01g15570 pycom07g18650
rosa_chinensis	RchiOBHm_Chr1g0367721
rosa_laevigata	RLG00000027268
rosa_multiflora	Rmu_co8328167.1_g000001 Rmu_sc0008470.1_g000003 Rmu_sc0033554.1_g000001
rosa_roxburghii	Rroxscaffold_4G00289280
rosa_rugosa	Rorug01G0336200
rosa_samantha	Rh1AG343300 Rh1BG305000 Rh1CG320700 Rh1DG337300 Rh6BG013900
rosa_wichuraiana	Rw1G030550

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AatII	GACGTC	1 cut(s)	718
AccII	CGCG	1 cut(s)	262
AciI	CCGC	3 cut(s)	17, 260, 262
AclWI	GGATC	4 cut(s)	136, 453, 747, 760
AcuI	CTGAAG	3 cut(s)	354, 411, 417
AcyI	GRCGYC	1 cut(s)	715
AfiI	CCNNNNNNNGG	5 cut(s)	41, 89, 204, 578, 762
AgsI	TTSAA	2 cut(s)	477, 738
AjiI	CACGTC	2 cut(s)	89, 500
AjnI	CCWGG	4 cut(s)	440, 619, 755, 761
AluBI	AGCT	2 cut(s)	187, 336
AluI	AGCT	2 cut(s)	187, 336
Alw26I	GTCTC	4 cut(s)	149, 234, 468, 663
AlwI	GGATC	4 cut(s)	136, 453, 747, 760
AoxI	GGCC	1 cut(s)	386
ApeKI	GCWGC	4 cut(s)	635, 638, 641, 644
ArsI	GACNNNNNNTTYG	2 cut(s)	553, 585
Asp700I	GAANNNNTTC	1 cut(s)	186
AspS9I	GGNCC	4 cut(s)	212, 569, 609, 759
AsuC2I	CCSGG	1 cut(s)	693
AvaII	GGWCC	4 cut(s)	212, 569, 609, 759
BaeI	ACNNNNGTAYC	2 cut(s)	37, 70
BamHI	GGATCC	1 cut(s)	752
BanII	GRGCYC	1 cut(s)	198
BarI	GAAGNNNNNNTAC	2 cut(s)	415, 447
BauI	CACGAG	1 cut(s)	576
BbsI	GAAGAC	1 cut(s)	413
BbvI	GCAGC	4 cut(s)	622, 625, 628, 631
BccI	CCATC	1 cut(s)	754
BciT130I	CCWGG	4 cut(s)	442, 621, 757, 763
BciVI	GTATCC	1 cut(s)	38
BcnI	CCSGG	1 cut(s)	693
BcoDI	GTCTC	4 cut(s)	149, 234, 468, 663
BfaI	CTAG	4 cut(s)	132, 378, 411, 516
BfuI	GTATCC	1 cut(s)	38
BisI	GCNGC	4 cut(s)	636, 639, 642, 645
BlsI	GCNGC	4 cut(s)	637, 640, 643, 646
Bme1390I	CCNGG	5 cut(s)	442, 621, 693, 757, 763
Bme18I	GGWCC	4 cut(s)	212, 569, 609, 759
BmgBI	CACGTC	2 cut(s)	89, 500
BmgT120I	GGNCC	4 cut(s)	212, 569, 609, 759
BmiI	GGNNCC	3 cut(s)	429, 439, 754
BmrFI	CCNGG	5 cut(s)	442, 621, 693, 757, 763
BmsI	GCATC	3 cut(s)	280, 289, 387
BpiI	GAAGAC	1 cut(s)	413
BpmI	CTGGAG	2 cut(s)	424, 633
BpuMI	CCSGG	1 cut(s)	693
BsaBI	GATNNNNATC	1 cut(s)	529
BsaHI	GRCGYC	1 cut(s)	715
BsaI	GGTCTC	1 cut(s)	468
BsaJI	CCNNGG	5 cut(s)	35, 136, 260, 441, 619
BsaXI	ACNNNNNCTCC	1 cut(s)	28
Bsc4I	CCNNNNNNNGG	5 cut(s)	41, 89, 204, 578, 762
Bse8I	GATNNNNATC	1 cut(s)	529
BseBI	CCWGG	4 cut(s)	442, 621, 757, 763
BseDI	CCNNGG	5 cut(s)	35, 136, 260, 441, 619
BseJI	GATNNNNATC	1 cut(s)	529
BseLI	CCNNNNNNNGG	5 cut(s)	41, 89, 204, 578, 762
BseMII	CTCAG	1 cut(s)	264
BseRI	GAGGAG	9 cut(s)	19, 52, 60, 63, 66, 69, 72, 564, 579
BseXI	GCAGC	4 cut(s)	622, 625, 628, 631
BseYI	CCCAGC	1 cut(s)	302
BsgI	GTGCAG	1 cut(s)	534
Bsh1236I	CGCG	1 cut(s)	262
BshFI	GGCC	1 cut(s)	388
BsiSI	CCGG	1 cut(s)	692
BslFI	GGGAC	1 cut(s)	671
BslI	CCNNNNNNNGG	5 cut(s)	41, 89, 204, 578, 762
BsmAI	GTCTC	4 cut(s)	149, 234, 468, 663
BsmFI	GGGAC	1 cut(s)	671
BsnI	GGCC	1 cut(s)	388
Bso31I	GGTCTC	1 cut(s)	468
Bsp1286I	GDGCHC	1 cut(s)	198
Bsp143I	GATC	6 cut(s)	128, 445, 485, 530, 652, 752
Bsp19I	CCATGG	1 cut(s)	136
BspACI	CCGC	3 cut(s)	17, 260, 262
BspANI	GGCC	1 cut(s)	388
BspCNI	CTCAG	1 cut(s)	263
BspFNI	CGCG	1 cut(s)	262
BspLI	GGNNCC	3 cut(s)	429, 439, 754
BspPI	GGATC	4 cut(s)	136, 453, 747, 760
BspQI	GCTCTTC	2 cut(s)	177, 721
BspTNI	GGTCTC	1 cut(s)	468
BssECI	CCNNGG	5 cut(s)	35, 136, 260, 441, 619
BssMI	GATC	6 cut(s)	128, 445, 485, 530, 652, 752
BssNI	GRCGYC	1 cut(s)	715
BssSI	CACGAG	1 cut(s)	576
BssT1I	CCWWGG	1 cut(s)	136
Bst2BI	CACGAG	1 cut(s)	576
Bst2UI	CCWGG	4 cut(s)	442, 621, 757, 763
Bst4CI	ACNGT	6 cut(s)	14, 29, 50, 358, 462, 602
Bst6I	CTCTTC	5 cut(s)	177, 340, 387, 556, 721
BstACI	GRCGYC	1 cut(s)	715
BstAPI	GCANNNNNTGC	1 cut(s)	299
BstDEI	CTNAG	1 cut(s)	250
BstDSI	CCRYGG	2 cut(s)	136, 260
BstENI	CCTNNNNNAGG	1 cut(s)	202
BstFNI	CGCG	1 cut(s)	262
BstKTI	GATC	6 cut(s)	131, 448, 488, 533, 655, 755
BstMAI	GTCTC	4 cut(s)	149, 234, 468, 663
BstMBI	GATC	6 cut(s)	128, 445, 485, 530, 652, 752
BstMWI	GCNNNNNNNGC	5 cut(s)	193, 299, 308, 641, 644
BstNI	CCWGG	4 cut(s)	442, 621, 757, 763
BstSCI	CCNGG	5 cut(s)	440, 619, 691, 755, 761
BstUI	CGCG	1 cut(s)	262
BstV1I	GCAGC	4 cut(s)	622, 625, 628, 631
BstV2I	GAAGAC	1 cut(s)	413
BstX2I	RGATCY	2 cut(s)	128, 752
BstXI	CCANNNNNNTGG	1 cut(s)	769
BstYI	RGATCY	2 cut(s)	128, 752
BsuI	GTATCC	1 cut(s)	38
BsuRI	GGCC	1 cut(s)	388
BtgI	CCRYGG	2 cut(s)	136, 260
BtrI	CACGTC	2 cut(s)	89, 500
Cfr13I	GGNCC	4 cut(s)	212, 569, 609, 759
Cfr42I	CCGCGG	1 cut(s)	263
CviAII	CATG	3 cut(s)	137, 322, 455
CviJI	RGCY	9 cut(s)	135, 187, 196, 311, 336, 388, 438, 624, 696
CviKI_1	RGCY	9 cut(s)	135, 187, 196, 311, 336, 388, 438, 624, 696
DdeI	CTNAG	1 cut(s)	250
DpnI	GATC	6 cut(s)	130, 447, 487, 532, 654, 754
DpnII	GATC	6 cut(s)	128, 445, 485, 530, 652, 752
Eam1104I	CTCTTC	5 cut(s)	177, 340, 387, 556, 721
EarI	CTCTTC	5 cut(s)	177, 340, 387, 556, 721
EciI	GGCGGA	1 cut(s)	6
Eco130I	CCWWGG	1 cut(s)	136
Eco147I	AGGCCT	1 cut(s)	388
Eco24I	GRGCYC	1 cut(s)	198
Eco31I	GGTCTC	1 cut(s)	468
Eco47I	GGWCC	4 cut(s)	212, 569, 609, 759
Eco57I	CTGAAG	3 cut(s)	354, 411, 417
EcoNI	CCTNNNNNAGG	1 cut(s)	202
EcoO109I	RGGNCCY	2 cut(s)	569, 609
EcoRII	CCWGG	4 cut(s)	440, 619, 755, 761
EcoT14I	CCWWGG	1 cut(s)	136
EcoT22I	ATGCAT	1 cut(s)	295
EcoT38I	GRGCYC	1 cut(s)	198
ErhI	CCWWGG	1 cut(s)	136
FaeI	CATG	3 cut(s)	140, 325, 458
FaiI	YATR	9 cut(s)	96, 138, 231, 295, 297, 323, 456, 627, 699
FaqI	GGGAC	1 cut(s)	671
FatI	CATG	3 cut(s)	136, 321, 454
FauI	CCCGC	1 cut(s)	255
FauNDI	CATATG	1 cut(s)	295
Fnu4HI	GCNGC	4 cut(s)	636, 639, 642, 645
FriOI	GRGCYC	1 cut(s)	198
Fsp4HI	GCNGC	4 cut(s)	636, 639, 642, 645
FspBI	CTAG	4 cut(s)	132, 378, 411, 516
GluI	GCNGC	4 cut(s)	636, 639, 642, 645
GsaI	CCCAGC	1 cut(s)	306
GsuI	CTGGAG	2 cut(s)	424, 633
HaeIII	GGCC	1 cut(s)	388
HapII	CCGG	1 cut(s)	692
Hin1I	GRCGYC	1 cut(s)	715
Hin1II	CATG	3 cut(s)	140, 325, 458
HindIII	AAGCTT	1 cut(s)	334
HinfI	GANTC	3 cut(s)	374, 415, 512
HpaII	CCGG	1 cut(s)	692
Hpy166II	GTNNAC	2 cut(s)	119, 470
Hpy188I	TCNGA	3 cut(s)	36, 373, 511
Hpy188III	TCNNGA	7 cut(s)	167, 191, 483, 516, 650, 656, 750
Hpy8I	GTNNAC	2 cut(s)	119, 470
Hpy99I	CGWCG	3 cut(s)	90, 504, 720
HpyAV	CCTTC	2 cut(s)	441, 623
HpyCH4III	ACNGT	6 cut(s)	14, 29, 50, 358, 462, 602
HpyCH4IV	ACGT	6 cut(s)	88, 121, 472, 490, 499, 715
HpyCH4V	TGCA	3 cut(s)	174, 293, 551
HpyF10VI	GCNNNNNNNGC	5 cut(s)	193, 299, 308, 641, 644
HpyF3I	CTNAG	1 cut(s)	250
HpySE526I	ACGT	6 cut(s)	88, 121, 472, 490, 499, 715
Hsp92I	GRCGYC	1 cut(s)	715
Hsp92II	CATG	3 cut(s)	140, 325, 458
KspI	CCGCGG	1 cut(s)	263
Kzo9I	GATC	6 cut(s)	128, 445, 485, 530, 652, 752
LguI	GCTCTTC	2 cut(s)	177, 721
LmnI	GCTCC	2 cut(s)	443, 652
Lsp1109I	GCAGC	4 cut(s)	622, 625, 628, 631
LweI	GCATC	3 cut(s)	280, 289, 387
MaeI	CTAG	4 cut(s)	132, 378, 411, 516
MaeII	ACGT	6 cut(s)	88, 121, 472, 490, 499, 715
MaeIII	GTNAC	1 cut(s)	155
MalI	GATC	6 cut(s)	130, 447, 487, 532, 654, 754
MboI	GATC	6 cut(s)	128, 445, 485, 530, 652, 752
MboII	GAAGA	8 cut(s)	194, 357, 404, 418, 573, 596, 599, 738
MflI	RGATCY	2 cut(s)	128, 752
MhlI	GDGCHC	1 cut(s)	198
MluCI	AATT	1 cut(s)	595
MlyI	GAGTC	2 cut(s)	383, 409
Mph1103I	ATGCAT	1 cut(s)	295
MroXI	GAANNNNTTC	1 cut(s)	186
MspA1I	CMGCKG	1 cut(s)	262
MspI	CCGG	1 cut(s)	692
MspR9I	CCNGG	5 cut(s)	442, 621, 693, 757, 763
MvaI	CCWGG	4 cut(s)	442, 621, 757, 763
MvnI	CGCG	1 cut(s)	262
MwoI	GCNNNNNNNGC	5 cut(s)	193, 299, 308, 641, 644
NciI	CCSGG	1 cut(s)	693
NcoI	CCATGG	1 cut(s)	136
NdeI	CATATG	1 cut(s)	295
NdeII	GATC	6 cut(s)	128, 445, 485, 530, 652, 752
NlaIII	CATG	3 cut(s)	140, 325, 458
NlaIV	GGNNCC	3 cut(s)	429, 439, 754
NsiI	ATGCAT	1 cut(s)	295
PceI	AGGCCT	1 cut(s)	388
PciSI	GCTCTTC	2 cut(s)	177, 721
PcsI	WCGNNNNNNNCGW	1 cut(s)	496
PdmI	GAANNNNTTC	1 cut(s)	186
PfeI	GAWTC	1 cut(s)	512
PkrI	GCNGC	4 cut(s)	637, 640, 643, 646
PleI	GAGTC	2 cut(s)	382, 409
PpsI	GAGTC	2 cut(s)	382, 409
PpuMI	RGGWCCY	2 cut(s)	569, 609
Psp5II	RGGWCCY	2 cut(s)	569, 609
Psp6I	CCWGG	4 cut(s)	440, 619, 755, 761
PspFI	CCCAGC	1 cut(s)	302
PspGI	CCWGG	4 cut(s)	440, 619, 755, 761
PspN4I	GGNNCC	3 cut(s)	429, 439, 754
PspPI	GGNCC	4 cut(s)	212, 569, 609, 759
PspPPI	RGGWCCY	2 cut(s)	569, 609
PsuI	RGATCY	2 cut(s)	128, 752
SacII	CCGCGG	1 cut(s)	263
SapI	GCTCTTC	2 cut(s)	177, 721
SatI	GCNGC	4 cut(s)	636, 639, 642, 645
Sau3AI	GATC	6 cut(s)	128, 445, 485, 530, 652, 752
Sau96I	GGNCC	4 cut(s)	212, 569, 609, 759
SchI	GAGTC	2 cut(s)	383, 409
ScrFI	CCNGG	5 cut(s)	442, 621, 693, 757, 763
SduI	GDGCHC	1 cut(s)	198
SfaNI	GCATC	3 cut(s)	280, 289, 387
Sfr303I	CCGCGG	1 cut(s)	263
SgrBI	CCGCGG	1 cut(s)	263
SinI	GGWCC	4 cut(s)	212, 569, 609, 759
Sse9I	AATT	1 cut(s)	595
SseBI	AGGCCT	1 cut(s)	388
SsiI	CCGC	3 cut(s)	17, 260, 262
SspMI	CTAG	4 cut(s)	132, 378, 411, 516
StuI	AGGCCT	1 cut(s)	388
StyD4I	CCNGG	5 cut(s)	440, 619, 691, 755, 761
StyI	CCWWGG	1 cut(s)	136
TaaI	ACNGT	6 cut(s)	14, 29, 50, 358, 462, 602
TaiI	ACGT	6 cut(s)	91, 124, 475, 493, 502, 718
TaqI	TCGA	3 cut(s)	55, 85, 484
TasI	AATT	1 cut(s)	595
TfiI	GAWTC	1 cut(s)	512
TseI	GCWGC	4 cut(s)	635, 638, 641, 644
TspDTI	ATGAA	4 cut(s)	338, 606, 642, 714
TspGWI	ACGGA	1 cut(s)	495
VpaK11BI	GGWCC	4 cut(s)	212, 569, 609, 759
XagI	CCTNNNNNAGG	1 cut(s)	202
XbaI	TCTAGA	1 cut(s)	515
XmnI	GAANNNNTTC	1 cut(s)	186
XspI	CTAG	4 cut(s)	132, 378, 411, 516
ZraI	GACGTC	1 cut(s)	716
Zsp2I	ATGCAT	1 cut(s)	295

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