AT1G53120

RNA-binding S4 domain-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
1
OG0011251
Physical Location & Seq
Forward (+)
19792751 .. 19794778
2028 bp
Loading structure...
UTR
Exon/CDS
Intron
AT1G53120.1

Sequence Viewer

Length: 963 bp
ATGGCTGTCACAAGCTTGGCTCCTCCATGGGTCATCTTGAGACTAGCTTTCCGGTCAGTAGCAGCTTCTTCTTGTCTCCACACAAATCAAAAAACCCTAATCACGAATCTCTCCATTCCCACTTCGTTTCCTCTCCGACAGTCAGCTTTGAGAAGATGTTACAGTGCAGAAGCTATAAAAGGAGATGTAGATTTTCTCCTCAAAGGAGTTGGAGACCAAGCTGTTGCCAAAGAAGTCAAGCAAATTCTTGAAATGGCAAGACGTGCATCATCAAAAAGAGAAGTTCTTCATACAGATTTTCTCACACCACCTATTGTTAAGGAATCAGTTTCACTATTGGAAAAATTTGCTGATGTTAAGATAGTTGCTCAAGGAGGTTACCCTGAGGCTGAACGGTGTAGGATCTCGATTGGACATCCTGATGTCCTAACTAGTGATCCAGATATAGTTGCTGCTTTGAGTATCACAGGGAATTTCGGGTTTCAACCTTGTTCTCACGGTGACTTCCTTGGTGCTATTCTTGGCACGGGAATTTCCAGGGAAAAACTTGGAGATATCTTAATTCAGGAAGAAAAGGGAGCCCAAGTCCTGATAGTTCCTGAACTAGTTGACTTTGTTGTTACCGCTCTTGACAAGGTTGGAAATGTTGGTGTAACTTGTAGTAAGATACCTTTGCTTGCTCTTGAATACGAACCGCCTAGGACTAATTCCTTTAAAACCGTGGAGGCCTCGTTGAGAATTGATGCAGTAGCTAGTGCTGGTTTCAAGATTTCGCGGTCAAAGCTAGTTGATTTGATTAGTAGCAAGGATGTTCGGGTTAACTGGGCAACCGTTACAAAGAACGGAACCATAGTGAAGACTGGTGATGTTGTCTCCGTTAGCGGGAAAGGGAGACTCAAGATTGGAGAGATCAATGAAACGAAGAAAGGTAAATTTGCAGTTGAAATCATCAGATATCTTTAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
S4

Protein Analysis

320

Amino Acids

34.55

Weight (kDa)

9.11

Isoelectric Point (pI)

18.87

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
YlmH_RBD PF17774 153 - 225 8e-13 Putative RNA-binding domain in YlmH
S4 PF01479 246 - 291 3.1e-08 S4 domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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Orthologous Genes (Group: OG0011251)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G53120 AT1G53120
fragaria_vesca FvH4_3g19840
malus_domestica MD11G1248800.v1.1 MD11G1252400.v1.1
prunus_persica Prupe.4G180500_v2.0.a1
pyrus_communis pycom11g22390
rosa_chinensis RchiOBHm_Chr5g0033281
rosa_laevigata RLG00000033463
rosa_multiflora Rmu_sc0009715.1_g000003
rosa_roxburghii Rroxscaffold_1G00015440 Rroxscaffold_1G00046700
rosa_rugosa Rorug05G0139000 Rorug05G0139100 Rorug05G0250800
rosa_samantha Rh5AG230500 Rh5BG231400 Rh5CG259400 Rh5DG236600
rosa_wichuraiana Rw5G021070

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccBSI CCGCTC 1 cut(s) 626
AccII CGCG 1 cut(s) 775
AciI CCGC 4 cut(s) 624, 695, 775, 882
AclWI GGATC 2 cut(s) 410, 431
AcsI RAATTY 5 cut(s) 243, 344, 472, 531, 932
AfiI CCNNNNNNNGG 1 cut(s) 882
AgsI TTSAA 5 cut(s) 251, 485, 686, 766, 944
AhlI ACTAGT 2 cut(s) 431, 604
AjiI CACGTC 1 cut(s) 263
AjnI CCWGG 1 cut(s) 536
AluBI AGCT 8 cut(s) 15, 47, 65, 146, 173, 221, 752, 784
AluI AGCT 8 cut(s) 15, 47, 65, 146, 173, 221, 752, 784
Alw26I GTCTC 5 cut(s) 34, 80, 207, 877, 886
AlwI GGATC 2 cut(s) 410, 431
AoxI GGCC 1 cut(s) 726
ApeKI GCWGC 2 cut(s) 62, 452
ApoI RAATTY 5 cut(s) 243, 344, 472, 531, 932
Asp700I GAANNNNTTC 1 cut(s) 285
AspA2I CCTAGG 1 cut(s) 698
AsuHPI GGTGA 2 cut(s) 512, 875
AvrII CCTAGG 1 cut(s) 698
AxyI CCTNAGG 1 cut(s) 384
BanII GRGCYC 1 cut(s) 583
BbsI GAAGAC 1 cut(s) 863
BbvI GCAGC 2 cut(s) 74, 439
BciT130I CCWGG 1 cut(s) 538
BcoDI GTCTC 5 cut(s) 34, 80, 207, 877, 886
BcuI ACTAGT 2 cut(s) 431, 604
BfaI CTAG 6 cut(s) 44, 432, 605, 699, 753, 785
BisI GCNGC 2 cut(s) 63, 453
BlnI CCTAGG 1 cut(s) 698
BlsI GCNGC 2 cut(s) 64, 454
Bme1390I CCNGG 1 cut(s) 538
BmgBI CACGTC 1 cut(s) 263
BmiI GGNNCC 3 cut(s) 21, 580, 847
BmrFI CCNGG 1 cut(s) 538
BmrI ACTGGG 1 cut(s) 832
BmsI GCATC 2 cut(s) 275, 733
BmuI ACTGGG 1 cut(s) 832
BpiI GAAGAC 1 cut(s) 863
BpuEI CTTGAG 3 cut(s) 58, 354, 881
BsaI GGTCTC 1 cut(s) 207
BsaJI CCNNGG 5 cut(s) 26, 508, 537, 698, 720
BsaWI WCCGGW 1 cut(s) 51
BsaXI ACNNNNNCTCC 4 cut(s) 570, 600, 716, 746
Bsc4I CCNNNNNNNGG 1 cut(s) 882
Bse1I ACTGG 2 cut(s) 827, 865
Bse21I CCTNAGG 1 cut(s) 384
BseBI CCWGG 1 cut(s) 538
BseDI CCNNGG 5 cut(s) 26, 508, 537, 698, 720
BseGI GGATG 2 cut(s) 415, 814
BseLI CCNNNNNNNGG 1 cut(s) 882
BseMII CTCAG 1 cut(s) 375
BseNI ACTGG 2 cut(s) 827, 865
BseRI GAGGAG 2 cut(s) 12, 188
BseXI GCAGC 2 cut(s) 74, 439
BsgI GTGCAG 1 cut(s) 186
Bsh1236I CGCG 1 cut(s) 775
BshFI GGCC 1 cut(s) 728
BsiSI CCGG 1 cut(s) 52
BslI CCNNNNNNNGG 1 cut(s) 882
BsmAI GTCTC 5 cut(s) 34, 80, 207, 877, 886
BsnI GGCC 1 cut(s) 728
Bso31I GGTCTC 1 cut(s) 207
Bsp1286I GDGCHC 1 cut(s) 583
Bsp143I GATC 3 cut(s) 402, 436, 909
Bsp19I CCATGG 1 cut(s) 26
BspACI CCGC 4 cut(s) 624, 695, 775, 882
BspANI GGCC 1 cut(s) 728
BspCNI CTCAG 1 cut(s) 376
BspFNI CGCG 1 cut(s) 775
BspLI GGNNCC 3 cut(s) 21, 580, 847
BspPI GGATC 2 cut(s) 410, 431
BspTNI GGTCTC 1 cut(s) 207
BsrBI CCGCTC 1 cut(s) 626
BsrI ACTGG 2 cut(s) 827, 865
BssECI CCNNGG 5 cut(s) 26, 508, 537, 698, 720
BssMI GATC 3 cut(s) 402, 436, 909
BssT1I CCWWGG 3 cut(s) 26, 508, 698
Bst2UI CCWGG 1 cut(s) 538
Bst4CI ACNGT 6 cut(s) 141, 164, 396, 500, 721, 832
BstAPI GCANNNNNTGC 1 cut(s) 263
BstC8I GCNNGC 1 cut(s) 678
BstDEI CTNAG 1 cut(s) 384
BstDSI CCRYGG 2 cut(s) 26, 720
BstEII GGTNACC 1 cut(s) 377
BstF5I GGATG 2 cut(s) 415, 814
BstFNI CGCG 1 cut(s) 775
BstKTI GATC 3 cut(s) 405, 439, 912
BstMAI GTCTC 5 cut(s) 34, 80, 207, 877, 886
BstMBI GATC 3 cut(s) 402, 436, 909
BstMWI GCNNNNNNNGC 2 cut(s) 263, 781
BstNI CCWGG 1 cut(s) 538
BstPI GGTNACC 1 cut(s) 377
BstSCI CCNGG 1 cut(s) 536
BstUI CGCG 1 cut(s) 775
BstV1I GCAGC 2 cut(s) 74, 439
BstV2I GAAGAC 1 cut(s) 863
BstX2I RGATCY 1 cut(s) 402
BstYI RGATCY 1 cut(s) 402
Bsu36I CCTNAGG 1 cut(s) 384
BsuRI GGCC 1 cut(s) 728
BtgI CCRYGG 2 cut(s) 26, 720
BtrI CACGTC 1 cut(s) 263
BtsCI GGATG 2 cut(s) 415, 814
BtsIMutI CAGTG 1 cut(s) 169
Cac8I GCNNGC 1 cut(s) 678
CviAII CATG 1 cut(s) 27
DdeI CTNAG 1 cut(s) 384
DpnI GATC 3 cut(s) 404, 438, 911
DpnII GATC 3 cut(s) 402, 436, 909
DraI TTTAAA 1 cut(s) 715
Eco130I CCWWGG 3 cut(s) 26, 508, 698
Eco147I AGGCCT 1 cut(s) 728
Eco24I GRGCYC 1 cut(s) 583
Eco31I GGTCTC 1 cut(s) 207
Eco32I GATATC 2 cut(s) 556, 956
Eco81I CCTNAGG 1 cut(s) 384
Eco91I GGTNACC 1 cut(s) 377
EcoO65I GGTNACC 1 cut(s) 377
EcoRII CCWGG 1 cut(s) 536
EcoRV GATATC 2 cut(s) 556, 956
EcoT14I CCWWGG 3 cut(s) 26, 508, 698
EcoT38I GRGCYC 1 cut(s) 583
ErhI CCWWGG 3 cut(s) 26, 508, 698
FaeI CATG 1 cut(s) 30
FaiI YATR 5 cut(s) 28, 176, 291, 446, 851
FatI CATG 1 cut(s) 26
FauI CCCGC 1 cut(s) 875
Fnu4HI GCNGC 2 cut(s) 63, 453
FokI GGATG 2 cut(s) 402, 821
FriOI GRGCYC 1 cut(s) 583
Fsp4HI GCNGC 2 cut(s) 63, 453
FspBI CTAG 6 cut(s) 44, 432, 605, 699, 753, 785
GluI GCNGC 2 cut(s) 63, 453
HaeIII GGCC 1 cut(s) 728
HapII CCGG 1 cut(s) 52
Hin1II CATG 1 cut(s) 30
HincII GTYRAC 2 cut(s) 610, 820
HindII GTYRAC 2 cut(s) 610, 820
HindIII AAGCTT 1 cut(s) 13
HinfI GANTC 3 cut(s) 106, 323, 894
HpaI GTTAAC 1 cut(s) 820
HpaII CCGG 1 cut(s) 52
HphI GGTGA 2 cut(s) 512, 875
Hpy166II GTNNAC 2 cut(s) 610, 820
Hpy188I TCNGA 2 cut(s) 137, 953
Hpy8I GTNNAC 2 cut(s) 610, 820
HpyCH4III ACNGT 6 cut(s) 141, 164, 396, 500, 721, 832
HpyCH4IV ACGT 1 cut(s) 262
HpyCH4V TGCA 4 cut(s) 167, 266, 746, 938
HpyF10VI GCNNNNNNNGC 2 cut(s) 263, 781
HpyF3I CTNAG 1 cut(s) 384
HpySE526I ACGT 1 cut(s) 262
Hsp92II CATG 1 cut(s) 30
KspAI GTTAAC 1 cut(s) 820
Kzo9I GATC 3 cut(s) 402, 436, 909
LmnI GCTCC 2 cut(s) 25, 578
Lsp1109I GCAGC 2 cut(s) 74, 439
LweI GCATC 2 cut(s) 275, 733
MaeI CTAG 6 cut(s) 44, 432, 605, 699, 753, 785
MaeII ACGT 1 cut(s) 262
MaeIII GTNAC 7 cut(s) 7, 158, 377, 500, 619, 652, 832
MalI GATC 3 cut(s) 404, 438, 911
MbiI CCGCTC 1 cut(s) 626
MboI GATC 3 cut(s) 402, 436, 909
MboII GAAGA 6 cut(s) 60, 165, 278, 581, 868, 934
MflI RGATCY 1 cut(s) 402
MhlI GDGCHC 1 cut(s) 583
MluCI AATT 8 cut(s) 243, 344, 472, 531, 561, 706, 738, 932
MlyI GAGTC 1 cut(s) 888
MmeI TCCRAC 3 cut(s) 160, 190, 619
MnlI CCTC 7 cut(s) 33, 141, 209, 368, 379, 718, 739
MroXI GAANNNNTTC 1 cut(s) 285
MseI TTAA 5 cut(s) 318, 357, 560, 714, 819
MslI CAYNNNNRTG 1 cut(s) 420
MspI CCGG 1 cut(s) 52
MspR9I CCNGG 1 cut(s) 538
MvaI CCWGG 1 cut(s) 538
MvnI CGCG 1 cut(s) 775
MwoI GCNNNNNNNGC 2 cut(s) 263, 781
NcoI CCATGG 1 cut(s) 26
NdeII GATC 3 cut(s) 402, 436, 909
NlaIII CATG 1 cut(s) 30
NlaIV GGNNCC 3 cut(s) 21, 580, 847
NmuCI GTSAC 2 cut(s) 7, 500
PceI AGGCCT 1 cut(s) 728
PdmI GAANNNNTTC 1 cut(s) 285
PfeI GAWTC 2 cut(s) 106, 323
PkrI GCNGC 2 cut(s) 64, 454
PleI GAGTC 1 cut(s) 888
PpsI GAGTC 1 cut(s) 888
Psp6I CCWGG 1 cut(s) 536
PspEI GGTNACC 1 cut(s) 377
PspGI CCWGG 1 cut(s) 536
PspN4I GGNNCC 3 cut(s) 21, 580, 847
PsuI RGATCY 1 cut(s) 402
RseI CAYNNNNRTG 1 cut(s) 420
SaqAI TTAA 5 cut(s) 318, 357, 560, 714, 819
SatI GCNGC 2 cut(s) 63, 453
Sau3AI GATC 3 cut(s) 402, 436, 909
SchI GAGTC 1 cut(s) 888
ScrFI CCNGG 1 cut(s) 538
SduI GDGCHC 1 cut(s) 583
SfaNI GCATC 2 cut(s) 275, 733
SmiMI CAYNNNNRTG 1 cut(s) 420
SmlI CTYRAG 3 cut(s) 37, 369, 896
SmoI CTYRAG 3 cut(s) 37, 369, 896
SpeI ACTAGT 2 cut(s) 431, 604
Sse9I AATT 8 cut(s) 243, 344, 472, 531, 561, 706, 738, 932
SseBI AGGCCT 1 cut(s) 728
SsiI CCGC 4 cut(s) 624, 695, 775, 882
SspMI CTAG 6 cut(s) 44, 432, 605, 699, 753, 785
StuI AGGCCT 1 cut(s) 728
StyD4I CCNGG 1 cut(s) 536
StyI CCWWGG 3 cut(s) 26, 508, 698
TaaI ACNGT 6 cut(s) 141, 164, 396, 500, 721, 832
TaiI ACGT 1 cut(s) 265
TaqI TCGA 1 cut(s) 407
TasI AATT 8 cut(s) 243, 344, 472, 531, 561, 706, 738, 932
TfiI GAWTC 2 cut(s) 106, 323
Tru1I TTAA 5 cut(s) 318, 357, 560, 714, 819
Tru9I TTAA 5 cut(s) 318, 357, 560, 714, 819
TscAI CASTG 1 cut(s) 169
TseFI GTSAC 2 cut(s) 7, 500
TseI GCWGC 2 cut(s) 62, 452
Tsp45I GTSAC 2 cut(s) 7, 500
TspDTI ATGAA 2 cut(s) 278, 930
TspGWI ACGGA 2 cut(s) 858, 865
TspRI CASTG 1 cut(s) 169
XapI RAATTY 5 cut(s) 243, 344, 472, 531, 932
XmaJI CCTAGG 1 cut(s) 698
XmnI GAANNNNTTC 1 cut(s) 285
XspI CTAG 6 cut(s) 44, 432, 605, 699, 753, 785
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.