MD04G1034000.v1.1

U3-containing 90S pre-ribosomal complex subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr04
OG0012458
Physical Location & Seq
Forward (+)
3819388 .. 3822955
3568 bp
Loading structure...
UTR
Exon/CDS
Intron
MD04G1034000.v1.1.491

Sequence Viewer

Length: 906 bp
ATGGGGAGCGGGAAAGCAAAGAAGCCATCGAAGCTGTCTCACAGAAACCCTAAGAACAAGGGCAGGCCGCTCGGCCCTAAGACGAAGAAGACGAAGGCCAACTCCCACACCAAGAGCAAGAAGAAGAAGGAGAAGAAGCAACGGCTCAGCAATGGCGGCGGCAATGGAAACCCAACTGACGAGAAAGCGAGCAATCAAAACAGCCAAAACGACAATGGTTTAAGAGACGGTGCTGAGGTACAACCGGCATCGGCGTCCGCGCAGCTCAGCTTCTTCCTGGACAAGTTTCAGTCCGCCAATGGCGTTCAGCTTTCTTCTCTCGAGTTGGAGTCCTTTAATGATAAGTGTATTCTGGATCTGTCTGAAAGCTTGGATCAAGATGTCAGCAGCTTGTTGAAACATGTGAAGGAAGCTTTTGGTCCATCATGGAAACAAGAACTTTGTGGAAAGGATCTTGTGGATGGAAAAATTGATCCGGGGAGTCCAGCAGTTCTTATTATTAGTACATCTGCGTTGAGAGCGATAGAACTTCTTAGGGGCTTCCGGTTGTTGACTAATGAATGTCGTGCAGCAAAACTGTTCTCTAAGCATATGAAAGTTGAAGAACAGGTATCCTTGTTAAAAAACCGCGTCAATATTGCTAGTGGTACACCAAACAGGATAAAGAAGCTAATTGACATTGAGGCATTGGGGCTTTCACGACTGTCGGTGATTGTACTGGACATGCACCCAGATGTTAAGGGCTATTCCCTGATTACGCTTCCACAAGTCAGAGATGAATTCTGGGACTTGTACAAGAACTACTTTCACGATCGACTACAACAAGGTTGCTTGCGTCTCGGTCTTTATGGTCCGTTAACATCTGGGAAGGAGCTTAAGGGGAAAAAGAGGGGCCCGAATGAATAA
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
CMS1

Protein Analysis

302

Amino Acids

33.22

Weight (kDa)

9.74

Isoelectric Point (pI)

30.34

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
CMS1 PF14617 28 - 265 1.1e-29 U3-containing 90S pre-ribosomal complex subunit
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: OG0012458)

Species Orthologous Gene IDs
arabidopsis_thaliana AT2G43110 AT2G43110
fragaria_vesca FvH4_4g11840 FvH4_6g25320
malus_domestica MD04G1034000.v1.1 MD13G1276400.v1.1
prunus_persica Prupe.1G180600_v2.0.a1
pyrus_communis pycom04g02840
rosa_chinensis RchiOBHm_Chr4g0409281
rosa_laevigata RLG00000008581
rosa_multiflora Rmu_sc0002377.1_g000010
rosa_roxburghii Rroxscaffold_5G00353750 Rroxscaffold_7G00195060
rosa_rugosa Rorug04G0092000
rosa_samantha Rh4AG155000 Rh4BG152700 Rh4CG164000 Rh4DG148100
rosa_wichuraiana Rw4G012660

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccBSI CCGCTC 2 cut(s) 9, 70
AccII CGCG 2 cut(s) 260, 630
AciI CCGC 7 cut(s) 9, 68, 156, 159, 258, 294, 628
AclWI GGATC 4 cut(s) 363, 381, 459, 467
AcsI RAATTY 1 cut(s) 779
AcyI GRCGYC 1 cut(s) 254
AfaI GTAC 5 cut(s) 240, 505, 649, 717, 794
AflII CTTAAG 1 cut(s) 875
AflIII ACRYGT 1 cut(s) 400
AgsI TTSAA 2 cut(s) 397, 602
AjnI CCWGG 1 cut(s) 276
AluBI AGCT 9 cut(s) 34, 265, 270, 310, 369, 390, 413, 670, 874
AluI AGCT 9 cut(s) 34, 265, 270, 310, 369, 390, 413, 670, 874
Alw26I GTCTC 3 cut(s) 42, 219, 842
AlwI GGATC 4 cut(s) 363, 381, 459, 467
Ama87I CYCGRG 1 cut(s) 320
AoxI GGCC 4 cut(s) 65, 73, 96, 892
ApaI GGGCCC 1 cut(s) 896
ApeKI GCWGC 3 cut(s) 262, 387, 569
ApoI RAATTY 1 cut(s) 779
AspLEI GCGC 1 cut(s) 262
AspS9I GGNCC 5 cut(s) 74, 419, 851, 892, 893
AsuC2I CCSGG 1 cut(s) 477
AsuHPI GGTGA 1 cut(s) 721
AvaI CYCGRG 1 cut(s) 320
AvaII GGWCC 2 cut(s) 419, 851
BaeGI GKGCMC 1 cut(s) 896
BanII GRGCYC 1 cut(s) 896
BbsI GAAGAC 1 cut(s) 95
BbvCI CCTCAGC 1 cut(s) 234
BbvI GCAGC 3 cut(s) 274, 399, 581
BccI CCATC 3 cut(s) 34, 430, 455
BceAI ACGGC 1 cut(s) 158
BcgI CGANNNNNNTGC 2 cut(s) 52, 86
BciT130I CCWGG 1 cut(s) 278
BciVI GTATCC 1 cut(s) 622
BcnI CCSGG 1 cut(s) 477
BcoDI GTCTC 3 cut(s) 42, 219, 842
BfaI CTAG 1 cut(s) 642
BfrI CTTAAG 1 cut(s) 875
BfuI GTATCC 1 cut(s) 622
BisI GCNGC 6 cut(s) 68, 157, 160, 263, 388, 570
BlpI GCTNAGC 2 cut(s) 146, 266
BlsI GCNGC 6 cut(s) 69, 158, 161, 264, 389, 571
Bme1390I CCNGG 2 cut(s) 278, 477
Bme18I GGWCC 2 cut(s) 419, 851
BmeT110I CYCGRG 1 cut(s) 320
BmgT120I GGNCC 5 cut(s) 74, 419, 851, 892, 893
BmiI GGNNCC 2 cut(s) 893, 894
BmrFI CCNGG 2 cut(s) 278, 477
BmsI GCATC 1 cut(s) 257
BpiI GAAGAC 1 cut(s) 95
Bpu10I CCTNAGC 1 cut(s) 234
Bpu1102I GCTNAGC 2 cut(s) 146, 266
BpuMI CCSGG 1 cut(s) 477
BsaHI GRCGYC 1 cut(s) 254
BsaJI CCNNGG 1 cut(s) 476
BsaWI WCCGGW 1 cut(s) 543
Bse118I RCCGGY 1 cut(s) 244
Bse1I ACTGG 1 cut(s) 723
Bse3DI GCAATG 2 cut(s) 157, 169
BseBI CCWGG 1 cut(s) 278
BseDI CCNNGG 1 cut(s) 476
BseGI GGATG 1 cut(s) 466
BseMI GCAATG 2 cut(s) 157, 169
BseMII CTCAG 3 cut(s) 160, 225, 280
BseNI ACTGG 1 cut(s) 723
BseSI GKGCMC 1 cut(s) 896
BseXI GCAGC 3 cut(s) 274, 399, 581
BsgI GTGCAG 1 cut(s) 588
Bsh1236I CGCG 2 cut(s) 260, 630
Bsh1285I CGRYCG 1 cut(s) 814
BshFI GGCC 4 cut(s) 67, 75, 98, 894
BsiEI CGRYCG 1 cut(s) 814
BsiHKCI CYCGRG 1 cut(s) 320
BsiSI CCGG 3 cut(s) 245, 476, 544
BslFI GGGAC 1 cut(s) 800
BsmAI GTCTC 3 cut(s) 42, 219, 842
BsmBI CGTCTC 2 cut(s) 219, 842
BsmFI GGGAC 1 cut(s) 800
BsnI GGCC 4 cut(s) 67, 75, 98, 894
BsoBI CYCGRG 1 cut(s) 320
Bsp120I GGGCCC 1 cut(s) 892
Bsp1286I GDGCHC 1 cut(s) 896
Bsp1407I TGTACA 1 cut(s) 792
Bsp143I GATC 5 cut(s) 355, 373, 451, 472, 811
Bsp1720I GCTNAGC 2 cut(s) 146, 266
BspACI CCGC 7 cut(s) 9, 68, 156, 159, 258, 294, 628
BspANI GGCC 4 cut(s) 67, 75, 98, 894
BspCNI CTCAG 3 cut(s) 159, 226, 279
BspFNI CGCG 2 cut(s) 260, 630
BspLI GGNNCC 2 cut(s) 893, 894
BspPI GGATC 4 cut(s) 363, 381, 459, 467
BspTI CTTAAG 1 cut(s) 875
BsrBI CCGCTC 2 cut(s) 9, 70
BsrDI GCAATG 2 cut(s) 157, 169
BsrFI RCCGGY 1 cut(s) 244
BsrGI TGTACA 1 cut(s) 792
BsrI ACTGG 1 cut(s) 723
BssAI RCCGGY 1 cut(s) 244
BssECI CCNNGG 1 cut(s) 476
BssMI GATC 5 cut(s) 355, 373, 451, 472, 811
BssNI GRCGYC 1 cut(s) 254
Bst2UI CCWGG 1 cut(s) 278
Bst4CI ACNGT 3 cut(s) 230, 579, 705
BstACI GRCGYC 1 cut(s) 254
BstAFI CTTAAG 1 cut(s) 875
BstAUI TGTACA 1 cut(s) 792
BstC8I GCNNGC 3 cut(s) 65, 190, 833
BstDEI CTNAG 7 cut(s) 51, 78, 146, 234, 266, 533, 585
BstF5I GGATG 1 cut(s) 466
BstFNI CGCG 2 cut(s) 260, 630
BstHHI GCGC 1 cut(s) 262
BstKTI GATC 5 cut(s) 358, 376, 454, 475, 814
BstMAI GTCTC 3 cut(s) 42, 219, 842
BstMBI GATC 5 cut(s) 355, 373, 451, 472, 811
BstMCI CGRYCG 1 cut(s) 814
BstMWI GCNNNNNNNGC 3 cut(s) 31, 156, 518
BstNI CCWGG 1 cut(s) 278
BstNSI RCATGY 2 cut(s) 404, 727
BstSCI CCNGG 2 cut(s) 276, 475
BstSLI GKGCMC 1 cut(s) 896
BstUI CGCG 2 cut(s) 260, 630
BstV1I GCAGC 3 cut(s) 274, 399, 581
BstV2I GAAGAC 1 cut(s) 95
BstX2I RGATCY 2 cut(s) 355, 451
BstYI RGATCY 2 cut(s) 355, 451
BsuI GTATCC 1 cut(s) 622
BsuRI GGCC 4 cut(s) 67, 75, 98, 894
BtsCI GGATG 1 cut(s) 466
Cac8I GCNNGC 3 cut(s) 65, 190, 833
CfoI GCGC 1 cut(s) 262
Cfr10I RCCGGY 1 cut(s) 244
Cfr13I GGNCC 5 cut(s) 74, 419, 851, 892, 893
CseI GACGC 3 cut(s) 243, 619, 824
Csp6I GTAC 5 cut(s) 239, 504, 648, 716, 793
CviAII CATG 3 cut(s) 401, 426, 724
CviQI GTAC 5 cut(s) 239, 504, 648, 716, 793
DdeI CTNAG 7 cut(s) 51, 78, 146, 234, 266, 533, 585
DpnI GATC 5 cut(s) 357, 375, 453, 474, 813
DpnII GATC 5 cut(s) 355, 373, 451, 472, 811
EciI GGCGGA 1 cut(s) 283
Eco24I GRGCYC 1 cut(s) 896
Eco47I GGWCC 2 cut(s) 419, 851
Eco88I CYCGRG 1 cut(s) 320
EcoO109I RGGNCCY 1 cut(s) 892
EcoRI GAATTC 1 cut(s) 779
EcoRII CCWGG 1 cut(s) 276
EcoT38I GRGCYC 1 cut(s) 896
Esp3I CGTCTC 2 cut(s) 219, 842
FaeI CATG 3 cut(s) 404, 429, 727
FaiI YATR 6 cut(s) 402, 427, 591, 593, 725, 849
FalI AAGNNNNNCTT 2 cut(s) 788, 820
FaqI GGGAC 1 cut(s) 800
FatI CATG 3 cut(s) 400, 425, 723
FauI CCCGC 1 cut(s) 2
FauNDI CATATG 1 cut(s) 591
Fnu4HI GCNGC 6 cut(s) 68, 157, 160, 263, 388, 570
FokI GGATG 1 cut(s) 473
FriOI GRGCYC 1 cut(s) 896
Fsp4HI GCNGC 6 cut(s) 68, 157, 160, 263, 388, 570
FspBI CTAG 1 cut(s) 642
GlaI GCGC 1 cut(s) 261
GluI GCNGC 6 cut(s) 68, 157, 160, 263, 388, 570
HaeIII GGCC 4 cut(s) 67, 75, 98, 894
HapII CCGG 3 cut(s) 245, 476, 544
HgaI GACGC 3 cut(s) 243, 619, 824
HhaI GCGC 1 cut(s) 262
Hin1I GRCGYC 1 cut(s) 254
Hin1II CATG 3 cut(s) 404, 429, 727
Hin6I GCGC 1 cut(s) 260
HinP1I GCGC 1 cut(s) 260
HincII GTYRAC 2 cut(s) 552, 858
HindII GTYRAC 2 cut(s) 552, 858
HindIII AAGCTT 2 cut(s) 367, 411
HinfI GANTC 2 cut(s) 329, 481
HpaI GTTAAC 1 cut(s) 858
HpaII CCGG 3 cut(s) 245, 476, 544
HphI GGTGA 1 cut(s) 721
Hpy166II GTNNAC 3 cut(s) 552, 650, 858
Hpy188I TCNGA 2 cut(s) 364, 773
Hpy188III TCNNGA 5 cut(s) 320, 353, 377, 699, 809
Hpy8I GTNNAC 3 cut(s) 552, 650, 858
HpyAV CCTTC 4 cut(s) 88, 121, 400, 862
HpyCH4III ACNGT 3 cut(s) 230, 579, 705
HpyCH4V TGCA 2 cut(s) 569, 727
HpyF10VI GCNNNNNNNGC 3 cut(s) 31, 156, 518
HpyF3I CTNAG 7 cut(s) 51, 78, 146, 234, 266, 533, 585
Hsp92I GRCGYC 1 cut(s) 254
Hsp92II CATG 3 cut(s) 404, 429, 727
HspAI GCGC 1 cut(s) 260
KspAI GTTAAC 1 cut(s) 858
Kzo9I GATC 5 cut(s) 355, 373, 451, 472, 811
LmnI GCTCC 2 cut(s) 6, 871
Lsp1109I GCAGC 3 cut(s) 274, 399, 581
LweI GCATC 1 cut(s) 257
MaeI CTAG 1 cut(s) 642
MalI GATC 5 cut(s) 357, 375, 453, 474, 813
MbiI CCGCTC 2 cut(s) 9, 70
MboI GATC 5 cut(s) 355, 373, 451, 472, 811
MboII GAAGA 8 cut(s) 97, 100, 133, 136, 145, 265, 306, 614
MflI RGATCY 2 cut(s) 355, 451
MhlI GDGCHC 1 cut(s) 896
MluCI AATT 3 cut(s) 468, 672, 779
MlyI GAGTC 2 cut(s) 338, 490
MmeI TCCRAC 1 cut(s) 306
MnlI CCTC 3 cut(s) 229, 676, 882
MseI TTAA 6 cut(s) 221, 336, 620, 738, 857, 876
MslI CAYNNNNRTG 1 cut(s) 732
MspCI CTTAAG 1 cut(s) 875
MspI CCGG 3 cut(s) 245, 476, 544
MspR9I CCNGG 2 cut(s) 278, 477
MvaI CCWGG 1 cut(s) 278
MvnI CGCG 2 cut(s) 260, 630
MwoI GCNNNNNNNGC 3 cut(s) 31, 156, 518
NciI CCSGG 1 cut(s) 477
NdeI CATATG 1 cut(s) 591
NdeII GATC 5 cut(s) 355, 373, 451, 472, 811
NlaIII CATG 3 cut(s) 404, 429, 727
NlaIV GGNNCC 2 cut(s) 893, 894
NmeAIII GCCGAG 1 cut(s) 51
NspI RCATGY 2 cut(s) 404, 727
PaeR7I CTCGAG 1 cut(s) 320
PciI ACATGT 1 cut(s) 400
PcsI WCGNNNNNNNCGW 1 cut(s) 89
PfoI TCCNGGA 1 cut(s) 276
PkrI GCNGC 6 cut(s) 69, 158, 161, 264, 389, 571
Ple19I CGATCG 1 cut(s) 814
PleI GAGTC 2 cut(s) 337, 489
PpsI GAGTC 2 cut(s) 337, 489
PscI ACATGT 1 cut(s) 400
Psp6I CCWGG 1 cut(s) 276
PspGI CCWGG 1 cut(s) 276
PspN4I GGNNCC 2 cut(s) 893, 894
PspOMI GGGCCC 1 cut(s) 892
PspPI GGNCC 5 cut(s) 74, 419, 851, 892, 893
PsuI RGATCY 2 cut(s) 355, 451
PvuI CGATCG 1 cut(s) 814
RsaI GTAC 5 cut(s) 240, 505, 649, 717, 794
RsaNI GTAC 5 cut(s) 239, 504, 648, 716, 793
RseI CAYNNNNRTG 1 cut(s) 732
SaqAI TTAA 6 cut(s) 221, 336, 620, 738, 857, 876
SatI GCNGC 6 cut(s) 68, 157, 160, 263, 388, 570
Sau3AI GATC 5 cut(s) 355, 373, 451, 472, 811
Sau96I GGNCC 5 cut(s) 74, 419, 851, 892, 893
SchI GAGTC 2 cut(s) 338, 490
ScrFI CCNGG 2 cut(s) 278, 477
SduI GDGCHC 1 cut(s) 896
SfaNI GCATC 1 cut(s) 257
Sfr274I CTCGAG 1 cut(s) 320
SinI GGWCC 2 cut(s) 419, 851
SlaI CTCGAG 1 cut(s) 320
SmiMI CAYNNNNRTG 1 cut(s) 732
SmlI CTYRAG 2 cut(s) 320, 875
SmoI CTYRAG 2 cut(s) 320, 875
Sse9I AATT 3 cut(s) 468, 672, 779
SsiI CCGC 7 cut(s) 9, 68, 156, 159, 258, 294, 628
SspI AATATT 1 cut(s) 637
SspMI CTAG 1 cut(s) 642
StyD4I CCNGG 2 cut(s) 276, 475
TaaI ACNGT 3 cut(s) 230, 579, 705
TaqI TCGA 3 cut(s) 29, 321, 814
TaqII GACCGA 1 cut(s) 830
TasI AATT 3 cut(s) 468, 672, 779
TatI WGTACW 3 cut(s) 503, 715, 792
TauI GCSGC 3 cut(s) 70, 159, 162
Tru1I TTAA 6 cut(s) 221, 336, 620, 738, 857, 876
Tru9I TTAA 6 cut(s) 221, 336, 620, 738, 857, 876
TseI GCWGC 3 cut(s) 262, 387, 569
TspDTI ATGAA 3 cut(s) 573, 608, 792
TspGWI ACGGA 1 cut(s) 843
Vha464I CTTAAG 1 cut(s) 875
VpaK11BI GGWCC 2 cut(s) 419, 851
XapI RAATTY 1 cut(s) 779
XceI RCATGY 2 cut(s) 404, 727
XcmI CCANNNNNNNNNTGG 1 cut(s) 212
XhoI CTCGAG 1 cut(s) 320
XspI CTAG 1 cut(s) 642
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.