MD13G1276400.v1.1

U3-containing 90S pre-ribosomal complex subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr13
OG0012458
Physical Location & Seq
Reverse (-)
38472956 .. 38477366
4411 bp
Loading structure...
UTR
Exon/CDS
Intron
MD13G1276400.v1.1.491

Sequence Viewer

Length: 585 bp
ATGGGGAGCGGGAAGGCGAAGAAGCCATCGAAGCTGTCTCACAGAAACAACAAGGGCAATCCGCTTGGCCCTAAGACAAAGAAGAGGAAGAAGGAGAAGAAGCAACGGCTCAGCAATGGCGGCAGCAATGAAAACCCAATTGACGAGAAAGCGAGCAATCAAAGCAACCAAAACAGCGACGGTTTAAGAGACGGTGAGGTACAACCGGCGTCAGTGTCGGCGCAGCTCAGATTCTTTCTGGACAAGTTTCAGTCTGCCAACGGCGTTAGCTTTCTTACCTCGAGTTGGAGTCCTTCAATGTGTTTTCTGGATCAGTCTGAAAGCTTGGATCAAGATGTCAGCATCTGGGGGAAACATGTGAAGGAAGCTTTTGGTCCATCATGGAAACAAGAAGTTTGTGAAAAGGATCTCGTGGATGGAAAAATTGATCCAGGGAGTCCAGCAATTCTTATTATTAGTACATCTGCGTTGAGAGCATTAGAACTTCTAAGGGGCTTCCGGTTGTTGACTAATGAATGTCGTGCAGCAAAGCTGTTCTCTAAGCATATGAAGGTTGAAGAACAGGTAGTTTCTCGGAATCTTTAA
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

195

Amino Acids

21.46

Weight (kDa)

9.63

Isoelectric Point (pI)

39.5

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
CMS1 PF14617 135 - 189 8.7e-10 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 1 cut(s) 9
AciI CCGC 3 cut(s) 9, 62, 120
AclWI GGATC 4 cut(s) 318, 336, 414, 422
AcyI GRCGYC 1 cut(s) 209
AfaI GTAC 2 cut(s) 201, 460
AfiI CCNNNNNNNGG 1 cut(s) 285
AflIII ACRYGT 1 cut(s) 355
AgsI TTSAA 2 cut(s) 297, 557
AjnI CCWGG 1 cut(s) 430
AluBI AGCT 6 cut(s) 34, 226, 270, 324, 368, 532
AluI AGCT 6 cut(s) 34, 226, 270, 324, 368, 532
Alw26I GTCTC 2 cut(s) 42, 183
AlwI GGATC 4 cut(s) 318, 336, 414, 422
AlwNI CAGNNNCTG 1 cut(s) 345
Ama87I CYCGRG 1 cut(s) 280
AoxI GGCC 1 cut(s) 67
ApeKI GCWGC 3 cut(s) 123, 223, 524
AspLEI GCGC 1 cut(s) 223
AspS9I GGNCC 2 cut(s) 68, 374
AsuHPI GGTGA 1 cut(s) 206
AvaI CYCGRG 1 cut(s) 280
AvaII GGWCC 1 cut(s) 374
BauI CACGAG 1 cut(s) 410
BbvI GCAGC 3 cut(s) 135, 235, 536
BccI CCATC 3 cut(s) 34, 385, 410
BceAI ACGGC 2 cut(s) 122, 277
BciT130I CCWGG 1 cut(s) 432
BcoDI GTCTC 2 cut(s) 42, 183
BisI GCNGC 4 cut(s) 121, 124, 224, 525
BlpI GCTNAGC 1 cut(s) 110
BlsI GCNGC 4 cut(s) 122, 125, 225, 526
Bme1390I CCNGG 1 cut(s) 432
Bme18I GGWCC 1 cut(s) 374
BmeT110I CYCGRG 1 cut(s) 280
BmgT120I GGNCC 2 cut(s) 68, 374
BmrFI CCNGG 1 cut(s) 432
BmsI GCATC 1 cut(s) 351
Bpu1102I GCTNAGC 1 cut(s) 110
BsaHI GRCGYC 1 cut(s) 209
BsaJI CCNNGG 1 cut(s) 431
BsaWI WCCGGW 1 cut(s) 498
Bsc4I CCNNNNNNNGG 1 cut(s) 285
Bse118I RCCGGY 1 cut(s) 205
Bse3DI GCAATG 2 cut(s) 121, 133
BseBI CCWGG 1 cut(s) 432
BseDI CCNNGG 1 cut(s) 431
BseGI GGATG 1 cut(s) 421
BseLI CCNNNNNNNGG 1 cut(s) 285
BseMI GCAATG 2 cut(s) 121, 133
BseMII CTCAG 2 cut(s) 124, 241
BseXI GCAGC 3 cut(s) 135, 235, 536
BsgI GTGCAG 1 cut(s) 543
BshFI GGCC 1 cut(s) 69
BsiHKCI CYCGRG 1 cut(s) 280
BsiSI CCGG 2 cut(s) 206, 499
BslI CCNNNNNNNGG 1 cut(s) 285
BsmAI GTCTC 2 cut(s) 42, 183
BsmBI CGTCTC 1 cut(s) 183
BsnI GGCC 1 cut(s) 69
BsoBI CYCGRG 1 cut(s) 280
Bsp143I GATC 4 cut(s) 310, 328, 406, 427
Bsp1720I GCTNAGC 1 cut(s) 110
BspACI CCGC 3 cut(s) 9, 62, 120
BspANI GGCC 1 cut(s) 69
BspCNI CTCAG 2 cut(s) 123, 240
BspPI GGATC 4 cut(s) 318, 336, 414, 422
BsrBI CCGCTC 1 cut(s) 9
BsrDI GCAATG 2 cut(s) 121, 133
BsrFI RCCGGY 1 cut(s) 205
BssAI RCCGGY 1 cut(s) 205
BssECI CCNNGG 1 cut(s) 431
BssMI GATC 4 cut(s) 310, 328, 406, 427
BssNI GRCGYC 1 cut(s) 209
BssSI CACGAG 1 cut(s) 410
Bst2BI CACGAG 1 cut(s) 410
Bst2UI CCWGG 1 cut(s) 432
Bst4CI ACNGT 2 cut(s) 182, 194
Bst6I CTCTTC 1 cut(s) 77
BstACI GRCGYC 1 cut(s) 209
BstC8I GCNNGC 1 cut(s) 154
BstDEI CTNAG 5 cut(s) 72, 110, 227, 488, 540
BstF5I GGATG 1 cut(s) 421
BstHHI GCGC 1 cut(s) 223
BstKTI GATC 4 cut(s) 313, 331, 409, 430
BstMAI GTCTC 2 cut(s) 42, 183
BstMBI GATC 4 cut(s) 310, 328, 406, 427
BstMWI GCNNNNNNNGC 4 cut(s) 31, 120, 162, 473
BstNI CCWGG 1 cut(s) 432
BstNSI RCATGY 1 cut(s) 359
BstSCI CCNGG 1 cut(s) 430
BstV1I GCAGC 3 cut(s) 135, 235, 536
BstX2I RGATCY 1 cut(s) 406
BstYI RGATCY 1 cut(s) 406
BsuRI GGCC 1 cut(s) 69
BtsCI GGATG 1 cut(s) 421
BtsIMutI CAGTG 1 cut(s) 219
Cac8I GCNNGC 1 cut(s) 154
CaiI CAGNNNCTG 1 cut(s) 345
CfoI GCGC 1 cut(s) 223
Cfr10I RCCGGY 1 cut(s) 205
Cfr13I GGNCC 2 cut(s) 68, 374
CseI GACGC 1 cut(s) 198
Csp6I GTAC 2 cut(s) 200, 459
CviAII CATG 2 cut(s) 356, 381
CviQI GTAC 2 cut(s) 200, 459
DdeI CTNAG 5 cut(s) 72, 110, 227, 488, 540
DpnI GATC 4 cut(s) 312, 330, 408, 429
DpnII GATC 4 cut(s) 310, 328, 406, 427
Eam1104I CTCTTC 1 cut(s) 77
EarI CTCTTC 1 cut(s) 77
Eco47I GGWCC 1 cut(s) 374
Eco88I CYCGRG 1 cut(s) 280
EcoRII CCWGG 1 cut(s) 430
Esp3I CGTCTC 1 cut(s) 183
FaeI CATG 2 cut(s) 359, 384
FaiI YATR 4 cut(s) 357, 382, 546, 548
FatI CATG 2 cut(s) 355, 380
FauI CCCGC 1 cut(s) 2
FauNDI CATATG 1 cut(s) 546
Fnu4HI GCNGC 4 cut(s) 121, 124, 224, 525
FokI GGATG 1 cut(s) 428
Fsp4HI GCNGC 4 cut(s) 121, 124, 224, 525
GlaI GCGC 1 cut(s) 222
GluI GCNGC 4 cut(s) 121, 124, 224, 525
HaeIII GGCC 1 cut(s) 69
HapII CCGG 2 cut(s) 206, 499
HgaI GACGC 1 cut(s) 198
HhaI GCGC 1 cut(s) 223
Hin1I GRCGYC 1 cut(s) 209
Hin1II CATG 2 cut(s) 359, 384
Hin6I GCGC 1 cut(s) 221
HinP1I GCGC 1 cut(s) 221
HincII GTYRAC 1 cut(s) 507
HindII GTYRAC 1 cut(s) 507
HindIII AAGCTT 2 cut(s) 322, 366
HinfI GANTC 4 cut(s) 231, 289, 436, 577
HpaII CCGG 2 cut(s) 206, 499
HphI GGTGA 1 cut(s) 206
Hpy166II GTNNAC 1 cut(s) 507
Hpy188I TCNGA 3 cut(s) 230, 319, 576
Hpy188III TCNNGA 3 cut(s) 239, 308, 332
Hpy8I GTNNAC 1 cut(s) 507
Hpy99I CGWCG 1 cut(s) 182
HpyAV CCTTC 5 cut(s) 7, 85, 303, 355, 544
HpyCH4III ACNGT 2 cut(s) 182, 194
HpyCH4V TGCA 1 cut(s) 524
HpyF10VI GCNNNNNNNGC 4 cut(s) 31, 120, 162, 473
HpyF3I CTNAG 5 cut(s) 72, 110, 227, 488, 540
Hsp92I GRCGYC 1 cut(s) 209
Hsp92II CATG 2 cut(s) 359, 384
HspAI GCGC 1 cut(s) 221
Kzo9I GATC 4 cut(s) 310, 328, 406, 427
LmnI GCTCC 1 cut(s) 6
LpnPI CCDG 9 cut(s) 219, 224, 293, 331, 417, 444, 453, 512, 548
Lsp1109I GCAGC 3 cut(s) 135, 235, 536
LweI GCATC 1 cut(s) 351
MalI GATC 4 cut(s) 312, 330, 408, 429
MbiI CCGCTC 1 cut(s) 9
MboI GATC 4 cut(s) 310, 328, 406, 427
MboII GAAGA 5 cut(s) 31, 94, 100, 109, 569
MfeI CAATTG 1 cut(s) 138
MflI RGATCY 1 cut(s) 406
MluCI AATT 3 cut(s) 138, 423, 444
MlyI GAGTC 2 cut(s) 298, 445
MmeI TCCRAC 1 cut(s) 266
MnlI CCTC 3 cut(s) 78, 190, 289
MseI TTAA 2 cut(s) 185, 583
MspI CCGG 2 cut(s) 206, 499
MspR9I CCNGG 1 cut(s) 432
MunI CAATTG 1 cut(s) 138
MvaI CCWGG 1 cut(s) 432
MwoI GCNNNNNNNGC 4 cut(s) 31, 120, 162, 473
NdeI CATATG 1 cut(s) 546
NdeII GATC 4 cut(s) 310, 328, 406, 427
NlaIII CATG 2 cut(s) 359, 384
NspI RCATGY 1 cut(s) 359
PaeR7I CTCGAG 1 cut(s) 280
PciI ACATGT 1 cut(s) 355
PfeI GAWTC 2 cut(s) 231, 577
PkrI GCNGC 4 cut(s) 122, 125, 225, 526
PleI GAGTC 2 cut(s) 297, 444
PpsI GAGTC 2 cut(s) 297, 444
PscI ACATGT 1 cut(s) 355
Psp6I CCWGG 1 cut(s) 430
PspGI CCWGG 1 cut(s) 430
PspPI GGNCC 2 cut(s) 68, 374
PspXI VCTCGAGB 1 cut(s) 280
PstNI CAGNNNCTG 1 cut(s) 345
PsuI RGATCY 1 cut(s) 406
RsaI GTAC 2 cut(s) 201, 460
RsaNI GTAC 2 cut(s) 200, 459
SaqAI TTAA 2 cut(s) 185, 583
SatI GCNGC 4 cut(s) 121, 124, 224, 525
Sau3AI GATC 4 cut(s) 310, 328, 406, 427
Sau96I GGNCC 2 cut(s) 68, 374
SchI GAGTC 2 cut(s) 298, 445
ScrFI CCNGG 1 cut(s) 432
SfaNI GCATC 1 cut(s) 351
Sfr274I CTCGAG 1 cut(s) 280
SinI GGWCC 1 cut(s) 374
SlaI CTCGAG 1 cut(s) 280
SmlI CTYRAG 1 cut(s) 280
SmoI CTYRAG 1 cut(s) 280
Sse9I AATT 3 cut(s) 138, 423, 444
SsiI CCGC 3 cut(s) 9, 62, 120
StyD4I CCNGG 1 cut(s) 430
TaaI ACNGT 2 cut(s) 182, 194
TaqI TCGA 2 cut(s) 29, 281
TasI AATT 3 cut(s) 138, 423, 444
TatI WGTACW 1 cut(s) 458
TauI GCSGC 1 cut(s) 123
TfiI GAWTC 2 cut(s) 231, 577
Tru1I TTAA 2 cut(s) 185, 583
Tru9I TTAA 2 cut(s) 185, 583
TscAI CASTG 1 cut(s) 219
TseI GCWGC 3 cut(s) 123, 223, 524
TspDTI ATGAA 3 cut(s) 144, 528, 563
TspRI CASTG 1 cut(s) 219
VpaK11BI GGWCC 1 cut(s) 374
XceI RCATGY 1 cut(s) 359
XhoI CTCGAG 1 cut(s) 280
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.