MD16G1243600.v1.1

U5 small nuclear ribonucleoprotein 40

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr16
OG0012055
Physical Location & Seq
Forward (+)
26498193 .. 26504829
6637 bp
Loading structure...
UTR
Exon/CDS
Intron
MD16G1243600.v1.1.491

Sequence Viewer

Length: 1035 bp
ATGATGCATTTTGCTCCTAGTGAGGGTGAAAATGCTTTGTCGGTTGTTGGTCCAAGGCCAATGGATTTGTCTACATACAATGGTCGCCCAGCACCTGGACCAAATGGGAAACAAAGGACTTCCAGCTTGGAATCACCGATCATGTTGCTGACAGGCCATCAGAGTGCTGTATACACAATGAAATTTAACCCTGCTGGAACAGTTATTGCGTCTGGGTCCCATGACAAAGAAATCTTTTTATGGAATGTTCATGGGGAATGCAAGAACTTTATGGTTTTGAAGGGGCACAAGAATGCTGTATTGGATCTTCACTGGACAACCGATGGTTCACAGATTATATCAGCCAGTCCAGACAAAACTGTGGGGGCATGGGATGTTGAAACAGGAAAAAGGATAAAGAAGATGGCTGAGCACTCTTCGTTTGTGAATTCTTGCCATCCTGCTCGAAGGGGACCTCCTCTTATTGTCAGTGGATCTGATGATGGAACTGCCAAACTCTGGGATATGCGTCTGAGGGGAGCGATCCAAACATTCCCTGATAAATATCAAATTACAGCTGTCAGCTTCTCTGATGCATCCGATAAAATCTTTACGGGAGGTATTGACAATGACATTAAGGTATGGGATTTGCGCAAAGTTGAAGTAATGATGACACTTCAAGGCCATCAAGATATGATAACAGGTATGTCATTGAGTCCTGATGGCTCTTATCTTCTGACTAATGGAATGGACAGCAAACTCTGCATTTGGGATATGCGCCCGTATGCACCGCAAAATCGCTGTGTGAAGATAATGGAAGGTCACCAGCACAATTTTGAAAAGAACCTGTTGAAATGTGGCTGGTCCCCTGATGGAAGCAAGGTCACGGCTGGCAGTTCTGATCGGATGGTCTACGTATGGGACACCACTTCCCGACGCATCTTGTATATGCTGCCTGGCCACAGTGGATCCGTCAACGAGTCTGTTTTCCATCCCAACGAACCCATCATTGGATCGTGCAGTAGTGATAAACAGATCTATCTAGGGGAAATCTGA

Protein Analysis

345

Amino Acids

37.95

Weight (kDa)

6.89

Isoelectric Point (pI)

37.92

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Beta-prop_Aladin PF25460 42 - 128 9.7e-07 Aladin seven-bladed propeller
Beta-prop_TEP1_2nd PF25047 45 - 145 3.2e-15 TEP-1 second beta-propeller
WD40 PF00400 46 - 82 1.8e-08 WD domain, G-beta repeat
EIF3I PF24805 46 - 253 3.3e-21 EIF3I
Beta-prop_WDR3_1st PF25173 47 - 169 3e-28 WDR3 first beta-propeller domain
WD40_Prp19 PF24814 49 - 223 2.5e-27 Prp19 WD40 domain
WD40_WDHD1_1st PF24817 49 - 137 1.3e-11 WDHD1 first WD40 domain
Beta-prop_WDR3_2nd PF25172 49 - 168 1.5e-13 WDR3 second beta-propeller domain
Beta-prop_WDR5 PF25175 50 - 339 3.3e-63 WDR5 beta-propeller domain
Beta-prop_WDR36-Utp21_1st PF25171 50 - 160 1.6e-07 WDR36/Utp21 first beta-propeller
WD40_CDC20-Fz PF24807 50 - 250 7e-30 CDC20/Fizzy WD40 domain
Beta-prop_CAF1B_HIR1 PF24105 50 - 146 1.9e-15 CAF1B/HIR1 beta-propeller domain
Beta-prop_EML_2 PF23414 51 - 137 1.2e-14 Echinoderm microtubule-associated protein second beta-propeller
Beta-prop_EML PF23409 53 - 135 4.4e-06 Echinoderm microtubule-associated protein first beta-propeller
Beta-prop_THOC3 PF25174 53 - 269 4.7e-42 THOC3 beta-propeller domain
WDR55 PF24796 54 - 179 1.9e-18 WDR55
WD40_Gbeta PF25391 54 - 301 1.7e-22 G protein beta WD-40 repeat protein
WD40_MABP1-WDR62_2nd PF24782 54 - 167 1.2e-06 MABP1/WDR62 second WD40 domain
Beta-prop_WDR36-Utp21_2nd PF25168 55 - 134 1.6e-06 WDR36/Utp21 second beta-propeller domain
Beta-prop_WDR41 PF25178 66 - 150 1.7e-07 WDR41
Beta-prop_TEP1_2nd PF25047 138 - 216 4.2e-07 TEP-1 second beta-propeller
Beta-prop_EML_2 PF23414 153 - 263 9.6e-11 Echinoderm microtubule-associated protein second beta-propeller
Beta-prop_WDR3_2nd PF25172 154 - 251 4.4e-14 WDR3 second beta-propeller domain
Beta-prop_WDR3_1st PF25173 155 - 271 8.3e-20 WDR3 first beta-propeller domain
Beta-prop_WDR36-Utp21_1st PF25171 155 - 265 2.2e-09 WDR36/Utp21 first beta-propeller
Beta-prop_WDR36-Utp21_2nd PF25168 155 - 253 4.9e-10 WDR36/Utp21 second beta-propeller domain
Beta-prop_WDR90_POC16_2nd PF23393 157 - 253 4.8e-08 WDR90/POC16, second beta-propeller
Beta-prop_EML PF23409 182 - 339 7.2e-09 Echinoderm microtubule-associated protein first beta-propeller
WD40_WDHD1_1st PF24817 183 - 283 3e-12 WDHD1 first WD40 domain
Beta-prop_CAF1B_HIR1 PF24105 184 - 265 1.8e-09 CAF1B/HIR1 beta-propeller domain
WD40_MABP1-WDR62_2nd PF24782 193 - 251 1e-05 MABP1/WDR62 second WD40 domain
WDR55 PF24796 194 - 336 1.9e-12 WDR55
Beta-prop_TEP1_2nd PF25047 214 - 327 2.1e-11 TEP-1 second beta-propeller
WD40 PF00400 216 - 251 6.3e-08 WD domain, G-beta repeat
Beta-prop_Aladin PF25460 218 - 305 3.6e-06 Aladin seven-bladed propeller
WD40_Prp19 PF24814 226 - 341 3.3e-12 Prp19 WD40 domain
Beta-prop_EML_2 PF23414 239 - 341 7.1e-06 Echinoderm microtubule-associated protein second beta-propeller
WD40 PF00400 260 - 301 9e-06 WD domain, G-beta repeat
Beta-prop_CAF1B_HIR1 PF24105 261 - 340 1.1e-06 CAF1B/HIR1 beta-propeller domain
Beta-prop_THOC3 PF25174 276 - 340 1.3e-09 THOC3 beta-propeller domain
Beta-prop_WDR3_1st PF25173 280 - 339 1.7e-10 WDR3 first beta-propeller domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Orthologous Genes (Group: OG0012055)

Species Orthologous Gene IDs
arabidopsis_thaliana AT2G43770
fragaria_vesca FvH4_4g10290 FvH4_4g10290 FvH4_4g10290 FvH4_4g10290 FvH4_4g10290
malus_domestica MD16G1243600.v1.1
prunus_persica Prupe.1G071000_v2.0.a1
pyrus_communis pycom16g20470
rosa_chinensis RchiOBHm_Chr4g0405641
rosa_laevigata RLG00000008830
rosa_multiflora Rmu_sc0001200.1_g000049
rosa_roxburghii Rroxscaffold_5G00350120
rosa_rugosa Rorug04G0061600
rosa_samantha Rh4AG133000 Rh4BG128000 Rh4CG140700 Rh4DG127400
rosa_wichuraiana Rw4G010780

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc16I TGCGCA 1 cut(s) 632
AccB7I CCANNNNNTGG 2 cut(s) 95, 498
AccI GTMKAC 3 cut(s) 71, 171, 891
AciI CCGC 1 cut(s) 770
AclWI GGATC 6 cut(s) 312, 481, 517, 942, 955, 1000
AcoI YGGCCR 1 cut(s) 937
AcsI RAATTY 2 cut(s) 182, 427
AfiI CCNNNNNNNGG 4 cut(s) 23, 95, 498, 989
AgsI TTSAA 6 cut(s) 280, 380, 641, 659, 818, 832
AjnI CCWGG 2 cut(s) 94, 934
AjuI GAANNNNNNNTTGG 4 cut(s) 284, 316, 972, 1004
AluBI AGCT 3 cut(s) 126, 557, 564
AluI AGCT 3 cut(s) 126, 557, 564
Alw21I GWGCWC 1 cut(s) 414
AlwI GGATC 6 cut(s) 312, 481, 517, 942, 955, 1000
AlwNI CAGNNNCTG 1 cut(s) 95
AoxI GGCC 4 cut(s) 56, 154, 661, 937
ApeKI GCWGC 1 cut(s) 931
ApoI RAATTY 2 cut(s) 182, 427
AspLEI GCGC 2 cut(s) 633, 759
AspS9I GGNCC 5 cut(s) 50, 98, 216, 452, 843
AsuHPI GGTGA 3 cut(s) 38, 126, 794
AvaII GGWCC 5 cut(s) 50, 98, 216, 452, 843
BaeGI GKGCMC 1 cut(s) 288
BalI TGGCCA 1 cut(s) 939
BamHI GGATCC 1 cut(s) 947
BarI GAAGNNNNNNTAC 2 cut(s) 291, 323
Bbv12I GWGCWC 1 cut(s) 414
BbvI GCAGC 1 cut(s) 918
BceAI ACGGC 1 cut(s) 882
BcgI CGANNNNNNTGC 2 cut(s) 127, 161
BciT130I CCWGG 2 cut(s) 96, 936
BfaI CTAG 2 cut(s) 18, 1022
BglII AGATCT 1 cut(s) 1014
BisI GCNGC 1 cut(s) 932
BlpI GCTNAGC 1 cut(s) 408
BlsI GCNGC 1 cut(s) 933
Bme1390I CCNGG 2 cut(s) 96, 936
Bme18I GGWCC 5 cut(s) 50, 98, 216, 452, 843
BmgT120I GGNCC 5 cut(s) 50, 98, 216, 452, 843
BmiI GGNNCC 5 cut(s) 217, 218, 453, 845, 949
BmrFI CCNGG 2 cut(s) 96, 936
BmsI GCATC 3 cut(s) 562, 584, 927
Bpu1102I GCTNAGC 1 cut(s) 408
BsaAI YACGTR 1 cut(s) 895
BsaBI GATNNNNATC 1 cut(s) 543
BsaJI CCNNGG 1 cut(s) 53
Bsc4I CCNNNNNNNGG 4 cut(s) 23, 95, 498, 989
Bse1I ACTGG 2 cut(s) 317, 345
Bse8I GATNNNNATC 1 cut(s) 543
BseBI CCWGG 2 cut(s) 96, 936
BseDI CCNNGG 1 cut(s) 53
BseGI GGATG 5 cut(s) 379, 436, 575, 891, 970
BseJI GATNNNNATC 1 cut(s) 543
BseLI CCNNNNNNNGG 4 cut(s) 23, 95, 498, 989
BseMII CTCAG 2 cut(s) 399, 503
BseNI ACTGG 2 cut(s) 317, 345
BseRI GAGGAG 1 cut(s) 447
BseSI GKGCMC 1 cut(s) 288
BseXI GCAGC 1 cut(s) 918
BseYI CCCAGC 1 cut(s) 88
BsgI GTGCAG 1 cut(s) 1018
BshFI GGCC 4 cut(s) 58, 156, 663, 939
BsiHKAI GWGCWC 1 cut(s) 414
BslFI GGGAC 4 cut(s) 202, 465, 829, 914
BslI CCNNNNNNNGG 4 cut(s) 23, 95, 498, 989
BsmFI GGGAC 4 cut(s) 202, 465, 829, 914
BsmI GAATGC 2 cut(s) 263, 298
BsnI GGCC 4 cut(s) 58, 156, 663, 939
Bsp1286I GDGCHC 2 cut(s) 288, 414
Bsp143I GATC 8 cut(s) 138, 304, 473, 522, 880, 947, 992, 1014
Bsp1720I GCTNAGC 1 cut(s) 408
BspACI CCGC 1 cut(s) 770
BspANI GGCC 4 cut(s) 58, 156, 663, 939
BspCNI CTCAG 2 cut(s) 400, 504
BspLI GGNNCC 5 cut(s) 217, 218, 453, 845, 949
BspPI GGATC 6 cut(s) 312, 481, 517, 942, 955, 1000
BsrI ACTGG 2 cut(s) 317, 345
BssECI CCNNGG 1 cut(s) 53
BssMI GATC 8 cut(s) 138, 304, 473, 522, 880, 947, 992, 1014
BssNAI GTATAC 1 cut(s) 172
BssT1I CCWWGG 1 cut(s) 53
Bst1107I GTATAC 1 cut(s) 172
Bst2UI CCWGG 2 cut(s) 96, 936
Bst4CI ACNGT 3 cut(s) 202, 361, 944
Bst6I CTCTTC 1 cut(s) 421
BstAPI GCANNNNNTGC 1 cut(s) 741
BstBAI YACGTR 1 cut(s) 895
BstC8I GCNNGC 1 cut(s) 871
BstDEI CTNAG 2 cut(s) 408, 512
BstEII GGTNACC 1 cut(s) 800
BstF5I GGATG 5 cut(s) 379, 436, 575, 891, 970
BstHHI GCGC 2 cut(s) 633, 759
BstKTI GATC 8 cut(s) 141, 307, 476, 525, 883, 950, 995, 1017
BstMBI GATC 8 cut(s) 138, 304, 473, 522, 880, 947, 992, 1014
BstMWI GCNNNNNNNGC 1 cut(s) 741
BstNI CCWGG 2 cut(s) 96, 936
BstPI GGTNACC 1 cut(s) 800
BstSCI CCNGG 2 cut(s) 94, 934
BstSLI GKGCMC 1 cut(s) 288
BstSNI TACGTA 1 cut(s) 895
BstV1I GCAGC 1 cut(s) 918
BstX2I RGATCY 4 cut(s) 304, 473, 947, 1014
BstYI RGATCY 4 cut(s) 304, 473, 947, 1014
BstZ17I GTATAC 1 cut(s) 172
BsuRI GGCC 4 cut(s) 58, 156, 663, 939
BtsCI GGATG 5 cut(s) 379, 436, 575, 891, 970
BtsIMutI CAGTG 3 cut(s) 310, 475, 949
Cac8I GCNNGC 1 cut(s) 871
CaiI CAGNNNCTG 1 cut(s) 95
CfoI GCGC 2 cut(s) 633, 759
Cfr13I GGNCC 5 cut(s) 50, 98, 216, 452, 843
CseI GACGC 3 cut(s) 198, 497, 924
CviAII CATG 4 cut(s) 142, 221, 251, 369
DdeI CTNAG 2 cut(s) 408, 512
DpnI GATC 8 cut(s) 140, 306, 475, 524, 882, 949, 994, 1016
DpnII GATC 8 cut(s) 138, 304, 473, 522, 880, 947, 992, 1014
EaeI YGGCCR 1 cut(s) 937
Eam1104I CTCTTC 1 cut(s) 421
EarI CTCTTC 1 cut(s) 421
Eco105I TACGTA 1 cut(s) 895
Eco130I CCWWGG 1 cut(s) 53
Eco47I GGWCC 5 cut(s) 50, 98, 216, 452, 843
Eco91I GGTNACC 1 cut(s) 800
EcoO109I RGGNCCY 2 cut(s) 216, 452
EcoO65I GGTNACC 1 cut(s) 800
EcoRI GAATTC 1 cut(s) 427
EcoRII CCWGG 2 cut(s) 94, 934
EcoT14I CCWWGG 1 cut(s) 53
EcoT22I ATGCAT 2 cut(s) 9, 577
ErhI CCWWGG 1 cut(s) 53
FaeI CATG 4 cut(s) 145, 224, 254, 372
FaqI GGGAC 4 cut(s) 202, 465, 829, 914
FatI CATG 4 cut(s) 141, 220, 250, 368
FblI GTMKAC 3 cut(s) 71, 171, 891
Fnu4HI GCNGC 1 cut(s) 932
FokI GGATG 5 cut(s) 386, 423, 562, 898, 957
Fsp4HI GCNGC 1 cut(s) 932
FspBI CTAG 2 cut(s) 18, 1022
FspI TGCGCA 1 cut(s) 632
GlaI GCGC 2 cut(s) 632, 758
GluI GCNGC 1 cut(s) 932
GsaI CCCAGC 1 cut(s) 92
HaeIII GGCC 4 cut(s) 58, 156, 663, 939
HgaI GACGC 3 cut(s) 198, 497, 924
HhaI GCGC 2 cut(s) 633, 759
Hin1II CATG 4 cut(s) 145, 224, 254, 372
Hin6I GCGC 2 cut(s) 631, 757
HinP1I GCGC 2 cut(s) 631, 757
HincII GTYRAC 1 cut(s) 955
HindII GTYRAC 1 cut(s) 955
HinfI GANTC 3 cut(s) 131, 694, 959
HphI GGTGA 3 cut(s) 38, 126, 794
Hpy166II GTNNAC 5 cut(s) 72, 172, 329, 892, 955
Hpy188I TCNGA 9 cut(s) 162, 478, 513, 571, 580, 717, 880, 885, 1034
Hpy188III TCNNGA 4 cut(s) 350, 668, 698, 912
Hpy8I GTNNAC 5 cut(s) 72, 172, 329, 892, 955
Hpy99I CGWCG 1 cut(s) 918
HpyAV CCTTC 3 cut(s) 274, 441, 791
HpyCH4III ACNGT 3 cut(s) 202, 361, 944
HpyCH4IV ACGT 1 cut(s) 894
HpyCH4V TGCA 6 cut(s) 7, 261, 575, 744, 767, 999
HpyF10VI GCNNNNNNNGC 1 cut(s) 741
HpyF3I CTNAG 2 cut(s) 408, 512
HpySE526I ACGT 1 cut(s) 894
Hsp92II CATG 4 cut(s) 145, 224, 254, 372
HspAI GCGC 2 cut(s) 631, 757
KflI GGGWCCC 1 cut(s) 216
Kzo9I GATC 8 cut(s) 138, 304, 473, 522, 880, 947, 992, 1014
LmnI GCTCC 2 cut(s) 19, 518
Lsp1109I GCAGC 1 cut(s) 918
LweI GCATC 3 cut(s) 562, 584, 927
MaeI CTAG 2 cut(s) 18, 1022
MaeII ACGT 1 cut(s) 894
MaeIII GTNAC 2 cut(s) 800, 862
MalI GATC 8 cut(s) 140, 306, 475, 524, 882, 949, 994, 1016
MboI GATC 8 cut(s) 138, 304, 473, 522, 880, 947, 992, 1014
MboII GAAGA 5 cut(s) 299, 408, 412, 704, 799
MflI RGATCY 4 cut(s) 304, 473, 947, 1014
MhlI GDGCHC 2 cut(s) 288, 414
MlsI TGGCCA 1 cut(s) 939
MluCI AATT 4 cut(s) 182, 427, 549, 811
MluNI TGGCCA 1 cut(s) 939
MlyI GAGTC 2 cut(s) 703, 968
MnlI CCTC 5 cut(s) 16, 465, 468, 507, 590
Mox20I TGGCCA 1 cut(s) 939
Mph1103I ATGCAT 2 cut(s) 9, 577
MscI TGGCCA 1 cut(s) 939
MseI TTAA 2 cut(s) 186, 615
MslI CAYNNNNRTG 2 cut(s) 162, 291
Msp20I TGGCCA 1 cut(s) 939
MspA1I CMGCKG 1 cut(s) 557
MspR9I CCNGG 2 cut(s) 96, 936
Mva1269I GAATGC 2 cut(s) 263, 298
MvaI CCWGG 2 cut(s) 96, 936
MwoI GCNNNNNNNGC 1 cut(s) 741
NdeII GATC 8 cut(s) 138, 304, 473, 522, 880, 947, 992, 1014
NlaIII CATG 4 cut(s) 145, 224, 254, 372
NlaIV GGNNCC 5 cut(s) 217, 218, 453, 845, 949
NmuCI GTSAC 2 cut(s) 800, 862
NsbI TGCGCA 1 cut(s) 632
NsiI ATGCAT 2 cut(s) 9, 577
PctI GAATGC 2 cut(s) 263, 298
PfeI GAWTC 1 cut(s) 131
PflMI CCANNNNNTGG 2 cut(s) 95, 498
PkrI GCNGC 1 cut(s) 933
PleI GAGTC 2 cut(s) 702, 967
PpsI GAGTC 2 cut(s) 702, 967
Ppu21I YACGTR 1 cut(s) 895
PpuMI RGGWCCY 2 cut(s) 216, 452
Psp5II RGGWCCY 2 cut(s) 216, 452
Psp6I CCWGG 2 cut(s) 94, 934
PspEI GGTNACC 1 cut(s) 800
PspFI CCCAGC 1 cut(s) 88
PspGI CCWGG 2 cut(s) 94, 934
PspN4I GGNNCC 5 cut(s) 217, 218, 453, 845, 949
PspPI GGNCC 5 cut(s) 50, 98, 216, 452, 843
PspPPI RGGWCCY 2 cut(s) 216, 452
PstNI CAGNNNCTG 1 cut(s) 95
PsuI RGATCY 4 cut(s) 304, 473, 947, 1014
PvuII CAGCTG 1 cut(s) 557
RseI CAYNNNNRTG 2 cut(s) 162, 291
SaqAI TTAA 2 cut(s) 186, 615
SatI GCNGC 1 cut(s) 932
Sau3AI GATC 8 cut(s) 138, 304, 473, 522, 880, 947, 992, 1014
Sau96I GGNCC 5 cut(s) 50, 98, 216, 452, 843
SchI GAGTC 2 cut(s) 703, 968
ScrFI CCNGG 2 cut(s) 96, 936
SduI GDGCHC 2 cut(s) 288, 414
SfaNI GCATC 3 cut(s) 562, 584, 927
SinI GGWCC 5 cut(s) 50, 98, 216, 452, 843
SmiMI CAYNNNNRTG 2 cut(s) 162, 291
SnaBI TACGTA 1 cut(s) 895
Sse9I AATT 4 cut(s) 182, 427, 549, 811
SsiI CCGC 1 cut(s) 770
SspMI CTAG 2 cut(s) 18, 1022
StyD4I CCNGG 2 cut(s) 94, 934
StyI CCWWGG 1 cut(s) 53
TaaI ACNGT 3 cut(s) 202, 361, 944
TaiI ACGT 1 cut(s) 897
TaqI TCGA 1 cut(s) 445
TasI AATT 4 cut(s) 182, 427, 549, 811
TfiI GAWTC 1 cut(s) 131
Tru1I TTAA 2 cut(s) 186, 615
Tru9I TTAA 2 cut(s) 186, 615
TscAI CASTG 3 cut(s) 317, 475, 949
TseFI GTSAC 2 cut(s) 800, 862
TseI GCWGC 1 cut(s) 931
Tsp45I GTSAC 2 cut(s) 800, 862
TspDTI ATGAA 2 cut(s) 194, 239
TspGWI ACGGA 1 cut(s) 940
TspRI CASTG 3 cut(s) 317, 475, 949
Van91I CCANNNNNTGG 2 cut(s) 95, 498
VpaK11BI GGWCC 5 cut(s) 50, 98, 216, 452, 843
XapI RAATTY 2 cut(s) 182, 427
XmiI GTMKAC 3 cut(s) 71, 171, 891
XspI CTAG 2 cut(s) 18, 1022
Zsp2I ATGCAT 2 cut(s) 9, 577
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.