Rh4BG128000

U5 small nuclear ribonucleoprotein 40

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr4B
OG0012055
Physical Location & Seq
Forward (+)
21514875 .. 21519400
4526 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh4BG128000.1

Sequence Viewer

Length: 1035 bp
ATGATGCAGTTTGCTCCAAGTGAGGGTGAAAATGCTTTGTCTGTAGTTGGTCCCAGGCCAATGGATTTGTCTACATATAATGTTCGCCCTGGATCTGGGCCTAATGGAAAACAAAGGACTTCAAGTTTGGAGGCACCAATCATGCTGCTGACTGGTCATCAAAGTGCTATATACACAATGAAATTTAACCCTGCCGGAACAGTCATAGCATCGGGGTCTCATGACAAGGAAATTTTCTTATGGAATGTTCATGGGGAATGCAAAAACTTCATGGTTTTAAAGGGGCATAAGAATGCTGTGTTGGATCTTCACTGGACAACTGATGGGTCTCAGATAGTATCAGCCAGTCCAGACAAAACTGTGGGGGCATGGGATGTTGAGACGGGAAAAAGAATTAAAAAGATGGCAGAACACTCTTCATTTGTGAATTCTTGTCATCCTGCTCGGAGAGGACCACCTCTTGTTGTCAGTGGATCTGATGATGGAACTGCCAAACTATGGGATATGCGTGTGAGGGGTGCCATCCAAACATATCCTGATAAATACCAAATCACAGCAGTCAGCTTCTCGGATGCATCAGATAAAATCTTTACAGGAGGTATTGATAATGATATTAAGGTTTGGGACTTGCGCAAGGCTGAAGTACTGATGACACTTCAAGGACATCAAGATATGATAACAGGTATGTCATTGAGTCCTGATGGCTCTTATCTTCTGACTAATGGAATGGACTGCAAACTCTGCATTTGGGATATGCGCCCGTATGCACCACAAAATCGTTGTGTAAAGATAATGGAAGGGCACCAGCACAACTTTGAAAAGAACTTGTTGAAATGTAGCTGGTCACCTGATGGAAGCAAGGTCACGGCCGGCAGTTCTGATAGGATGGTCTACATATGGGATACTACTTCTCGACGCATCTTGTTTATGCTGCCGGGCCACACTGGATCTGTCAATGAGTCTGTCTTCCACCCCAAAGAGCCCATTATTGGATCTTGCAGTAGTGATAAGCAGATATATCTGGGGGAAATCTGA

Protein Analysis

344

Amino Acids

37.96

Weight (kDa)

7.18

Isoelectric Point (pI)

30.93

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Beta-prop_Aladin PF25460 39 - 128 1.1e-06 Aladin seven-bladed propeller
WD40 PF00400 46 - 82 4.4e-08 WD domain, G-beta repeat
EIF3I PF24805 46 - 253 8.5e-22 EIF3I
Beta-prop_TEP1_2nd PF25047 46 - 168 3.3e-17 TEP-1 second beta-propeller
Beta-prop_WDR3_1st PF25173 47 - 169 6.8e-28 WDR3 first beta-propeller domain
WD40_Prp19 PF24814 49 - 218 3.5e-25 Prp19 WD40 domain
WD40_WDHD1_1st PF24817 50 - 137 2.1e-11 WDHD1 first WD40 domain
WD40_CDC20-Fz PF24807 50 - 250 3.3e-29 CDC20/Fizzy WD40 domain
Beta-prop_CAF1B_HIR1 PF24105 50 - 169 5.2e-15 CAF1B/HIR1 beta-propeller domain
Beta-prop_WDR5 PF25175 50 - 339 6.4e-63 WDR5 beta-propeller domain
Beta-prop_WDR36-Utp21_1st PF25171 51 - 160 9.5e-08 WDR36/Utp21 first beta-propeller
Beta-prop_EML_2 PF23414 51 - 137 6e-15 Echinoderm microtubule-associated protein second beta-propeller
Beta-prop_EML PF23409 53 - 135 5.4e-06 Echinoderm microtubule-associated protein first beta-propeller
Beta-prop_THOC3 PF25174 53 - 269 1.9e-41 THOC3 beta-propeller domain
WDR55 PF24796 54 - 178 2.9e-18 WDR55
WD40_MABP1-WDR62_2nd PF24782 54 - 167 1.2e-06 MABP1/WDR62 second WD40 domain
Beta-prop_WDR41 PF25178 67 - 144 1e-06 WDR41
Beta-prop_WDR3_2nd PF25172 87 - 176 6.9e-08 WDR3 second beta-propeller domain
WD40_Prp19 PF24814 146 - 339 2.4e-26 Prp19 WD40 domain
Beta-prop_EML_2 PF23414 153 - 263 3.2e-11 Echinoderm microtubule-associated protein second beta-propeller
Beta-prop_WDR36-Utp21_2nd PF25168 154 - 253 4.8e-11 WDR36/Utp21 second beta-propeller domain
Beta-prop_WDR3_2nd PF25172 154 - 251 5.9e-13 WDR3 second beta-propeller domain
Beta-prop_WDR36-Utp21_1st PF25171 155 - 266 1.6e-09 WDR36/Utp21 first beta-propeller
Beta-prop_WDR3_1st PF25173 156 - 271 2e-19 WDR3 first beta-propeller domain
Beta-prop_WDR90_POC16_2nd PF23393 157 - 253 2e-08 WDR90/POC16, second beta-propeller
Beta-prop_DCAF4 PF23761 172 - 321 3.1e-06 DDB1- and CUL4-associated factor 4 beta-propeller domain
Beta-prop_EML PF23409 181 - 339 2.5e-09 Echinoderm microtubule-associated protein first beta-propeller
WD40_WDHD1_1st PF24817 183 - 284 7.1e-13 WDHD1 first WD40 domain
Beta-prop_CAF1B_HIR1 PF24105 184 - 265 2.2e-09 CAF1B/HIR1 beta-propeller domain
Beta-prop_SCAP PF24017 190 - 304 1.9e-06 SCAP Beta-propeller
EIF3I PF24805 193 - 341 2.2e-08 EIF3I
WDR55 PF24796 194 - 320 2.7e-12 WDR55
WD40 PF00400 215 - 251 1.7e-08 WD domain, G-beta repeat
Beta-prop_TEP1_2nd PF25047 216 - 329 1.5e-11 TEP-1 second beta-propeller
Beta-prop_Aladin PF25460 218 - 304 5e-06 Aladin seven-bladed propeller
Beta-prop_EML_2 PF23414 239 - 341 5.2e-06 Echinoderm microtubule-associated protein second beta-propeller
WD40 PF00400 260 - 301 1.3e-06 WD domain, G-beta repeat
Beta-prop_CAF1B_HIR1 PF24105 261 - 340 1.3e-07 CAF1B/HIR1 beta-propeller domain
Beta-prop_WDR3_1st PF25173 262 - 339 5.5e-11 WDR3 first beta-propeller domain
Beta-prop_THOC3 PF25174 276 - 340 6.9e-10 THOC3 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
AccB1I GGYRCC 3 cut(s) 133, 518, 801
AccB7I CCANNNNNTGG 1 cut(s) 498
AccI GTMKAC 2 cut(s) 71, 891
AclWI GGATC 5 cut(s) 100, 312, 481, 955, 1000
AcoI YGGCCR 1 cut(s) 867
AcsI RAATTY 3 cut(s) 182, 231, 427
AcuI CTGAAG 1 cut(s) 660
AfaI GTAC 1 cut(s) 645
AfiI CCNNNNNNNGG 4 cut(s) 23, 95, 498, 989
AgsI TTSAA 4 cut(s) 123, 659, 818, 832
AjnI CCWGG 2 cut(s) 53, 88
AjuI GAANNNNNNNTTGG 2 cut(s) 284, 316
AluBI AGCT 2 cut(s) 564, 840
AluI AGCT 2 cut(s) 564, 840
Alw26I GTCTC 3 cut(s) 222, 333, 374
AlwI GGATC 5 cut(s) 100, 312, 481, 955, 1000
AoxI GGCC 4 cut(s) 56, 98, 867, 937
ApeKI GCWGC 2 cut(s) 145, 931
ApoI RAATTY 3 cut(s) 182, 231, 427
ArsI GACNNNNNNTTYG 2 cut(s) 109, 141
AspLEI GCGC 2 cut(s) 633, 759
AspS9I GGNCC 4 cut(s) 50, 98, 452, 937
AsuC2I CCSGG 1 cut(s) 936
AsuHPI GGTGA 2 cut(s) 38, 837
AvaII GGWCC 2 cut(s) 50, 452
BaeGI GKGCMC 1 cut(s) 804
BanI GGYRCC 3 cut(s) 133, 518, 801
BanII GRGCYC 1 cut(s) 984
BbsI GAAGAC 1 cut(s) 958
BbvI GCAGC 2 cut(s) 132, 918
BccI CCATC 7 cut(s) 317, 397, 476, 530, 695, 845, 880
BceAI ACGGC 1 cut(s) 882
BciT130I CCWGG 2 cut(s) 55, 90
BciVI GTATCC 1 cut(s) 895
BcnI CCSGG 1 cut(s) 936
BcoDI GTCTC 3 cut(s) 222, 333, 374
BfmI CTRYAG 1 cut(s) 42
BfuI GTATCC 1 cut(s) 895
BisI GCNGC 2 cut(s) 146, 932
BlsI GCNGC 2 cut(s) 147, 933
BmcAI AGTACT 1 cut(s) 645
Bme1390I CCNGG 3 cut(s) 55, 90, 936
Bme18I GGWCC 2 cut(s) 50, 452
BmgT120I GGNCC 4 cut(s) 50, 98, 452, 937
BmiI GGNNCC 4 cut(s) 52, 135, 520, 803
BmrFI CCNGG 3 cut(s) 55, 90, 936
BmsI GCATC 4 cut(s) 218, 562, 584, 927
BpiI GAAGAC 1 cut(s) 958
BpuMI CCSGG 1 cut(s) 936
BsaI GGTCTC 2 cut(s) 222, 333
BsaJI CCNNGG 2 cut(s) 53, 88
Bsc4I CCNNNNNNNGG 4 cut(s) 23, 95, 498, 989
Bse118I RCCGGY 1 cut(s) 869
Bse1I ACTGG 4 cut(s) 157, 317, 345, 949
BseBI CCWGG 2 cut(s) 55, 90
BseDI CCNNGG 2 cut(s) 53, 88
BseGI GGATG 5 cut(s) 379, 436, 522, 577, 891
BseLI CCNNNNNNNGG 4 cut(s) 23, 95, 498, 989
BseMII CTCAG 1 cut(s) 344
BseNI ACTGG 4 cut(s) 157, 317, 345, 949
BseSI GKGCMC 1 cut(s) 804
BseX3I CGGCCG 1 cut(s) 867
BseXI GCAGC 2 cut(s) 132, 918
Bsh1285I CGRYCG 1 cut(s) 870
BshFI GGCC 4 cut(s) 58, 100, 869, 939
BshNI GGYRCC 3 cut(s) 133, 518, 801
BsiEI CGRYCG 1 cut(s) 870
BsiSI CCGG 3 cut(s) 195, 870, 935
BslFI GGGAC 2 cut(s) 36, 638
BslI CCNNNNNNNGG 4 cut(s) 23, 95, 498, 989
BsmAI GTCTC 3 cut(s) 222, 333, 374
BsmBI CGTCTC 1 cut(s) 374
BsmFI GGGAC 2 cut(s) 36, 638
BsmI GAATGC 2 cut(s) 263, 298
BsnI GGCC 4 cut(s) 58, 100, 869, 939
Bso31I GGTCTC 2 cut(s) 222, 333
Bsp1286I GDGCHC 2 cut(s) 804, 984
Bsp143I GATC 5 cut(s) 92, 304, 473, 947, 992
BspANI GGCC 4 cut(s) 58, 100, 869, 939
BspCNI CTCAG 1 cut(s) 343
BspHI TCATGA 1 cut(s) 220
BspLI GGNNCC 4 cut(s) 52, 135, 520, 803
BspPI GGATC 5 cut(s) 100, 312, 481, 955, 1000
BspT107I GGYRCC 3 cut(s) 133, 518, 801
BspTNI GGTCTC 2 cut(s) 222, 333
BsrFI RCCGGY 1 cut(s) 869
BsrI ACTGG 4 cut(s) 157, 317, 345, 949
BssAI RCCGGY 1 cut(s) 869
BssECI CCNNGG 2 cut(s) 53, 88
BssMI GATC 5 cut(s) 92, 304, 473, 947, 992
Bst2UI CCWGG 2 cut(s) 55, 90
Bst4CI ACNGT 2 cut(s) 202, 361
Bst6I CTCTTC 1 cut(s) 421
BstAPI GCANNNNNTGC 1 cut(s) 741
BstC8I GCNNGC 1 cut(s) 871
BstDEI CTNAG 1 cut(s) 330
BstEII GGTNACC 1 cut(s) 843
BstF5I GGATG 5 cut(s) 379, 436, 522, 577, 891
BstHHI GCGC 2 cut(s) 633, 759
BstKTI GATC 5 cut(s) 95, 307, 476, 950, 995
BstMAI GTCTC 3 cut(s) 222, 333, 374
BstMBI GATC 5 cut(s) 92, 304, 473, 947, 992
BstMCI CGRYCG 1 cut(s) 870
BstMWI GCNNNNNNNGC 1 cut(s) 741
BstNI CCWGG 2 cut(s) 55, 90
BstPI GGTNACC 1 cut(s) 843
BstSCI CCNGG 3 cut(s) 53, 88, 934
BstSFI CTRYAG 1 cut(s) 42
BstSLI GKGCMC 1 cut(s) 804
BstV1I GCAGC 2 cut(s) 132, 918
BstV2I GAAGAC 1 cut(s) 958
BstX2I RGATCY 5 cut(s) 92, 304, 473, 947, 992
BstXI CCANNNNNNTGG 1 cut(s) 61
BstYI RGATCY 5 cut(s) 92, 304, 473, 947, 992
BstZI CGGCCG 1 cut(s) 867
BsuI GTATCC 1 cut(s) 895
BsuRI GGCC 4 cut(s) 58, 100, 869, 939
BtsCI GGATG 5 cut(s) 379, 436, 522, 577, 891
BtsIMutI CAGTG 3 cut(s) 310, 475, 942
Cac8I GCNNGC 1 cut(s) 871
CciI TCATGA 1 cut(s) 220
CfoI GCGC 2 cut(s) 633, 759
Cfr10I RCCGGY 1 cut(s) 869
Cfr13I GGNCC 4 cut(s) 50, 98, 452, 937
CseI GACGC 1 cut(s) 924
Csp6I GTAC 1 cut(s) 644
CviAII CATG 5 cut(s) 142, 221, 251, 271, 369
CviQI GTAC 1 cut(s) 644
DdeI CTNAG 1 cut(s) 330
DpnI GATC 5 cut(s) 94, 306, 475, 949, 994
DpnII GATC 5 cut(s) 92, 304, 473, 947, 992
DraI TTTAAA 1 cut(s) 279
EaeI YGGCCR 1 cut(s) 867
EagI CGGCCG 1 cut(s) 867
Eam1104I CTCTTC 1 cut(s) 421
EarI CTCTTC 1 cut(s) 421
EclXI CGGCCG 1 cut(s) 867
Eco24I GRGCYC 1 cut(s) 984
Eco31I GGTCTC 2 cut(s) 222, 333
Eco47I GGWCC 2 cut(s) 50, 452
Eco52I CGGCCG 1 cut(s) 867
Eco57I CTGAAG 1 cut(s) 660
Eco91I GGTNACC 1 cut(s) 843
EcoO65I GGTNACC 1 cut(s) 843
EcoRI GAATTC 1 cut(s) 427
EcoRII CCWGG 2 cut(s) 53, 88
EcoT22I ATGCAT 1 cut(s) 577
EcoT38I GRGCYC 1 cut(s) 984
Esp3I CGTCTC 1 cut(s) 374
FaeI CATG 5 cut(s) 145, 224, 254, 274, 372
FaqI GGGAC 2 cut(s) 36, 638
FatI CATG 5 cut(s) 141, 220, 250, 270, 368
FauNDI CATATG 1 cut(s) 896
FblI GTMKAC 2 cut(s) 71, 891
Fnu4HI GCNGC 2 cut(s) 146, 932
FokI GGATG 5 cut(s) 386, 423, 509, 584, 898
FriOI GRGCYC 1 cut(s) 984
Fsp4HI GCNGC 2 cut(s) 146, 932
FspI TGCGCA 1 cut(s) 632
GlaI GCGC 2 cut(s) 632, 758
GluI GCNGC 2 cut(s) 146, 932
HaeIII GGCC 4 cut(s) 58, 100, 869, 939
HapII CCGG 3 cut(s) 195, 870, 935
HgaI GACGC 1 cut(s) 924
HhaI GCGC 2 cut(s) 633, 759
Hin1II CATG 5 cut(s) 145, 224, 254, 274, 372
Hin6I GCGC 2 cut(s) 631, 757
HinP1I GCGC 2 cut(s) 631, 757
HinfI GANTC 2 cut(s) 694, 959
HpaII CCGG 3 cut(s) 195, 870, 935
HphI GGTGA 2 cut(s) 38, 837
Hpy166II GTNNAC 2 cut(s) 72, 892
Hpy188I TCNGA 8 cut(s) 333, 447, 478, 571, 580, 717, 880, 1034
Hpy188III TCNNGA 6 cut(s) 221, 350, 536, 668, 698, 912
Hpy8I GTNNAC 2 cut(s) 72, 892
Hpy99I CGWCG 1 cut(s) 918
HpyAV CCTTC 1 cut(s) 791
HpyCH4III ACNGT 2 cut(s) 202, 361
HpyCH4V TGCA 7 cut(s) 7, 261, 575, 735, 744, 767, 999
HpyF10VI GCNNNNNNNGC 1 cut(s) 741
HpyF3I CTNAG 1 cut(s) 330
Hsp92II CATG 5 cut(s) 145, 224, 254, 274, 372
HspAI GCGC 2 cut(s) 631, 757
KroI GCCGGC 1 cut(s) 869
KroNI GCCGGC 1 cut(s) 871
Kzo9I GATC 5 cut(s) 92, 304, 473, 947, 992
LmnI GCTCC 1 cut(s) 19
Lsp1109I GCAGC 2 cut(s) 132, 918
LweI GCATC 4 cut(s) 218, 562, 584, 927
MaeIII GTNAC 2 cut(s) 843, 862
MalI GATC 5 cut(s) 94, 306, 475, 949, 994
MboI GATC 5 cut(s) 92, 304, 473, 947, 992
MboII GAAGA 4 cut(s) 299, 408, 704, 958
MflI RGATCY 5 cut(s) 92, 304, 473, 947, 992
MhlI GDGCHC 2 cut(s) 804, 984
MluCI AATT 4 cut(s) 182, 231, 393, 427
MlyI GAGTC 2 cut(s) 703, 968
MmeI TCCRAC 1 cut(s) 282
MnlI CCTC 6 cut(s) 16, 124, 443, 468, 507, 590
Mph1103I ATGCAT 1 cut(s) 577
MroNI GCCGGC 1 cut(s) 869
MseI TTAA 4 cut(s) 186, 278, 396, 615
MslI CAYNNNNRTG 2 cut(s) 162, 291
MspI CCGG 3 cut(s) 195, 870, 935
MspR9I CCNGG 3 cut(s) 55, 90, 936
Mva1269I GAATGC 2 cut(s) 263, 298
MvaI CCWGG 2 cut(s) 55, 90
MwoI GCNNNNNNNGC 1 cut(s) 741
NaeI GCCGGC 1 cut(s) 871
NciI CCSGG 1 cut(s) 936
NdeI CATATG 1 cut(s) 896
NdeII GATC 5 cut(s) 92, 304, 473, 947, 992
NgoMIV GCCGGC 1 cut(s) 869
NlaIII CATG 5 cut(s) 145, 224, 254, 274, 372
NlaIV GGNNCC 4 cut(s) 52, 135, 520, 803
NmuCI GTSAC 2 cut(s) 843, 862
NsbI TGCGCA 1 cut(s) 632
NsiI ATGCAT 1 cut(s) 577
PagI TCATGA 1 cut(s) 220
PctI GAATGC 2 cut(s) 263, 298
PdiI GCCGGC 1 cut(s) 871
PflMI CCANNNNNTGG 1 cut(s) 498
PkrI GCNGC 2 cut(s) 147, 933
PleI GAGTC 2 cut(s) 702, 967
PpsI GAGTC 2 cut(s) 702, 967
Psp6I CCWGG 2 cut(s) 53, 88
PspEI GGTNACC 1 cut(s) 843
PspGI CCWGG 2 cut(s) 53, 88
PspN4I GGNNCC 4 cut(s) 52, 135, 520, 803
PspPI GGNCC 4 cut(s) 50, 98, 452, 937
PsuI RGATCY 5 cut(s) 92, 304, 473, 947, 992
RsaI GTAC 1 cut(s) 645
RsaNI GTAC 1 cut(s) 644
RseI CAYNNNNRTG 2 cut(s) 162, 291
SaqAI TTAA 4 cut(s) 186, 278, 396, 615
SatI GCNGC 2 cut(s) 146, 932
Sau3AI GATC 5 cut(s) 92, 304, 473, 947, 992
Sau96I GGNCC 4 cut(s) 50, 98, 452, 937
ScaI AGTACT 1 cut(s) 645
SchI GAGTC 2 cut(s) 703, 968
ScrFI CCNGG 3 cut(s) 55, 90, 936
SduI GDGCHC 2 cut(s) 804, 984
SetI ASST 8 cut(s) 460, 566, 601, 621, 685, 842, 850, 864
SfaNI GCATC 4 cut(s) 218, 562, 584, 927
SfcI CTRYAG 1 cut(s) 42
SinI GGWCC 2 cut(s) 50, 452
SmiMI CAYNNNNRTG 2 cut(s) 162, 291
Sse9I AATT 4 cut(s) 182, 231, 393, 427
StyD4I CCNGG 3 cut(s) 53, 88, 934
TaaI ACNGT 2 cut(s) 202, 361
TaqI TCGA 1 cut(s) 913
TasI AATT 4 cut(s) 182, 231, 393, 427
TatI WGTACW 1 cut(s) 643
Tru1I TTAA 4 cut(s) 186, 278, 396, 615
Tru9I TTAA 4 cut(s) 186, 278, 396, 615
TscAI CASTG 3 cut(s) 317, 475, 949
TseFI GTSAC 2 cut(s) 843, 862
TseI GCWGC 2 cut(s) 145, 931
Tsp45I GTSAC 2 cut(s) 843, 862
TspDTI ATGAA 4 cut(s) 194, 239, 259, 408
TspRI CASTG 3 cut(s) 317, 475, 949
Van91I CCANNNNNTGG 1 cut(s) 498
VpaK11BI GGWCC 2 cut(s) 50, 452
XapI RAATTY 3 cut(s) 182, 231, 427
XmiI GTMKAC 2 cut(s) 71, 891
ZrmI AGTACT 1 cut(s) 645
Zsp2I ATGCAT 1 cut(s) 577
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.