Rh3BG087400

zinc finger CCCH domain-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr3B
OG0018453
Physical Location & Seq
Reverse (-)
6832460 .. 6833965
1506 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh3BG087400.1

Sequence Viewer

Length: 1428 bp
ATGCGCTCAATTCCGAGATATCGAAACTCATTGCGTTCATCTACCAATATGAAGAAGAATCAGAGATCAACGAACAAAGATCACATGAATGATTATTCAGAGTCAGAGGATTGGTGCTTCATCTGCAAAGACGGTGGGGTTCTAATTCTATGCGACCACGAGGGCTGCTCCAAAGCCTATCACCCTCGCTGCGTTGGAAAGAAGATATCTTTCCTCAAGAAACAAAAGCGCTGGATTTGTAGTCACCACTCCTGCTCAGCGTGCGGTGTTGGCGCCCCTGGAACTAAGATCCTCTCTTGCCTTCTTTGCACTTATGCAGTGTGTGGTAGTTGCTGCAAAAGCAGCGATGCTAATTCGGAGTTTGCAGTGGTGAGAGGGAAGGAGAAACTTGGCCTTTGCAATGACTGCTTAGGGATTGTTAGGCTTGCAGAAGAAAATGGACCGTATGGAGTAGATGGAAAGAAATTAGGCTTCGAGGATCCGGAAACATTTGAATACGGATTCAAAGAATGTTGGGAAATCATCAAGGAAAAGGAGGGCTTGACCTTGGATGATCTCTACTTCCCATATTCCAAAGGGGTAACAGATAGTCATGACAGTGAAGACACAGAAACTCACAAGTCAACATTGGGCAAACGGAAGGCGGAAGCCGCAATTTGTGAGGATAACAAAGATGAATTTGGTAGTGACGATGTTGCTGCAAGCAACCACAAGAAGCAAAAATTAGTGAGCTCATCAGAGCATATGACATCAGAATCTGTTTTGCATGAGGAAAATAACTCCGAGGAAAAGGAGGAAATGATTCCTAGTCCGACTAGGAATGACGAATCAGAGTGGCGCTTTGCATCTATAGTTGCTAGTAATATGAAGCTTGTCTACTTGAGAAGGAGCTTAGTGGAGGAGCTGATATCCAAGCAGCCTGATAGTTGGGAAAGAAAACTAGTTGGAAGTTATGTGAGAGTGGAAAATGAACCCGAGGACTATTTTCAGATAAAATCTTCTTACCAACTTTCACAAGTGAAAGGCATAATTAGGAACCACAACAATGGAGAAGAAATTCTCCTGCATCTGCTAACAAGAGAGGTTCCAATTTCTATGCTATCGGATTGTGACTTCACTGAGGAAGATTGTGAAGATTTGCAAGAAAGGGTGAACAATTACCTGATGAGGAGACCGACGGTTGTTGAAATTGAACAAAAAGCGAGAGAGCTACATGAAGATATAACAAAGGATTGGATTGAGAGAGAGTTGGTCCGGTTACAGAAATGCATTATTCATCACGAGAAAAATCAGCATGGATGGATCAGCAGAGAGTTATGTGAGTATTTGAAACAGAGAAATATGCTAAAGCAACCATCTGAGCAGGAAAGACTCCGAAAAGAGGTGCCACAAGTCATTGCAGAGGACTTGGACTCCAGCAATTTATGA
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
Plus-3 SWIB

Protein Analysis

475

Amino Acids

54.67

Weight (kDa)

5.58

Isoelectric Point (pI)

55.48

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PHD_NSD PF22908 38 - 83 4e-06 Histone-lysine N-methyltransferase NSD-like, PHD zinc finger
Plus-3 PF03126 288 - 384 9.1e-11 Plus-3 domain
NERD_plant PF25980 406 - 458 1.3e-10 Plant NERD 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: OG0018453)

Species Orthologous Gene IDs
fragaria_vesca FvH4_6g08140
rosa_chinensis RchiOBHm_Chr3g0458001
rosa_laevigata RLG00000025180
rosa_multiflora Rmu_sc0000384.1_g000008
rosa_rugosa Rorug03G0024100
rosa_samantha Rh3BG087400 Rh3CG087900 Rh3DG088200
rosa_wichuraiana Rw0G012390 Rw3G007210

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 2 cut(s) 272, 1384
AccI GTMKAC 1 cut(s) 876
AccIII TCCGGA 1 cut(s) 481
AciI CCGC 3 cut(s) 264, 644, 651
AclWI GGATC 4 cut(s) 283, 473, 486, 1310
AcsI RAATTY 2 cut(s) 677, 1056
AcyI GRCGYC 1 cut(s) 273
AfeI AGCGCT 1 cut(s) 230
AfiI CCNNNNNNNGG 1 cut(s) 1381
AgsI TTSAA 5 cut(s) 494, 505, 1187, 1193, 1330
AhlI ACTAGT 1 cut(s) 940
AjnI CCWGG 1 cut(s) 277
AluBI AGCT 5 cut(s) 732, 871, 891, 904, 1210
AluI AGCT 5 cut(s) 732, 871, 891, 904, 1210
Alw21I GWGCWC 1 cut(s) 734
Alw26I GTCTC 1 cut(s) 1165
AlwI GGATC 4 cut(s) 283, 473, 486, 1310
AlwNI CAGNNNCTG 1 cut(s) 758
Ama87I CYCGRG 1 cut(s) 974
Aor13HI TCCGGA 1 cut(s) 481
Aor51HI AGCGCT 1 cut(s) 230
AoxI GGCC 1 cut(s) 391
ApeKI GCWGC 6 cut(s) 165, 189, 333, 342, 698, 916
ApoI RAATTY 2 cut(s) 677, 1056
Asp700I GAANNNNTTC 2 cut(s) 801, 1056
AspLEI GCGC 4 cut(s) 6, 231, 275, 840
AspS9I GGNCC 2 cut(s) 440, 1252
AsuHPI GGTGA 4 cut(s) 173, 236, 382, 1162
AvaI CYCGRG 1 cut(s) 974
AvaII GGWCC 2 cut(s) 440, 1252
BamHI GGATCC 1 cut(s) 478
BanI GGYRCC 2 cut(s) 272, 1384
BanII GRGCYC 1 cut(s) 734
BarI GAAGNNNNNNTAC 2 cut(s) 860, 892
BauI CACGAG 2 cut(s) 158, 1280
BbsI GAAGAC 1 cut(s) 609
Bbv12I GWGCWC 1 cut(s) 734
BbvI GCAGC 6 cut(s) 152, 176, 320, 354, 685, 928
BccI CCATC 3 cut(s) 449, 1293, 1363
BcgI CGANNNNNNTGC 2 cut(s) 680, 714
BciT130I CCWGG 1 cut(s) 279
BcoDI GTCTC 1 cut(s) 1165
BcuI ACTAGT 1 cut(s) 940
BfaI CTAG 4 cut(s) 807, 816, 858, 941
BfmI CTRYAG 1 cut(s) 849
BfoI RGCGCY 3 cut(s) 232, 276, 841
BisI GCNGC 7 cut(s) 166, 190, 334, 343, 651, 699, 917
BlpI GCTNAGC 1 cut(s) 256
BlsI GCNGC 7 cut(s) 167, 191, 335, 344, 652, 700, 918
Bme1390I CCNGG 1 cut(s) 279
Bme18I GGWCC 2 cut(s) 440, 1252
BmeT110I CYCGRG 1 cut(s) 974
BmgT120I GGNCC 2 cut(s) 440, 1252
BmiI GGNNCC 5 cut(s) 274, 480, 1037, 1086, 1386
BmrFI CCNGG 1 cut(s) 279
BmsI GCATC 3 cut(s) 337, 854, 1075
BpiI GAAGAC 1 cut(s) 609
BplI GAGNNNNNCTC 2 cut(s) 152, 184
BpmI CTGGAG 1 cut(s) 1399
Bpu10I CCTNAGC 1 cut(s) 409
Bpu1102I GCTNAGC 1 cut(s) 256
BpuEI CTTGAG 2 cut(s) 200, 901
BsaHI GRCGYC 1 cut(s) 273
BsaI GGTCTC 1 cut(s) 1165
BsaJI CCNNGG 4 cut(s) 277, 546, 783, 975
BsaWI WCCGGW 2 cut(s) 481, 1254
BsaXI ACNNNNNCTCC 2 cut(s) 1397, 1427
Bsc4I CCNNNNNNNGG 1 cut(s) 1381
Bse3DI GCAATG 3 cut(s) 29, 406, 1395
BseAI TCCGGA 1 cut(s) 481
BseBI CCWGG 1 cut(s) 279
BseDI CCNNGG 4 cut(s) 277, 546, 783, 975
BseGI GGATG 2 cut(s) 556, 1304
BseLI CCNNNNNNNGG 1 cut(s) 1381
BseMI GCAATG 3 cut(s) 29, 406, 1395
BseMII CTCAG 3 cut(s) 270, 1110, 1350
BseRI GAGGAG 2 cut(s) 914, 1183
BseXI GCAGC 6 cut(s) 152, 176, 320, 354, 685, 928
BshFI GGCC 1 cut(s) 393
BshNI GGYRCC 2 cut(s) 272, 1384
BsiHKAI GWGCWC 1 cut(s) 734
BsiHKCI CYCGRG 1 cut(s) 974
BsiSI CCGG 2 cut(s) 482, 1255
BslI CCNNNNNNNGG 1 cut(s) 1381
BsmAI GTCTC 1 cut(s) 1165
BsnI GGCC 1 cut(s) 393
Bso31I GGTCTC 1 cut(s) 1165
BsoBI CYCGRG 1 cut(s) 974
Bsp1286I GDGCHC 1 cut(s) 734
Bsp13I TCCGGA 1 cut(s) 481
Bsp143I GATC 6 cut(s) 65, 79, 288, 478, 553, 1302
Bsp1720I GCTNAGC 1 cut(s) 256
BspACI CCGC 3 cut(s) 264, 644, 651
BspANI GGCC 1 cut(s) 393
BspCNI CTCAG 3 cut(s) 269, 1111, 1351
BspEI TCCGGA 1 cut(s) 481
BspHI TCATGA 1 cut(s) 592
BspLI GGNNCC 5 cut(s) 274, 480, 1037, 1086, 1386
BspPI GGATC 4 cut(s) 283, 473, 486, 1310
BspT107I GGYRCC 2 cut(s) 272, 1384
BspTNI GGTCTC 1 cut(s) 1165
BsrDI GCAATG 3 cut(s) 29, 406, 1395
BssECI CCNNGG 4 cut(s) 277, 546, 783, 975
BssMI GATC 6 cut(s) 65, 79, 288, 478, 553, 1302
BssNI GRCGYC 1 cut(s) 273
BssSI CACGAG 2 cut(s) 158, 1280
BssT1I CCWWGG 1 cut(s) 546
Bst2BI CACGAG 2 cut(s) 158, 1280
Bst2UI CCWGG 1 cut(s) 279
Bst4CI ACNGT 4 cut(s) 134, 444, 599, 1180
BstACI GRCGYC 1 cut(s) 273
BstAPI GCANNNNNTGC 1 cut(s) 405
BstC8I GCNNGC 3 cut(s) 262, 426, 703
BstDEI CTNAG 6 cut(s) 256, 285, 409, 892, 1119, 1359
BstF5I GGATG 2 cut(s) 556, 1304
BstH2I RGCGCY 3 cut(s) 232, 276, 841
BstHHI GCGC 4 cut(s) 6, 231, 275, 840
BstKTI GATC 6 cut(s) 68, 82, 291, 481, 556, 1305
BstMAI GTCTC 1 cut(s) 1165
BstMBI GATC 6 cut(s) 65, 79, 288, 478, 553, 1302
BstMWI GCNNNNNNNGC 8 cut(s) 123, 261, 270, 306, 339, 342, 405, 650
BstNI CCWGG 1 cut(s) 279
BstSCI CCNGG 1 cut(s) 277
BstSFI CTRYAG 1 cut(s) 849
BstV1I GCAGC 6 cut(s) 152, 176, 320, 354, 685, 928
BstV2I GAAGAC 1 cut(s) 609
BstX2I RGATCY 2 cut(s) 288, 478
BstXI CCANNNNNNTGG 1 cut(s) 1046
BstYI RGATCY 2 cut(s) 288, 478
BsuRI GGCC 1 cut(s) 393
BtgZI GCGATG 1 cut(s) 360
BtsCI GGATG 2 cut(s) 556, 1304
BtsI GCAGTG 2 cut(s) 324, 372
BtsIMutI CAGTG 4 cut(s) 324, 372, 604, 1116
Cac8I GCNNGC 3 cut(s) 262, 426, 703
CaiI CAGNNNCTG 1 cut(s) 758
CciI TCATGA 1 cut(s) 592
CfoI GCGC 4 cut(s) 6, 231, 275, 840
Cfr13I GGNCC 2 cut(s) 440, 1252
CspCI CAANNNNNGTGG 2 cut(s) 115, 150
CviAII CATG 5 cut(s) 85, 593, 767, 1214, 1295
DdeI CTNAG 6 cut(s) 256, 285, 409, 892, 1119, 1359
DinI GGCGCC 1 cut(s) 274
DpnI GATC 6 cut(s) 67, 81, 290, 480, 555, 1304
DpnII GATC 6 cut(s) 65, 79, 288, 478, 553, 1302
EciI GGCGGA 1 cut(s) 659
Ecl136II GAGCTC 1 cut(s) 732
Eco130I CCWWGG 1 cut(s) 546
Eco24I GRGCYC 1 cut(s) 734
Eco31I GGTCTC 1 cut(s) 1165
Eco32I GATATC 3 cut(s) 20, 207, 909
Eco47I GGWCC 2 cut(s) 440, 1252
Eco47III AGCGCT 1 cut(s) 230
Eco53kI GAGCTC 1 cut(s) 732
Eco88I CYCGRG 1 cut(s) 974
EcoICRI GAGCTC 1 cut(s) 732
EcoRII CCWGG 1 cut(s) 277
EcoRV GATATC 3 cut(s) 20, 207, 909
EcoT14I CCWWGG 1 cut(s) 546
EcoT22I ATGCAT 1 cut(s) 1271
EcoT38I GRGCYC 1 cut(s) 734
EgeI GGCGCC 1 cut(s) 274
EheI GGCGCC 1 cut(s) 274
ErhI CCWWGG 1 cut(s) 546
FaeI CATG 5 cut(s) 88, 596, 770, 1217, 1298
FalI AAGNNNNNCTT 2 cut(s) 524, 556
FatI CATG 5 cut(s) 84, 592, 766, 1213, 1294
FauNDI CATATG 1 cut(s) 744
FblI GTMKAC 1 cut(s) 876
Fnu4HI GCNGC 7 cut(s) 166, 190, 334, 343, 651, 699, 917
FokI GGATG 2 cut(s) 563, 1311
FriOI GRGCYC 1 cut(s) 734
Fsp4HI GCNGC 7 cut(s) 166, 190, 334, 343, 651, 699, 917
FspBI CTAG 4 cut(s) 807, 816, 858, 941
GlaI GCGC 4 cut(s) 5, 230, 274, 839
GluI GCNGC 7 cut(s) 166, 190, 334, 343, 651, 699, 917
GsuI CTGGAG 1 cut(s) 1399
HaeII RGCGCY 3 cut(s) 232, 276, 841
HaeIII GGCC 1 cut(s) 393
HapII CCGG 2 cut(s) 482, 1255
HhaI GCGC 4 cut(s) 6, 231, 275, 840
Hin1I GRCGYC 1 cut(s) 273
Hin1II CATG 5 cut(s) 88, 596, 770, 1217, 1298
Hin6I GCGC 4 cut(s) 4, 229, 273, 838
HinP1I GCGC 4 cut(s) 4, 229, 273, 838
HincII GTYRAC 1 cut(s) 624
HindII GTYRAC 1 cut(s) 624
HindIII AAGCTT 1 cut(s) 869
HinfI GANTC 8 cut(s) 58, 101, 501, 755, 802, 827, 1371, 1412
HpaII CCGG 2 cut(s) 482, 1255
HphI GGTGA 4 cut(s) 173, 236, 382, 1162
Hpy166II GTNNAC 3 cut(s) 624, 877, 1153
Hpy188III TCNNGA 4 cut(s) 217, 482, 593, 1280
Hpy8I GTNNAC 3 cut(s) 624, 877, 1153
Hpy99I CGWCG 1 cut(s) 1180
HpyAV CCTTC 4 cut(s) 311, 373, 634, 879
HpyCH4III ACNGT 4 cut(s) 134, 444, 599, 1180
HpyF10VI GCNNNNNNNGC 8 cut(s) 123, 261, 270, 306, 339, 342, 405, 650
HpyF3I CTNAG 6 cut(s) 256, 285, 409, 892, 1119, 1359
Hsp92I GRCGYC 1 cut(s) 273
Hsp92II CATG 5 cut(s) 88, 596, 770, 1217, 1298
HspAI GCGC 4 cut(s) 4, 229, 273, 838
KasI GGCGCC 1 cut(s) 272
Kpn2I TCCGGA 1 cut(s) 481
Kzo9I GATC 6 cut(s) 65, 79, 288, 478, 553, 1302
LmnI GCTCC 3 cut(s) 173, 888, 901
Lsp1109I GCAGC 6 cut(s) 152, 176, 320, 354, 685, 928
LweI GCATC 3 cut(s) 337, 854, 1075
MaeI CTAG 4 cut(s) 807, 816, 858, 941
MaeIII GTNAC 5 cut(s) 242, 580, 686, 1109, 1257
MalI GATC 6 cut(s) 67, 81, 290, 480, 555, 1304
MboI GATC 6 cut(s) 65, 79, 288, 478, 553, 1302
MflI RGATCY 2 cut(s) 288, 478
MhlI GDGCHC 1 cut(s) 734
Mly113I GGCGCC 1 cut(s) 273
MlyI GAGTC 3 cut(s) 110, 1365, 1406
MmeI TCCRAC 3 cut(s) 175, 836, 925
Mph1103I ATGCAT 1 cut(s) 1271
MroI TCCGGA 1 cut(s) 481
MroXI GAANNNNTTC 2 cut(s) 801, 1056
MslI CAYNNNNRTG 3 cut(s) 87, 597, 1044
MspI CCGG 2 cut(s) 482, 1255
MspR9I CCNGG 1 cut(s) 279
MvaI CCWGG 1 cut(s) 279
MwoI GCNNNNNNNGC 8 cut(s) 123, 261, 270, 306, 339, 342, 405, 650
NarI GGCGCC 1 cut(s) 273
NdeI CATATG 1 cut(s) 744
NdeII GATC 6 cut(s) 65, 79, 288, 478, 553, 1302
NlaIII CATG 5 cut(s) 88, 596, 770, 1217, 1298
NlaIV GGNNCC 5 cut(s) 274, 480, 1037, 1086, 1386
NmuCI GTSAC 3 cut(s) 242, 686, 1109
NsiI ATGCAT 1 cut(s) 1271
PagI TCATGA 1 cut(s) 592
PdmI GAANNNNTTC 2 cut(s) 801, 1056
PfeI GAWTC 5 cut(s) 58, 501, 755, 802, 827
PkrI GCNGC 7 cut(s) 167, 191, 335, 344, 652, 700, 918
PleI GAGTC 3 cut(s) 109, 1365, 1406
PluTI GGCGCC 1 cut(s) 276
PpsI GAGTC 3 cut(s) 109, 1365, 1406
Psp124BI GAGCTC 1 cut(s) 734
Psp6I CCWGG 1 cut(s) 277
PspGI CCWGG 1 cut(s) 277
PspN4I GGNNCC 5 cut(s) 274, 480, 1037, 1086, 1386
PspPI GGNCC 2 cut(s) 440, 1252
PstNI CAGNNNCTG 1 cut(s) 758
PsuI RGATCY 2 cut(s) 288, 478
RseI CAYNNNNRTG 3 cut(s) 87, 597, 1044
SacI GAGCTC 1 cut(s) 734
SatI GCNGC 7 cut(s) 166, 190, 334, 343, 651, 699, 917
Sau3AI GATC 6 cut(s) 65, 79, 288, 478, 553, 1302
Sau96I GGNCC 2 cut(s) 440, 1252
SchI GAGTC 3 cut(s) 110, 1365, 1406
ScrFI CCNGG 1 cut(s) 279
SduI GDGCHC 1 cut(s) 734
SetI ASST 9 cut(s) 548, 734, 873, 893, 906, 1086, 1164, 1212, 1386
SfaNI GCATC 3 cut(s) 337, 854, 1075
SfcI CTRYAG 1 cut(s) 849
SfoI GGCGCC 1 cut(s) 274
SinI GGWCC 2 cut(s) 440, 1252
SmiMI CAYNNNNRTG 3 cut(s) 87, 597, 1044
SmlI CTYRAG 2 cut(s) 215, 880
SmoI CTYRAG 2 cut(s) 215, 880
SpeI ACTAGT 1 cut(s) 940
SsiI CCGC 3 cut(s) 264, 644, 651
SspDI GGCGCC 1 cut(s) 272
SspMI CTAG 4 cut(s) 807, 816, 858, 941
SstI GAGCTC 1 cut(s) 734
StyD4I CCNGG 1 cut(s) 277
StyI CCWWGG 1 cut(s) 546
TaaI ACNGT 4 cut(s) 134, 444, 599, 1180
TaqI TCGA 2 cut(s) 22, 474
TaqII GACCGA 1 cut(s) 1189
TauI GCSGC 1 cut(s) 653
TfiI GAWTC 5 cut(s) 58, 501, 755, 802, 827
TscAI CASTG 4 cut(s) 324, 372, 604, 1123
TseFI GTSAC 3 cut(s) 242, 686, 1109
TseI GCWGC 6 cut(s) 165, 189, 333, 342, 698, 916
Tsp45I GTSAC 3 cut(s) 242, 686, 1109
TspDTI ATGAA 9 cut(s) 27, 65, 101, 109, 690, 881, 984, 1230, 1265
TspGWI ACGGA 2 cut(s) 513, 652
TspRI CASTG 4 cut(s) 324, 372, 604, 1123
VpaK11BI GGWCC 2 cut(s) 440, 1252
XapI RAATTY 2 cut(s) 677, 1056
XmiI GTMKAC 1 cut(s) 876
XmnI GAANNNNTTC 2 cut(s) 801, 1056
XspI CTAG 4 cut(s) 807, 816, 858, 941
Zsp2I ATGCAT 1 cut(s) 1271
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.