RchiOBHm_Chr3g0458001

zinc finger CCCH domain-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
3
OG0018453
Physical Location & Seq
Reverse (-)
6875525 .. 6876865
1341 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ42471

Sequence Viewer

Length: 1341 bp
ATGAATGATTATTCAGAGTCAGAGGATTGGTGCTTCATCTGCAAAGACGGTGGGGTTCTAATTCTATGCGACCACGAGGGCTGCTCCAAAGCCTATCACCCTCGCTGCGTTGGAAAGAAGATATCTTTCCTCAAGAAACAAAAGCGCTGGATTTGTAGTCACCACTCCTGCTCAGCATGCGGTGTTGCCGCCTCTGGAACTAAGATCCTCTCTTGCCTTCTTTGCACTTATGCAGTGTGTGGTAGTTGCTGCAAAAGCAGCGATACTAATTCGGAGTTTGCAGTGGTGAGAGGGAAGGAGAAACTTGGCCTTTGCAATGACTGCTTAGGGATTGTTAGGCTTGCAGAAGAAAATGGACCTTATGGAGTAGATGGAAAGAAATTAGGCTTCGAGGATCCGGAAACATTTGAATACGGATTCAAAGAATGTTGGGAAAACATCAAGGAAAAGGAGGGCTTGACCTTGGATGATCTCTACTTCCCATATTCCAAAGGGGTAACAGATAGTCATGACAGTGAAGGCACAGAAACTCACAAGTTAACATTGAGCAAACGGAAGGCAGAAGCCGCAATTTGTGAGGATAACAAAGATGAATTTGGTAGTGACGATCTTGCTGCAAGCAACCACAAGAAGAAAAAATTAGTGAGCTCATCAGAGTATATGACATCAGAATCTGATTTGCATGAGGAAAATAACTCCGAGGAAAAAGAGGAAATGATTCCTAGTCCGACTAGGAATGACGAATCAGAGTGGCGCTTTGCATCTATAGTTGCTAGTAATATGAAGCTTGTCTACTTGAGAAGGAGCTTAGTGGAGGAGCTGATATCCAAGCAGCCTGATAGTTGGGAAAGAAAACTAGTTGGAAGTTATGTGAGAGTGGAAAATGAACCCGAGGACTATTTTCAGATAAAATCTTCTTACCAACTTTCACAAGTGAAAGGCATAATTAGGAACCACAACAATGGAGAAGAAATTCTCCTGCATCTGCTAACAAGAGAGGTTCCAATTTATATGCTATCGGATTGTGACTTCACTGAGGAAGATTGTGAAGATTTGCAAGAAAGGGTGAAAAATTACCTGATGAGGAGACCGACGGTTGTTGAAATTGAACAAAAAGCGAGAGAGCTACATGAAGATATAACAAAGGATTGGATTGAGAGAGAGTTGGTCCGGTTACTGAAATGCATTGATCACGAGGAATATCAGCATGGATGGATCAGCAGAGAGTTTTGTGAGTATTTGAAACAGAGAAATATGCTAAAGCAACCATCTGAGCAGGAAAGACTCCGAAAAGAGGTGCCACAAGTCATTTCAGAGGACTTGGACTCCAGCAATTTATGA
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

446

Amino Acids

51.41

Weight (kDa)

5.1

Isoelectric Point (pI)

56.82

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PHD_NSD PF22908 10 - 55 3.2e-06 Histone-lysine N-methyltransferase NSD-like, PHD zinc finger
Plus-3 PF03126 260 - 356 3.2e-10 Plus-3 domain
NERD_plant PF25980 378 - 429 2.3e-09 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 1 cut(s) 1297
AccI GTMKAC 1 cut(s) 792
AccIII TCCGGA 1 cut(s) 397
AciI CCGC 3 cut(s) 180, 189, 567
AclWI GGATC 4 cut(s) 199, 389, 402, 1223
AcsI RAATTY 2 cut(s) 593, 972
AfeI AGCGCT 1 cut(s) 146
AfiI CCNNNNNNNGG 1 cut(s) 1294
AgsI TTSAA 5 cut(s) 410, 421, 1103, 1109, 1243
AhlI ACTAGT 1 cut(s) 856
AluBI AGCT 5 cut(s) 648, 787, 807, 820, 1126
AluI AGCT 5 cut(s) 648, 787, 807, 820, 1126
Alw21I GWGCWC 1 cut(s) 650
Alw26I GTCTC 1 cut(s) 1081
AlwI GGATC 4 cut(s) 199, 389, 402, 1223
AlwNI CAGNNNCTG 1 cut(s) 674
Ama87I CYCGRG 1 cut(s) 890
Aor13HI TCCGGA 1 cut(s) 397
Aor51HI AGCGCT 1 cut(s) 146
AoxI GGCC 1 cut(s) 307
ApeKI GCWGC 6 cut(s) 81, 105, 249, 258, 614, 832
ApoI RAATTY 2 cut(s) 593, 972
Asp700I GAANNNNTTC 2 cut(s) 717, 972
AspLEI GCGC 2 cut(s) 147, 756
AspS9I GGNCC 2 cut(s) 356, 1168
AsuHPI GGTGA 4 cut(s) 89, 152, 298, 1078
AvaI CYCGRG 1 cut(s) 890
AvaII GGWCC 2 cut(s) 356, 1168
BamHI GGATCC 1 cut(s) 394
BanI GGYRCC 1 cut(s) 1297
BanII GRGCYC 1 cut(s) 650
BarI GAAGNNNNNNTAC 2 cut(s) 776, 808
BauI CACGAG 2 cut(s) 74, 1193
Bbv12I GWGCWC 1 cut(s) 650
BbvI GCAGC 6 cut(s) 68, 92, 236, 270, 601, 844
BccI CCATC 3 cut(s) 365, 1206, 1276
BcgI CGANNNNNNTGC 2 cut(s) 596, 630
BclI TGATCA 1 cut(s) 1189
BcoDI GTCTC 1 cut(s) 1081
BcuI ACTAGT 1 cut(s) 856
BfaI CTAG 4 cut(s) 723, 732, 774, 857
BfmI CTRYAG 1 cut(s) 765
BfoI RGCGCY 2 cut(s) 148, 757
BisI GCNGC 8 cut(s) 82, 106, 189, 250, 259, 567, 615, 833
BlpI GCTNAGC 1 cut(s) 172
BlsI GCNGC 8 cut(s) 83, 107, 190, 251, 260, 568, 616, 834
Bme18I GGWCC 2 cut(s) 356, 1168
BmeT110I CYCGRG 1 cut(s) 890
BmgT120I GGNCC 2 cut(s) 356, 1168
BmiI GGNNCC 4 cut(s) 396, 953, 1002, 1299
BmsI GCATC 2 cut(s) 770, 991
BplI GAGNNNNNCTC 2 cut(s) 68, 100
BpmI CTGGAG 1 cut(s) 1312
Bpu10I CCTNAGC 1 cut(s) 325
Bpu1102I GCTNAGC 1 cut(s) 172
BpuEI CTTGAG 2 cut(s) 116, 817
BsaI GGTCTC 1 cut(s) 1081
BsaJI CCNNGG 3 cut(s) 462, 699, 891
BsaWI WCCGGW 2 cut(s) 397, 1170
BsaXI ACNNNNNCTCC 2 cut(s) 1310, 1340
Bsc4I CCNNNNNNNGG 1 cut(s) 1294
Bse3DI GCAATG 1 cut(s) 322
BseAI TCCGGA 1 cut(s) 397
BseDI CCNNGG 3 cut(s) 462, 699, 891
BseGI GGATG 2 cut(s) 472, 1217
BseLI CCNNNNNNNGG 1 cut(s) 1294
BseMI GCAATG 1 cut(s) 322
BseMII CTCAG 3 cut(s) 186, 1026, 1263
BseRI GAGGAG 2 cut(s) 830, 1099
BseXI GCAGC 6 cut(s) 68, 92, 236, 270, 601, 844
BshFI GGCC 1 cut(s) 309
BshNI GGYRCC 1 cut(s) 1297
BsiHKAI GWGCWC 1 cut(s) 650
BsiHKCI CYCGRG 1 cut(s) 890
BsiSI CCGG 2 cut(s) 398, 1171
BslI CCNNNNNNNGG 1 cut(s) 1294
BsmAI GTCTC 1 cut(s) 1081
BsnI GGCC 1 cut(s) 309
Bso31I GGTCTC 1 cut(s) 1081
BsoBI CYCGRG 1 cut(s) 890
Bsp1286I GDGCHC 1 cut(s) 650
Bsp13I TCCGGA 1 cut(s) 397
Bsp143I GATC 6 cut(s) 204, 394, 469, 607, 1189, 1215
Bsp1720I GCTNAGC 1 cut(s) 172
BspACI CCGC 3 cut(s) 180, 189, 567
BspANI GGCC 1 cut(s) 309
BspCNI CTCAG 3 cut(s) 185, 1027, 1264
BspEI TCCGGA 1 cut(s) 397
BspHI TCATGA 1 cut(s) 508
BspLI GGNNCC 4 cut(s) 396, 953, 1002, 1299
BspPI GGATC 4 cut(s) 199, 389, 402, 1223
BspT107I GGYRCC 1 cut(s) 1297
BspTNI GGTCTC 1 cut(s) 1081
BsrDI GCAATG 1 cut(s) 322
BssECI CCNNGG 3 cut(s) 462, 699, 891
BssMI GATC 6 cut(s) 204, 394, 469, 607, 1189, 1215
BssSI CACGAG 2 cut(s) 74, 1193
BssT1I CCWWGG 1 cut(s) 462
Bst2BI CACGAG 2 cut(s) 74, 1193
Bst4CI ACNGT 3 cut(s) 50, 515, 1096
BstAPI GCANNNNNTGC 1 cut(s) 321
BstC8I GCNNGC 3 cut(s) 178, 342, 619
BstDEI CTNAG 6 cut(s) 172, 201, 325, 808, 1035, 1272
BstF5I GGATG 2 cut(s) 472, 1217
BstH2I RGCGCY 2 cut(s) 148, 757
BstHHI GCGC 2 cut(s) 147, 756
BstKTI GATC 6 cut(s) 207, 397, 472, 610, 1192, 1218
BstMAI GTCTC 1 cut(s) 1081
BstMBI GATC 6 cut(s) 204, 394, 469, 607, 1189, 1215
BstMWI GCNNNNNNNGC 7 cut(s) 39, 177, 222, 255, 258, 321, 566
BstNSI RCATGY 1 cut(s) 180
BstSFI CTRYAG 1 cut(s) 765
BstV1I GCAGC 6 cut(s) 68, 92, 236, 270, 601, 844
BstX2I RGATCY 2 cut(s) 204, 394
BstXI CCANNNNNNTGG 1 cut(s) 962
BstYI RGATCY 2 cut(s) 204, 394
BsuRI GGCC 1 cut(s) 309
BtsCI GGATG 2 cut(s) 472, 1217
BtsI GCAGTG 2 cut(s) 240, 288
BtsIMutI CAGTG 4 cut(s) 240, 288, 520, 1032
Cac8I GCNNGC 3 cut(s) 178, 342, 619
CaiI CAGNNNCTG 1 cut(s) 674
CciI TCATGA 1 cut(s) 508
CfoI GCGC 2 cut(s) 147, 756
Cfr13I GGNCC 2 cut(s) 356, 1168
CspCI CAANNNNNGTGG 2 cut(s) 31, 66
CviAII CATG 5 cut(s) 177, 509, 683, 1130, 1208
DdeI CTNAG 6 cut(s) 172, 201, 325, 808, 1035, 1272
DpnI GATC 6 cut(s) 206, 396, 471, 609, 1191, 1217
DpnII GATC 6 cut(s) 204, 394, 469, 607, 1189, 1215
Ecl136II GAGCTC 1 cut(s) 648
Eco130I CCWWGG 1 cut(s) 462
Eco24I GRGCYC 1 cut(s) 650
Eco31I GGTCTC 1 cut(s) 1081
Eco32I GATATC 2 cut(s) 123, 825
Eco47I GGWCC 2 cut(s) 356, 1168
Eco47III AGCGCT 1 cut(s) 146
Eco53kI GAGCTC 1 cut(s) 648
Eco88I CYCGRG 1 cut(s) 890
EcoICRI GAGCTC 1 cut(s) 648
EcoRV GATATC 2 cut(s) 123, 825
EcoT14I CCWWGG 1 cut(s) 462
EcoT22I ATGCAT 1 cut(s) 1187
EcoT38I GRGCYC 1 cut(s) 650
ErhI CCWWGG 1 cut(s) 462
FaeI CATG 5 cut(s) 180, 512, 686, 1133, 1211
FalI AAGNNNNNCTT 2 cut(s) 440, 472
FatI CATG 5 cut(s) 176, 508, 682, 1129, 1207
FbaI TGATCA 1 cut(s) 1189
FblI GTMKAC 1 cut(s) 792
Fnu4HI GCNGC 8 cut(s) 82, 106, 189, 250, 259, 567, 615, 833
FokI GGATG 2 cut(s) 479, 1224
FriOI GRGCYC 1 cut(s) 650
Fsp4HI GCNGC 8 cut(s) 82, 106, 189, 250, 259, 567, 615, 833
FspBI CTAG 4 cut(s) 723, 732, 774, 857
GlaI GCGC 2 cut(s) 146, 755
GluI GCNGC 8 cut(s) 82, 106, 189, 250, 259, 567, 615, 833
GsuI CTGGAG 1 cut(s) 1312
HaeII RGCGCY 2 cut(s) 148, 757
HaeIII GGCC 1 cut(s) 309
HapII CCGG 2 cut(s) 398, 1171
HhaI GCGC 2 cut(s) 147, 756
Hin1II CATG 5 cut(s) 180, 512, 686, 1133, 1211
Hin6I GCGC 2 cut(s) 145, 754
HinP1I GCGC 2 cut(s) 145, 754
HincII GTYRAC 1 cut(s) 540
HindII GTYRAC 1 cut(s) 540
HindIII AAGCTT 1 cut(s) 785
HinfI GANTC 7 cut(s) 17, 417, 671, 718, 743, 1284, 1325
HpaI GTTAAC 1 cut(s) 540
HpaII CCGG 2 cut(s) 398, 1171
HphI GGTGA 4 cut(s) 89, 152, 298, 1078
Hpy166II GTNNAC 2 cut(s) 540, 793
Hpy188III TCNNGA 5 cut(s) 133, 195, 398, 509, 1193
Hpy8I GTNNAC 2 cut(s) 540, 793
Hpy99I CGWCG 1 cut(s) 1096
HpyAV CCTTC 5 cut(s) 227, 289, 512, 550, 795
HpyCH4III ACNGT 3 cut(s) 50, 515, 1096
HpyF10VI GCNNNNNNNGC 7 cut(s) 39, 177, 222, 255, 258, 321, 566
HpyF3I CTNAG 6 cut(s) 172, 201, 325, 808, 1035, 1272
Hsp92II CATG 5 cut(s) 180, 512, 686, 1133, 1211
HspAI GCGC 2 cut(s) 145, 754
Kpn2I TCCGGA 1 cut(s) 397
Ksp22I TGATCA 1 cut(s) 1189
KspAI GTTAAC 1 cut(s) 540
Kzo9I GATC 6 cut(s) 204, 394, 469, 607, 1189, 1215
LmnI GCTCC 3 cut(s) 89, 804, 817
LpnPI CCDG 9 cut(s) 133, 180, 181, 411, 849, 992, 1091, 1184, 1262
Lsp1109I GCAGC 6 cut(s) 68, 92, 236, 270, 601, 844
LweI GCATC 2 cut(s) 770, 991
MaeI CTAG 4 cut(s) 723, 732, 774, 857
MaeIII GTNAC 5 cut(s) 158, 496, 602, 1025, 1173
MalI GATC 6 cut(s) 206, 396, 471, 609, 1191, 1217
MboI GATC 6 cut(s) 204, 394, 469, 607, 1189, 1215
MboII GAAGA 8 cut(s) 130, 359, 643, 906, 980, 1052, 1061, 1145
MflI RGATCY 2 cut(s) 204, 394
MhlI GDGCHC 1 cut(s) 650
MlyI GAGTC 3 cut(s) 26, 1278, 1319
MmeI TCCRAC 3 cut(s) 91, 752, 841
Mph1103I ATGCAT 1 cut(s) 1187
MroI TCCGGA 1 cut(s) 397
MroXI GAANNNNTTC 2 cut(s) 717, 972
MseI TTAA 1 cut(s) 539
MslI CAYNNNNRTG 2 cut(s) 513, 960
MspI CCGG 2 cut(s) 398, 1171
MwoI GCNNNNNNNGC 7 cut(s) 39, 177, 222, 255, 258, 321, 566
NdeII GATC 6 cut(s) 204, 394, 469, 607, 1189, 1215
NlaIII CATG 5 cut(s) 180, 512, 686, 1133, 1211
NlaIV GGNNCC 4 cut(s) 396, 953, 1002, 1299
NmuCI GTSAC 3 cut(s) 158, 602, 1025
NsiI ATGCAT 1 cut(s) 1187
NspI RCATGY 1 cut(s) 180
PaeI GCATGC 1 cut(s) 180
PagI TCATGA 1 cut(s) 508
PdmI GAANNNNTTC 2 cut(s) 717, 972
PfeI GAWTC 4 cut(s) 417, 671, 718, 743
PkrI GCNGC 8 cut(s) 83, 107, 190, 251, 260, 568, 616, 834
PleI GAGTC 3 cut(s) 25, 1278, 1319
PpsI GAGTC 3 cut(s) 25, 1278, 1319
Psp124BI GAGCTC 1 cut(s) 650
PspN4I GGNNCC 4 cut(s) 396, 953, 1002, 1299
PspPI GGNCC 2 cut(s) 356, 1168
PstNI CAGNNNCTG 1 cut(s) 674
PsuI RGATCY 2 cut(s) 204, 394
RseI CAYNNNNRTG 2 cut(s) 513, 960
SacI GAGCTC 1 cut(s) 650
SaqAI TTAA 1 cut(s) 539
SatI GCNGC 8 cut(s) 82, 106, 189, 250, 259, 567, 615, 833
Sau3AI GATC 6 cut(s) 204, 394, 469, 607, 1189, 1215
Sau96I GGNCC 2 cut(s) 356, 1168
SchI GAGTC 3 cut(s) 26, 1278, 1319
SduI GDGCHC 1 cut(s) 650
SfaNI GCATC 2 cut(s) 770, 991
SfcI CTRYAG 1 cut(s) 765
SinI GGWCC 2 cut(s) 356, 1168
SmiMI CAYNNNNRTG 2 cut(s) 513, 960
SmlI CTYRAG 2 cut(s) 131, 796
SmoI CTYRAG 2 cut(s) 131, 796
SpeI ACTAGT 1 cut(s) 856
SphI GCATGC 1 cut(s) 180
SsiI CCGC 3 cut(s) 180, 189, 567
SspMI CTAG 4 cut(s) 723, 732, 774, 857
SstI GAGCTC 1 cut(s) 650
StyI CCWWGG 1 cut(s) 462
TaaI ACNGT 3 cut(s) 50, 515, 1096
TaqI TCGA 1 cut(s) 390
TaqII GACCGA 1 cut(s) 1105
TauI GCSGC 2 cut(s) 191, 569
TfiI GAWTC 4 cut(s) 417, 671, 718, 743
Tru1I TTAA 1 cut(s) 539
Tru9I TTAA 1 cut(s) 539
TscAI CASTG 4 cut(s) 240, 288, 520, 1039
TseFI GTSAC 3 cut(s) 158, 602, 1025
TseI GCWGC 6 cut(s) 81, 105, 249, 258, 614, 832
Tsp45I GTSAC 3 cut(s) 158, 602, 1025
TspDTI ATGAA 6 cut(s) 17, 25, 606, 797, 900, 1146
TspGWI ACGGA 2 cut(s) 429, 568
TspRI CASTG 4 cut(s) 240, 288, 520, 1039
VpaK11BI GGWCC 2 cut(s) 356, 1168
XapI RAATTY 2 cut(s) 593, 972
XceI RCATGY 1 cut(s) 180
XmiI GTMKAC 1 cut(s) 792
XmnI GAANNNNTTC 2 cut(s) 717, 972
XspI CTAG 4 cut(s) 723, 732, 774, 857
Zsp2I ATGCAT 1 cut(s) 1187
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.