Rh3DG088200

zinc finger CCCH domain-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr3D
OG0018453
Physical Location & Seq
Reverse (-)
6823833 .. 6825322
1490 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh3DG088200.1

Sequence Viewer

Length: 1413 bp
ATGAGTTCAATTCCGAGATATCGAAACTCATTGCGTTCATCTACCAATATGAAGAAGAATCAGAGATCAACGAACAAAGATCACATGAATGATTATTCAGAGTCAGAGGATTGGTGCTTCATCTGCAAAGACGGTGGGGTTCTAATTCTATGCGACCACGAGGGCTGCTCCAAAGCCTATCACCCTCGCTGCGTTGGAAAGAAGATATCTTTCCTCAAGAAACAAAAGCGCTGGATTTGTAGTCACCACTCCTGCTCAGCATGCGGTGTTGCCGCCTCTGGAACTAAGATCCTCTCTTGCCTTCTTTGCACTTATGCAGTGTGTGGTAGTTGCTGCAAAAGCAGCGATACTAATTCGGAGTTTGCAGTGGTGAGAGGGAAGGAGAAACTTGGCCTTTGCAATGACTGCTTAGGGATTGTTAGGCTTGCAGAAGAAAATGGACCGTATGGAGTAGATGGAAAGAAATTAGGCTTCGAGGATCCGGAAACATTTGAATACGGATTCAAAGAATGTTGGGAAATCATCAAGGAAAAGGAGGGCTTGACCTTGGATGATCTCTACTTCCCATATTCCAAAGGGGTAACAGATAGTCATGACAGTGAAGGCACAGAAACTCACAAGTTAACATTGAGCAAACGGAAGGCAGAAGCCGCAATTTGTGAGGATAACAAAGATGAATTTGGTAGTGACGATCTTGCTGCAAGCAACCACAAGAAGAAAAAATTAGTGAGCTCATCAGAGTATATGACATCAGAATCTGATTTGCATGAGGAAAATAACTCCGAGGAAAAAGAGGAAATGATTCCTAGTCCGACTAGGAATGACGAATCAGAGTGGCGCTTTGCATCTATAGTTGCTAGTAATATGAAGCTTGTCTACTTGAGAAGGAGCTTAGTGGAGGAGCTGATATCCAAGCAGCCTGATAGTTGGGAAAGAAAACTAGTTGGAAGTTATGTGAGAGTGGAAAATGAACCCGAGGACTATTTTCAGATAAAATCTTCTTACCAACTTTCACAAGTGAAAGGCATAATTAGGAACCACAACAATGGAGAAGAAATTCTCCTGCATCTGCTAACAAGAGAGGTTCCAATTTCTATGCTATCGGATTGTGACTTCACTGAGGAAGATTGTGAAGATTTGCAAGAAAGGGTGAACAATTACCTGATGAGGAGACCGACGGTTGTTGAAATTGAACAAAAAGCGAGAGAGCTACATGAAGATATAACAAAGGATTGGATTGAGAGAGAGTTGGTCCGGTTACTGAAATGCATTGATCACGAGGAATATCAGCATGGATGGATCAGCAGAGAGTTATGTGAGTATTATTTGCTAAAGCAACCATCTGAGCAGGAAAGACTCCGAAAAGAGGTGCCACAAGTCATTGCAGAGGACTTGGACTCCAGCAATTTATGA
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

470

Amino Acids

54.1

Weight (kDa)

5.26

Isoelectric Point (pI)

55.56

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PHD_NSD PF22908 38 - 83 3.5e-06 Histone-lysine N-methyltransferase NSD-like, PHD zinc finger
Plus-3 PF03126 288 - 384 9e-11 Plus-3 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) 1369
AccI GTMKAC 1 cut(s) 876
AccIII TCCGGA 1 cut(s) 481
AciI CCGC 3 cut(s) 264, 273, 651
AclWI GGATC 4 cut(s) 283, 473, 486, 1307
AcsI RAATTY 2 cut(s) 677, 1056
AfeI AGCGCT 1 cut(s) 230
AfiI CCNNNNNNNGG 1 cut(s) 1366
AgsI TTSAA 5 cut(s) 9, 494, 505, 1187, 1193
AhlI ACTAGT 1 cut(s) 940
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, 1307
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 2 cut(s) 231, 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 1 cut(s) 1369
BanII GRGCYC 1 cut(s) 734
BarI GAAGNNNNNNTAC 2 cut(s) 860, 892
BauI CACGAG 2 cut(s) 158, 1277
Bbv12I GWGCWC 1 cut(s) 734
BbvI GCAGC 6 cut(s) 152, 176, 320, 354, 685, 928
BccI CCATC 3 cut(s) 449, 1290, 1348
BcgI CGANNNNNNTGC 2 cut(s) 680, 714
BclI TGATCA 1 cut(s) 1273
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 2 cut(s) 232, 841
BisI GCNGC 8 cut(s) 166, 190, 273, 334, 343, 651, 699, 917
BlpI GCTNAGC 1 cut(s) 256
BlsI GCNGC 8 cut(s) 167, 191, 274, 335, 344, 652, 700, 918
Bme18I GGWCC 2 cut(s) 440, 1252
BmeT110I CYCGRG 1 cut(s) 974
BmgT120I GGNCC 2 cut(s) 440, 1252
BmiI GGNNCC 4 cut(s) 480, 1037, 1086, 1371
BmsI GCATC 2 cut(s) 854, 1075
BplI GAGNNNNNCTC 2 cut(s) 152, 184
BpmI CTGGAG 1 cut(s) 1384
Bpu10I CCTNAGC 1 cut(s) 409
Bpu1102I GCTNAGC 1 cut(s) 256
BpuEI CTTGAG 2 cut(s) 200, 901
BsaI GGTCTC 1 cut(s) 1165
BsaJI CCNNGG 3 cut(s) 546, 783, 975
BsaWI WCCGGW 2 cut(s) 481, 1254
BsaXI ACNNNNNCTCC 2 cut(s) 1382, 1412
Bsc4I CCNNNNNNNGG 1 cut(s) 1366
Bse3DI GCAATG 3 cut(s) 29, 406, 1380
BseAI TCCGGA 1 cut(s) 481
BseDI CCNNGG 3 cut(s) 546, 783, 975
BseGI GGATG 2 cut(s) 556, 1301
BseLI CCNNNNNNNGG 1 cut(s) 1366
BseMI GCAATG 3 cut(s) 29, 406, 1380
BseMII CTCAG 3 cut(s) 270, 1110, 1335
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 1 cut(s) 1369
BsiHKAI GWGCWC 1 cut(s) 734
BsiHKCI CYCGRG 1 cut(s) 974
BsiSI CCGG 2 cut(s) 482, 1255
BslI CCNNNNNNNGG 1 cut(s) 1366
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 8 cut(s) 65, 79, 288, 478, 553, 691, 1273, 1299
Bsp1720I GCTNAGC 1 cut(s) 256
BspACI CCGC 3 cut(s) 264, 273, 651
BspANI GGCC 1 cut(s) 393
BspCNI CTCAG 3 cut(s) 269, 1111, 1336
BspEI TCCGGA 1 cut(s) 481
BspHI TCATGA 1 cut(s) 592
BspLI GGNNCC 4 cut(s) 480, 1037, 1086, 1371
BspPI GGATC 4 cut(s) 283, 473, 486, 1307
BspT107I GGYRCC 1 cut(s) 1369
BspTNI GGTCTC 1 cut(s) 1165
BsrDI GCAATG 3 cut(s) 29, 406, 1380
BssECI CCNNGG 3 cut(s) 546, 783, 975
BssMI GATC 8 cut(s) 65, 79, 288, 478, 553, 691, 1273, 1299
BssSI CACGAG 2 cut(s) 158, 1277
BssT1I CCWWGG 1 cut(s) 546
Bst2BI CACGAG 2 cut(s) 158, 1277
Bst4CI ACNGT 4 cut(s) 134, 444, 599, 1180
BstAPI GCANNNNNTGC 1 cut(s) 405
BstC8I GCNNGC 3 cut(s) 262, 426, 703
BstDEI CTNAG 6 cut(s) 256, 285, 409, 892, 1119, 1344
BstF5I GGATG 2 cut(s) 556, 1301
BstH2I RGCGCY 2 cut(s) 232, 841
BstHHI GCGC 2 cut(s) 231, 840
BstKTI GATC 8 cut(s) 68, 82, 291, 481, 556, 694, 1276, 1302
BstMAI GTCTC 1 cut(s) 1165
BstMBI GATC 8 cut(s) 65, 79, 288, 478, 553, 691, 1273, 1299
BstMWI GCNNNNNNNGC 7 cut(s) 123, 261, 306, 339, 342, 405, 650
BstNSI RCATGY 1 cut(s) 264
BstSFI CTRYAG 1 cut(s) 849
BstV1I GCAGC 6 cut(s) 152, 176, 320, 354, 685, 928
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
BtsCI GGATG 2 cut(s) 556, 1301
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 2 cut(s) 231, 840
Cfr13I GGNCC 2 cut(s) 440, 1252
CspCI CAANNNNNGTGG 2 cut(s) 115, 150
CviAII CATG 6 cut(s) 85, 261, 593, 767, 1214, 1292
DdeI CTNAG 6 cut(s) 256, 285, 409, 892, 1119, 1344
DpnI GATC 8 cut(s) 67, 81, 290, 480, 555, 693, 1275, 1301
DpnII GATC 8 cut(s) 65, 79, 288, 478, 553, 691, 1273, 1299
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
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
ErhI CCWWGG 1 cut(s) 546
FaeI CATG 6 cut(s) 88, 264, 596, 770, 1217, 1295
FalI AAGNNNNNCTT 2 cut(s) 524, 556
FatI CATG 6 cut(s) 84, 260, 592, 766, 1213, 1291
FbaI TGATCA 1 cut(s) 1273
FblI GTMKAC 1 cut(s) 876
Fnu4HI GCNGC 8 cut(s) 166, 190, 273, 334, 343, 651, 699, 917
FokI GGATG 2 cut(s) 563, 1308
FriOI GRGCYC 1 cut(s) 734
Fsp4HI GCNGC 8 cut(s) 166, 190, 273, 334, 343, 651, 699, 917
FspBI CTAG 4 cut(s) 807, 816, 858, 941
GlaI GCGC 2 cut(s) 230, 839
GluI GCNGC 8 cut(s) 166, 190, 273, 334, 343, 651, 699, 917
GsuI CTGGAG 1 cut(s) 1384
HaeII RGCGCY 2 cut(s) 232, 841
HaeIII GGCC 1 cut(s) 393
HapII CCGG 2 cut(s) 482, 1255
HhaI GCGC 2 cut(s) 231, 840
Hin1II CATG 6 cut(s) 88, 264, 596, 770, 1217, 1295
Hin6I GCGC 2 cut(s) 229, 838
HinP1I GCGC 2 cut(s) 229, 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, 1356, 1397
HpaI GTTAAC 1 cut(s) 624
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 5 cut(s) 217, 279, 482, 593, 1277
Hpy8I GTNNAC 3 cut(s) 624, 877, 1153
Hpy99I CGWCG 1 cut(s) 1180
HpyAV CCTTC 5 cut(s) 311, 373, 596, 634, 879
HpyCH4III ACNGT 4 cut(s) 134, 444, 599, 1180
HpyF10VI GCNNNNNNNGC 7 cut(s) 123, 261, 306, 339, 342, 405, 650
HpyF3I CTNAG 6 cut(s) 256, 285, 409, 892, 1119, 1344
Hsp92II CATG 6 cut(s) 88, 264, 596, 770, 1217, 1295
HspAI GCGC 2 cut(s) 229, 838
Kpn2I TCCGGA 1 cut(s) 481
Ksp22I TGATCA 1 cut(s) 1273
KspAI GTTAAC 1 cut(s) 624
Kzo9I GATC 8 cut(s) 65, 79, 288, 478, 553, 691, 1273, 1299
LmnI GCTCC 3 cut(s) 173, 888, 901
LpnPI CCDG 9 cut(s) 217, 264, 265, 495, 933, 1076, 1175, 1268, 1334
Lsp1109I GCAGC 6 cut(s) 152, 176, 320, 354, 685, 928
LweI GCATC 2 cut(s) 854, 1075
MaeI CTAG 4 cut(s) 807, 816, 858, 941
MaeIII GTNAC 5 cut(s) 242, 580, 686, 1109, 1257
MalI GATC 8 cut(s) 67, 81, 290, 480, 555, 693, 1275, 1301
MboI GATC 8 cut(s) 65, 79, 288, 478, 553, 691, 1273, 1299
MflI RGATCY 2 cut(s) 288, 478
MhlI GDGCHC 1 cut(s) 734
MlyI GAGTC 3 cut(s) 110, 1350, 1391
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
MseI TTAA 1 cut(s) 623
MslI CAYNNNNRTG 3 cut(s) 87, 597, 1044
MspI CCGG 2 cut(s) 482, 1255
MwoI GCNNNNNNNGC 7 cut(s) 123, 261, 306, 339, 342, 405, 650
NdeII GATC 8 cut(s) 65, 79, 288, 478, 553, 691, 1273, 1299
NlaIII CATG 6 cut(s) 88, 264, 596, 770, 1217, 1295
NlaIV GGNNCC 4 cut(s) 480, 1037, 1086, 1371
NmuCI GTSAC 3 cut(s) 242, 686, 1109
NsiI ATGCAT 1 cut(s) 1271
NspI RCATGY 1 cut(s) 264
PaeI GCATGC 1 cut(s) 264
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 8 cut(s) 167, 191, 274, 335, 344, 652, 700, 918
PleI GAGTC 3 cut(s) 109, 1350, 1391
PpsI GAGTC 3 cut(s) 109, 1350, 1391
Psp124BI GAGCTC 1 cut(s) 734
PspN4I GGNNCC 4 cut(s) 480, 1037, 1086, 1371
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
SaqAI TTAA 1 cut(s) 623
SatI GCNGC 8 cut(s) 166, 190, 273, 334, 343, 651, 699, 917
Sau3AI GATC 8 cut(s) 65, 79, 288, 478, 553, 691, 1273, 1299
Sau96I GGNCC 2 cut(s) 440, 1252
SchI GAGTC 3 cut(s) 110, 1350, 1391
SduI GDGCHC 1 cut(s) 734
SetI ASST 9 cut(s) 548, 734, 873, 893, 906, 1086, 1164, 1212, 1371
SfaNI GCATC 2 cut(s) 854, 1075
SfcI CTRYAG 1 cut(s) 849
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
SphI GCATGC 1 cut(s) 264
SsiI CCGC 3 cut(s) 264, 273, 651
SspMI CTAG 4 cut(s) 807, 816, 858, 941
SstI GAGCTC 1 cut(s) 734
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 2 cut(s) 275, 653
TfiI GAWTC 5 cut(s) 58, 501, 755, 802, 827
Tru1I TTAA 1 cut(s) 623
Tru9I TTAA 1 cut(s) 623
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 8 cut(s) 27, 65, 101, 109, 690, 881, 984, 1230
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
XceI RCATGY 1 cut(s) 264
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.