Rroxscaffold_6G00406840

zinc finger CCCH domain-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000006
OG0017332
Physical Location & Seq
Forward (+)
29392566 .. 29396733
4168 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_6G00406840.1

Sequence Viewer

Length: 1179 bp
ATGGATGACTACTCAGAGGATTGGTGCTTCGTCTGCAAAGATGGTGGTGTTCTAATGCTTTGCGACCATGAAGGCTGCTCCAAAGTATATCATCCTAAATGTGTGGGAAGGAAGAATTCCTTCCTCAAAAGCAAGAAGCTCTGGACTTGTAGCAAGCATTCCTGTTATGTGTGCCGTAACAATGGATCAACCACCTCAGCAGCAATTAGTTTCTCATGCCTTTGTTGTCCGTACGCATTATGTGACCCTTGCTACACAGCAAGTACTACTACTAGTGGTGCTGAGTTTTCACTGCTAAGAGGGAAGGATAAGTCGGGCCTTTGCAATGACTGTTTAGAAGTTGTTAGGCTTGCAGAAGCAAACTCGGAGTATGGACCAGATGGAGAGAAACTAGACTTCAAAAACCATGACACATTTGAATGCCGACTCAAAGAGCATTGGGAATTCATAAAGAAAAACGAGGGCTTGACTTTAAATGATGTCTATTCCTCAAATGTTGGGAAAAGGAAAAGGCTAGACAAATTTTTAGGATGTTCAAAAGCTCTGCTTCAGTTCCATAACTATATGAAACCTGATGCAAAGAAACTGCGGACATCTGCTGTTAGAGATCATGGGCTGAGAGGGATCAAAACAGAGAGTGTTGAGAGTTGGAAGTTTGCTATTTTCCTAGTAGTTTATGCATGCTCAAGGCACCCTCCGGATGGTGCTTTTCATCAAAGAGTTGAGAATCTTGTTCTTTTGGCAGAGAGCCGGTGTGTTTGGGAGGTAGAGAAATCAAAGTGGCTTTCCCATGGAATTCACCTCAAGCGGGTGCGTTGTGATTCGATCGAATTATGCTCGGAAGGCACATTTTGTGGAAGGGATAGCAAAGATTCTTTCCAGCATATGTGTATCAAAGAAAGAGAGCCATATATTATCCGAAAACCGATTGAGGTGATTGAAGTGGCCGTCCCCTTGATCCCTATAGTTGTGCACCTAAGGGATACAACTATGCAAAAACTAGGTGCCGCCGTTCCCGCAACCGCATCAGCCATGGGACGGTTGGAGAATGTGACCCTCGCTTACTCAAATCCCTACTTGCTTACACCTTTTTCATGGAGATTGCCTCACCAAGTGGTCGTCGGGGACCAACTTGTGTCTAGTGTACCAGTGCCCATTAGAGCAAATCCACCGGTGTAG
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

392

Amino Acids

44.14

Weight (kDa)

8.52

Isoelectric Point (pI)

32.33

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PHD_NSD PF22908 8 - 53 9.8e-06 Histone-lysine N-methyltransferase NSD-like, PHD zinc finger
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0017332)

Species Orthologous Gene IDs
fragaria_vesca FvH4_6g19471
rosa_laevigata RLG00000023894 RLG00000023895
rosa_multiflora Rmu_sc0004848.1_g000006
rosa_roxburghii Rroxscaffold_6G00406840
rosa_rugosa Rorug03G0144000
rosa_samantha Rh3AG193700 Rh3AG193800 Rh3BG223500 Rh3BG223600 Rh3CG218400 Rh3CG218500 Rh3DG219500

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 2 cut(s) 690, 1004
AccIII TCCGGA 1 cut(s) 697
AciI CCGC 5 cut(s) 589, 808, 1008, 1017, 1023
AclWI GGATC 3 cut(s) 193, 632, 952
AcoI YGGCCR 1 cut(s) 945
AcsI RAATTY 4 cut(s) 115, 443, 521, 795
AcuI CTGAAG 1 cut(s) 533
AdeI CACNNNGTG 1 cut(s) 1114
AfaI GTAC 3 cut(s) 233, 265, 1146
AfiI CCNNNNNNNGG 3 cut(s) 701, 808, 1038
AgeI ACCGGT 1 cut(s) 1171
AgsI TTSAA 4 cut(s) 400, 419, 537, 941
AhlI ACTAGT 1 cut(s) 272
AluBI AGCT 2 cut(s) 139, 542
AluI AGCT 2 cut(s) 139, 542
Alw21I GWGCWC 1 cut(s) 975
Alw44I GTGCAC 1 cut(s) 971
AlwI GGATC 3 cut(s) 193, 632, 952
Aor13HI TCCGGA 1 cut(s) 697
AoxI GGCC 2 cut(s) 316, 945
ApaLI GTGCAC 1 cut(s) 971
ApeKI GCWGC 2 cut(s) 75, 200
ApoI RAATTY 4 cut(s) 115, 443, 521, 795
AsiGI ACCGGT 1 cut(s) 1171
Asp700I GAANNNNTTC 1 cut(s) 119
AspS9I GGNCC 3 cut(s) 316, 374, 1126
AsuHPI GGTGA 3 cut(s) 791, 946, 1100
AvaII GGWCC 2 cut(s) 374, 1126
AxyI CCTNAGG 1 cut(s) 977
BaeGI GKGCMC 2 cut(s) 975, 1155
BanI GGYRCC 2 cut(s) 690, 1004
Bbv12I GWGCWC 1 cut(s) 975
BbvCI CCTCAGC 1 cut(s) 196
BbvI GCAGC 2 cut(s) 62, 212
BccI CCATC 3 cut(s) 35, 374, 695
BceAI ACGGC 3 cut(s) 159, 932, 995
BciVI GTATCC 1 cut(s) 976
BcuI ACTAGT 1 cut(s) 272
BfaI CTAG 6 cut(s) 273, 392, 515, 668, 1001, 1140
BfmI CTRYAG 1 cut(s) 963
BfuI GTATCC 1 cut(s) 976
BisI GCNGC 3 cut(s) 76, 201, 1008
BlsI GCNGC 3 cut(s) 77, 202, 1009
BmcAI AGTACT 1 cut(s) 265
Bme18I GGWCC 2 cut(s) 374, 1126
BmgT120I GGNCC 3 cut(s) 316, 374, 1126
BmiI GGNNCC 3 cut(s) 692, 1006, 1127
BmsI GCATC 2 cut(s) 565, 1034
BplI GAGNNNNNCTC 2 cut(s) 1090, 1122
Bpu10I CCTNAGC 1 cut(s) 196
BpuEI CTTGAG 2 cut(s) 670, 788
BsaJI CCNNGG 2 cut(s) 790, 1032
BsaWI WCCGGW 2 cut(s) 697, 1171
Bsc4I CCNNNNNNNGG 3 cut(s) 701, 808, 1038
Bse118I RCCGGY 2 cut(s) 750, 1171
Bse1I ACTGG 1 cut(s) 1148
Bse21I CCTNAGG 1 cut(s) 977
Bse3DI GCAATG 1 cut(s) 331
BseAI TCCGGA 1 cut(s) 697
BseDI CCNNGG 2 cut(s) 790, 1032
BseGI GGATG 4 cut(s) 10, 91, 536, 706
BseLI CCNNNNNNNGG 3 cut(s) 701, 808, 1038
BseMI GCAATG 1 cut(s) 331
BseMII CTCAG 4 cut(s) 27, 210, 273, 608
BseNI ACTGG 1 cut(s) 1148
BseSI GKGCMC 2 cut(s) 975, 1155
BseXI GCAGC 2 cut(s) 62, 212
Bsh1285I CGRYCG 1 cut(s) 828
BshFI GGCC 2 cut(s) 318, 947
BshNI GGYRCC 2 cut(s) 690, 1004
BshTI ACCGGT 1 cut(s) 1171
BsiEI CGRYCG 1 cut(s) 828
BsiHKAI GWGCWC 1 cut(s) 975
BsiSI CCGG 3 cut(s) 698, 751, 1172
BsiWI CGTACG 1 cut(s) 231
BslFI GGGAC 3 cut(s) 935, 1050, 1139
BslI CCNNNNNNNGG 3 cut(s) 701, 808, 1038
BsmFI GGGAC 3 cut(s) 935, 1050, 1139
BsmI GAATGC 2 cut(s) 157, 425
BsnI GGCC 2 cut(s) 318, 947
Bsp1286I GDGCHC 2 cut(s) 975, 1155
Bsp13I TCCGGA 1 cut(s) 697
Bsp143I GATC 5 cut(s) 185, 607, 624, 825, 957
Bsp19I CCATGG 2 cut(s) 790, 1032
BspACI CCGC 5 cut(s) 589, 808, 1008, 1017, 1023
BspANI GGCC 2 cut(s) 318, 947
BspCNI CTCAG 4 cut(s) 26, 209, 274, 609
BspEI TCCGGA 1 cut(s) 697
BspLI GGNNCC 3 cut(s) 692, 1006, 1127
BspPI GGATC 3 cut(s) 193, 632, 952
BspT107I GGYRCC 2 cut(s) 690, 1004
BsrDI GCAATG 1 cut(s) 331
BsrFI RCCGGY 2 cut(s) 750, 1171
BsrI ACTGG 1 cut(s) 1148
BssAI RCCGGY 2 cut(s) 750, 1171
BssECI CCNNGG 2 cut(s) 790, 1032
BssMI GATC 5 cut(s) 185, 607, 624, 825, 957
BssT1I CCWWGG 2 cut(s) 790, 1032
Bst4CI ACNGT 2 cut(s) 332, 1041
BstC8I GCNNGC 3 cut(s) 155, 351, 682
BstDEI CTNAG 6 cut(s) 13, 196, 282, 296, 617, 977
BstDSI CCRYGG 2 cut(s) 790, 1032
BstF5I GGATG 4 cut(s) 10, 91, 536, 706
BstKTI GATC 5 cut(s) 188, 610, 627, 828, 960
BstMBI GATC 5 cut(s) 185, 607, 624, 825, 957
BstMCI CGRYCG 1 cut(s) 828
BstMWI GCNNNNNNNGC 3 cut(s) 33, 843, 1016
BstNSI RCATGY 1 cut(s) 684
BstSFI CTRYAG 1 cut(s) 963
BstSLI GKGCMC 2 cut(s) 975, 1155
BstV1I GCAGC 2 cut(s) 62, 212
Bsu36I CCTNAGG 1 cut(s) 977
BsuI GTATCC 1 cut(s) 976
BsuRI GGCC 2 cut(s) 318, 947
BtgI CCRYGG 2 cut(s) 790, 1032
BtsCI GGATG 4 cut(s) 10, 91, 536, 706
BtsI GCAGTG 1 cut(s) 290
BtsIMutI CAGTG 2 cut(s) 290, 1155
Cac8I GCNNGC 3 cut(s) 155, 351, 682
Cfr10I RCCGGY 2 cut(s) 750, 1171
Cfr13I GGNCC 3 cut(s) 316, 374, 1126
Csp6I GTAC 3 cut(s) 232, 264, 1145
CspAI ACCGGT 1 cut(s) 1171
CspCI CAANNNNNGTGG 2 cut(s) 25, 60
CviAII CATG 8 cut(s) 68, 216, 407, 611, 681, 791, 1033, 1095
CviQI GTAC 3 cut(s) 232, 264, 1145
DdeI CTNAG 6 cut(s) 13, 196, 282, 296, 617, 977
DpnI GATC 5 cut(s) 187, 609, 626, 827, 959
DpnII GATC 5 cut(s) 185, 607, 624, 825, 957
DraI TTTAAA 1 cut(s) 474
DraIII CACNNNGTG 1 cut(s) 1114
EaeI YGGCCR 1 cut(s) 945
Eco130I CCWWGG 2 cut(s) 790, 1032
Eco47I GGWCC 2 cut(s) 374, 1126
Eco57I CTGAAG 1 cut(s) 533
Eco81I CCTNAGG 1 cut(s) 977
EcoRI GAATTC 3 cut(s) 115, 443, 795
EcoT14I CCWWGG 2 cut(s) 790, 1032
EcoT22I ATGCAT 1 cut(s) 682
ErhI CCWWGG 2 cut(s) 790, 1032
FaeI CATG 8 cut(s) 71, 219, 410, 614, 684, 794, 1036, 1098
FalI AAGNNNNNCTT 4 cut(s) 104, 136, 531, 563
FaqI GGGAC 3 cut(s) 935, 1050, 1139
FatI CATG 8 cut(s) 67, 215, 406, 610, 680, 790, 1032, 1094
FauI CCCGC 2 cut(s) 801, 1024
FauNDI CATATG 1 cut(s) 885
Fnu4HI GCNGC 3 cut(s) 76, 201, 1008
FokI GGATG 4 cut(s) 17, 78, 543, 713
Fsp4HI GCNGC 3 cut(s) 76, 201, 1008
FspBI CTAG 6 cut(s) 273, 392, 515, 668, 1001, 1140
GluI GCNGC 3 cut(s) 76, 201, 1008
HaeIII GGCC 2 cut(s) 318, 947
HapII CCGG 3 cut(s) 698, 751, 1172
Hin1II CATG 8 cut(s) 71, 219, 410, 614, 684, 794, 1036, 1098
HinfI GANTC 4 cut(s) 426, 727, 821, 872
HpaII CCGG 3 cut(s) 698, 751, 1172
HphI GGTGA 3 cut(s) 791, 946, 1100
Hpy166II GTNNAC 2 cut(s) 973, 1145
Hpy188I TCNGA 4 cut(s) 16, 367, 841, 920
Hpy188III TCNNGA 2 cut(s) 142, 698
Hpy8I GTNNAC 2 cut(s) 973, 1145
Hpy99I CGWCG 1 cut(s) 1124
HpyAV CCTTC 6 cut(s) 65, 102, 130, 298, 836, 852
HpyCH4III ACNGT 2 cut(s) 332, 1041
HpyCH4V TGCA 7 cut(s) 36, 324, 353, 578, 680, 973, 994
HpyF10VI GCNNNNNNNGC 3 cut(s) 33, 843, 1016
HpyF3I CTNAG 6 cut(s) 13, 196, 282, 296, 617, 977
Hsp92II CATG 8 cut(s) 71, 219, 410, 614, 684, 794, 1036, 1098
Kpn2I TCCGGA 1 cut(s) 697
Kzo9I GATC 5 cut(s) 185, 607, 624, 825, 957
LmnI GCTCC 1 cut(s) 83
LpnPI CCDG 8 cut(s) 127, 175, 390, 585, 711, 764, 893, 1161
Lsp1109I GCAGC 2 cut(s) 62, 212
LweI GCATC 2 cut(s) 565, 1034
MaeI CTAG 6 cut(s) 273, 392, 515, 668, 1001, 1140
MaeIII GTNAC 3 cut(s) 176, 242, 1051
MalI GATC 5 cut(s) 187, 609, 626, 827, 959
MboI GATC 5 cut(s) 185, 607, 624, 825, 957
MboII GAAGA 1 cut(s) 124
MhlI GDGCHC 2 cut(s) 975, 1155
MluCI AATT 6 cut(s) 115, 204, 443, 521, 795, 830
MlyI GAGTC 1 cut(s) 420
MmeI TCCRAC 2 cut(s) 629, 1023
Mph1103I ATGCAT 1 cut(s) 682
MroI TCCGGA 1 cut(s) 697
MroXI GAANNNNTTC 1 cut(s) 119
MseI TTAA 1 cut(s) 473
MslI CAYNNNNRTG 1 cut(s) 418
MspI CCGG 3 cut(s) 698, 751, 1172
Mva1269I GAATGC 2 cut(s) 157, 425
MwoI GCNNNNNNNGC 3 cut(s) 33, 843, 1016
NcoI CCATGG 2 cut(s) 790, 1032
NdeI CATATG 1 cut(s) 885
NdeII GATC 5 cut(s) 185, 607, 624, 825, 957
NlaIII CATG 8 cut(s) 71, 219, 410, 614, 684, 794, 1036, 1098
NlaIV GGNNCC 3 cut(s) 692, 1006, 1127
NmuCI GTSAC 2 cut(s) 242, 1051
NsiI ATGCAT 1 cut(s) 682
NspI RCATGY 1 cut(s) 684
PaeI GCATGC 1 cut(s) 684
PctI GAATGC 2 cut(s) 157, 425
PdmI GAANNNNTTC 1 cut(s) 119
PfeI GAWTC 3 cut(s) 727, 821, 872
Pfl23II CGTACG 1 cut(s) 231
PinAI ACCGGT 1 cut(s) 1171
PkrI GCNGC 3 cut(s) 77, 202, 1009
Ple19I CGATCG 1 cut(s) 828
PleI GAGTC 1 cut(s) 420
PpsI GAGTC 1 cut(s) 420
PspLI CGTACG 1 cut(s) 231
PspN4I GGNNCC 3 cut(s) 692, 1006, 1127
PspPI GGNCC 3 cut(s) 316, 374, 1126
PvuI CGATCG 1 cut(s) 828
RsaI GTAC 3 cut(s) 233, 265, 1146
RsaNI GTAC 3 cut(s) 232, 264, 1145
RseI CAYNNNNRTG 1 cut(s) 418
SaqAI TTAA 1 cut(s) 473
SatI GCNGC 3 cut(s) 76, 201, 1008
Sau3AI GATC 5 cut(s) 185, 607, 624, 825, 957
Sau96I GGNCC 3 cut(s) 316, 374, 1126
ScaI AGTACT 1 cut(s) 265
SchI GAGTC 1 cut(s) 420
SduI GDGCHC 2 cut(s) 975, 1155
SfaNI GCATC 2 cut(s) 565, 1034
SfcI CTRYAG 1 cut(s) 963
SgrAI CRCCGGYG 1 cut(s) 1171
SinI GGWCC 2 cut(s) 374, 1126
SmiMI CAYNNNNRTG 1 cut(s) 418
SmlI CTYRAG 2 cut(s) 685, 803
SmoI CTYRAG 2 cut(s) 685, 803
SpeI ACTAGT 1 cut(s) 272
SphI GCATGC 1 cut(s) 684
Sse9I AATT 6 cut(s) 115, 204, 443, 521, 795, 830
SsiI CCGC 5 cut(s) 589, 808, 1008, 1017, 1023
SspMI CTAG 6 cut(s) 273, 392, 515, 668, 1001, 1140
StyI CCWWGG 2 cut(s) 790, 1032
TaaI ACNGT 2 cut(s) 332, 1041
TaqI TCGA 2 cut(s) 824, 828
TasI AATT 6 cut(s) 115, 204, 443, 521, 795, 830
TatI WGTACW 1 cut(s) 263
TauI GCSGC 1 cut(s) 1010
TfiI GAWTC 3 cut(s) 727, 821, 872
Tru1I TTAA 1 cut(s) 473
Tru9I TTAA 1 cut(s) 473
TscAI CASTG 2 cut(s) 297, 1155
TseFI GTSAC 2 cut(s) 242, 1051
TseI GCWGC 2 cut(s) 75, 200
Tsp45I GTSAC 2 cut(s) 242, 1051
TspDTI ATGAA 5 cut(s) 84, 436, 581, 701, 1083
TspGWI ACGGA 1 cut(s) 219
TspRI CASTG 2 cut(s) 297, 1155
VneI GTGCAC 1 cut(s) 971
VpaK11BI GGWCC 2 cut(s) 374, 1126
XapI RAATTY 4 cut(s) 115, 443, 521, 795
XceI RCATGY 1 cut(s) 684
XcmI CCANNNNNNNNNTGG 1 cut(s) 1039
XmnI GAANNNNTTC 1 cut(s) 119
XspI CTAG 6 cut(s) 273, 392, 515, 668, 1001, 1140
ZrmI AGTACT 1 cut(s) 265
Zsp2I ATGCAT 1 cut(s) 682
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.