Rroxscaffold_3G00257230

Replication factor C subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000003
OG0015060
Physical Location & Seq
Reverse (-)
51618213 .. 51621672
3460 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_3G00257230.1

Sequence Viewer

Length: 999 bp
ATGTCGTCGTCTTCTTCGTCTTCCGCGTCGGCCTACGACATGCCATGGGTGGAGAAGTACAGGCCGAACAAGGTCGGCGACATCGTCGGCAACGAAGACGCCGTGTCGAGGCTCCAGGTCATCGCCCGCGACGGCAACATGCCCAATCTCATCTTAGCCGGTCCTCCTGGAACTGGTAAGACCACTAGTATACTTGCTCTTGCACACGAGCTTTTGGGACCAAATTATAGGGAGGGTGTTTTAGAGCTGAATGCATCTGATGACAGGGGAATAGATGTGGTGAGGAACAAGATTAAAATGTTTGCTCAAAAGAAAGTAACACTTCCTCCTGGGCGCCATAAAATTGTCATCTTGGATGAAGCTGACAGCATGACATCTGGAGCGCAACAAGCTTTGAGGCGGACAATGGAAATATATTCAAATTCCACGCGGTTTGCTCTTGCATGCAATACTTCCTCCAAAATCATCGAGCCTATTCAGAGTAGATGTGCCTTAGTCCGATTTTCTAGATTATCTGATCAGGAGATACTTGGTCGTCTAATGGTTGTGGTCCAAGCTGAAAAGGTTCCCTATGTTCCAGAAGGTCTGGAAGCCATCATTTTTACTGCTGATGGTGATATGAGGCAGGCATTGAATAACTTGCAAGCTACAAACAGTGGATTCCGGTTTGTCAACCAAGAAAATGTTTTCAAGGTCTGTGACCAGCCTCATCCATTGCATGTAAAGAATATGGTTCGTAACATACTTGAAGGGAAATTTGACGACGCTTGTTCGGGTCTCAAGCAGCTCTATGATTTGGGCTATTCACCCACTGACATAATCACAACTTTTTTCCGTATCATTAAAAATTATGATATGGCTGAGTATTTGAAACTGGAATTCATGAAGGAAACTGGGTTTGCTCACATGAGAATCTGCGATGGAGTTGGCTCATATCTTCAGCTGTGTGGTCTTCTGGCTAAGCTTTCCCTAGTTCGTGACACAGCCAAAGCGACATAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0000166 GO:0000723 GO:0000731 GO:0003674 GO:0005488 GO:0005524 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005657 GO:0005663 GO:0005694 GO:0006139 GO:0006259 GO:0006260 GO:0006261 GO:0006275 GO:0006281 GO:0006283 GO:0006289 GO:0006296 GO:0006297 GO:0006301 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0006996 GO:0007049 GO:0008144 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009889 GO:0009891 GO:0009893 GO:0009987 GO:0010556 GO:0010557 GO:0010604 GO:0016043 GO:0017076 GO:0018130 GO:0019219 GO:0019222 GO:0019438 GO:0019725 GO:0019985 GO:0022402 GO:0030554 GO:0031323 GO:0031325 GO:0031326 GO:0031328 GO:0031390 GO:0031974 GO:0031981 GO:0032200 GO:0032201 GO:0032553 GO:0032555 GO:0032559 GO:0032991 GO:0033260 GO:0033554 GO:0033683 GO:0034641 GO:0034645 GO:0034654 GO:0035639 GO:0036094 GO:0042276 GO:0042592 GO:0042769 GO:0043085 GO:0043167 GO:0043168 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044093 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044427 GO:0044428 GO:0044446 GO:0044464 GO:0044786 GO:0045935 GO:0046483 GO:0048518 GO:0048522 GO:0050789 GO:0050790 GO:0050794 GO:0050896 GO:0051052 GO:0051054 GO:0051171 GO:0051173 GO:0051276 GO:0051338 GO:0051347 GO:0051606 GO:0051716 GO:0060249 GO:0060255 GO:0065007 GO:0065008 GO:0065009 GO:0070013 GO:0070987 GO:0071704 GO:0071840 GO:0071897 GO:0080090 GO:0090304 GO:0090305 GO:0090329 GO:0097159 GO:0097367 GO:1900262 GO:1900264 GO:1901265 GO:1901360 GO:1901362 GO:1901363 GO:1901576 GO:2000112 GO:2000278 GO:2000573
KEGG Pathways
Metabolic & Signaling
ko03030 ko03420 ko03430 map03030 map03420 map03430
Pfam Domains
Protein Families
AAA Rep_fac_C

Protein Analysis

332

Amino Acids

36.79

Weight (kDa)

8.13

Isoelectric Point (pI)

42.15

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
AAA_14 PF13173 49 - 150 2.7e-06 AAA domain
AAA PF00004 50 - 167 1.3e-13 ATPase family associated with various cellular activities (AAA)
DNA_pol3_delta2 PF13177 91 - 171 3.6e-08 DNA polymerase III, delta subunit
Rep_fac_C PF08542 236 - 321 9.9e-25 Replication factor C C-terminal domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Orthologous Genes (Group: OG0015060)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G63160
fragaria_vesca FvH4_5g01730 FvH4_5g01730
malus_domestica MD04G1065200.v1.1
prunus_persica Prupe.8G039600_v2.0.a1
pyrus_communis pycom04g05880
rosa_chinensis RchiOBHm_Chr7g0198991
rosa_laevigata RLG00000003826
rosa_multiflora Rmu_sc0006266.1_g000025 Rmu_sc0007328.1_g000009
rosa_roxburghii Rroxscaffold_3G00257230
rosa_rugosa Rorug07G0052000
rosa_samantha Rh7AG175000 Rh7BG178200 Rh7DG177600
rosa_wichuraiana Rw7G015350

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 1 cut(s) 333
AccI GTMKAC 1 cut(s) 190
AccII CGCG 3 cut(s) 26, 129, 430
AciI CCGC 4 cut(s) 24, 127, 400, 430
AcsI RAATTY 3 cut(s) 421, 755, 878
AcuI CTGAAG 1 cut(s) 923
AcyI GRCGYC 2 cut(s) 99, 334
AfaI GTAC 1 cut(s) 59
AfiI CCNNNNNNNGG 2 cut(s) 108, 173
AgsI TTSAA 5 cut(s) 420, 634, 691, 749, 871
AhdI GACNNNNNGTC 1 cut(s) 103
AhlI ACTAGT 1 cut(s) 185
AjnI CCWGG 3 cut(s) 114, 166, 328
AluBI AGCT 9 cut(s) 211, 247, 362, 392, 557, 647, 787, 943, 964
AluI AGCT 9 cut(s) 211, 247, 362, 392, 557, 647, 787, 943, 964
Alw26I GTCTC 1 cut(s) 782
AoxI GGCC 2 cut(s) 30, 62
ApeKI GCWGC 1 cut(s) 784
ApoI RAATTY 3 cut(s) 421, 755, 878
Asp700I GAANNNNTTC 1 cut(s) 564
AspLEI GCGC 2 cut(s) 336, 385
AspS9I GGNCC 3 cut(s) 161, 218, 550
AsuHPI GGTGA 3 cut(s) 292, 626, 798
AvaII GGWCC 3 cut(s) 161, 218, 550
BanI GGYRCC 1 cut(s) 333
BauI CACGAG 1 cut(s) 206
BbsI GAAGAC 4 cut(s) 3, 12, 102, 944
BbvI GCAGC 1 cut(s) 796
BccI CCATC 3 cut(s) 602, 605, 914
BceAI ACGGC 2 cut(s) 86, 148
BciT130I CCWGG 3 cut(s) 116, 168, 330
BclI TGATCA 1 cut(s) 517
BcoDI GTCTC 1 cut(s) 782
BcuI ACTAGT 1 cut(s) 185
BfaI CTAG 3 cut(s) 186, 507, 971
BfoI RGCGCY 1 cut(s) 337
BisI GCNGC 1 cut(s) 785
BlpI GCTNAGC 1 cut(s) 960
BlsI GCNGC 1 cut(s) 786
Bme1390I CCNGG 3 cut(s) 116, 168, 330
Bme18I GGWCC 3 cut(s) 161, 218, 550
BmeRI GACNNNNNGTC 1 cut(s) 103
BmgT120I GGNCC 3 cut(s) 161, 218, 550
BmiI GGNNCC 4 cut(s) 113, 219, 335, 567
BmrFI CCNGG 3 cut(s) 116, 168, 330
BmrI ACTGGG 1 cut(s) 903
BmsI GCATC 1 cut(s) 263
BmuI ACTGGG 1 cut(s) 903
BpiI GAAGAC 4 cut(s) 3, 12, 102, 944
BpmI CTGGAG 2 cut(s) 98, 399
Bpu1102I GCTNAGC 1 cut(s) 960
BpuEI CTTGAG 1 cut(s) 764
BsaHI GRCGYC 2 cut(s) 99, 334
BsaI GGTCTC 1 cut(s) 782
BsaJI CCNNGG 2 cut(s) 44, 329
BsaWI WCCGGW 1 cut(s) 663
BsaXI ACNNNNNCTCC 2 cut(s) 310, 340
Bsc4I CCNNNNNNNGG 2 cut(s) 108, 173
Bse118I RCCGGY 1 cut(s) 158
Bse1I ACTGG 3 cut(s) 178, 879, 898
Bse3DI GCAATG 1 cut(s) 713
BseBI CCWGG 3 cut(s) 116, 168, 330
BseDI CCNNGG 2 cut(s) 44, 329
BseGI GGATG 2 cut(s) 361, 709
BseLI CCNNNNNNNGG 2 cut(s) 108, 173
BseMI GCAATG 1 cut(s) 713
BseMII CTCAG 1 cut(s) 852
BseNI ACTGG 3 cut(s) 178, 879, 898
BseXI GCAGC 1 cut(s) 796
Bsh1236I CGCG 3 cut(s) 26, 129, 430
BshFI GGCC 2 cut(s) 32, 64
BshNI GGYRCC 1 cut(s) 333
BsiSI CCGG 2 cut(s) 159, 664
BslFI GGGAC 1 cut(s) 231
BslI CCNNNNNNNGG 2 cut(s) 108, 173
BsmAI GTCTC 1 cut(s) 782
BsmFI GGGAC 1 cut(s) 231
BsmI GAATGC 1 cut(s) 256
BsnI GGCC 2 cut(s) 32, 64
Bso31I GGTCTC 1 cut(s) 782
Bsp143I GATC 1 cut(s) 517
Bsp1720I GCTNAGC 1 cut(s) 960
Bsp19I CCATGG 1 cut(s) 44
BspACI CCGC 4 cut(s) 24, 127, 400, 430
BspANI GGCC 2 cut(s) 32, 64
BspCNI CTCAG 1 cut(s) 853
BspFNI CGCG 3 cut(s) 26, 129, 430
BspHI TCATGA 1 cut(s) 882
BspLI GGNNCC 4 cut(s) 113, 219, 335, 567
BspT107I GGYRCC 1 cut(s) 333
BspTNI GGTCTC 1 cut(s) 782
BsrDI GCAATG 1 cut(s) 713
BsrFI RCCGGY 1 cut(s) 158
BsrI ACTGG 3 cut(s) 178, 879, 898
BssAI RCCGGY 1 cut(s) 158
BssECI CCNNGG 2 cut(s) 44, 329
BssMI GATC 1 cut(s) 517
BssNAI GTATAC 1 cut(s) 191
BssNI GRCGYC 2 cut(s) 99, 334
BssSI CACGAG 1 cut(s) 206
BssT1I CCWWGG 1 cut(s) 44
Bst1107I GTATAC 1 cut(s) 191
Bst2BI CACGAG 1 cut(s) 206
Bst2UI CCWGG 3 cut(s) 116, 168, 330
Bst4CI ACNGT 1 cut(s) 656
BstACI GRCGYC 2 cut(s) 99, 334
BstC8I GCNNGC 4 cut(s) 127, 445, 627, 645
BstDEI CTNAG 4 cut(s) 154, 493, 861, 960
BstDSI CCRYGG 1 cut(s) 44
BstF5I GGATG 2 cut(s) 361, 709
BstFNI CGCG 3 cut(s) 26, 129, 430
BstH2I RGCGCY 1 cut(s) 337
BstHHI GCGC 2 cut(s) 336, 385
BstKTI GATC 1 cut(s) 520
BstMAI GTCTC 1 cut(s) 782
BstMBI GATC 1 cut(s) 517
BstMWI GCNNNNNNNGC 1 cut(s) 389
BstNI CCWGG 3 cut(s) 116, 168, 330
BstNSI RCATGY 4 cut(s) 43, 142, 447, 722
BstSCI CCNGG 3 cut(s) 114, 166, 328
BstUI CGCG 3 cut(s) 26, 129, 430
BstV1I GCAGC 1 cut(s) 796
BstV2I GAAGAC 4 cut(s) 3, 12, 102, 944
BstZ17I GTATAC 1 cut(s) 191
BsuRI GGCC 2 cut(s) 32, 64
BtgI CCRYGG 1 cut(s) 44
BtgZI GCGATG 2 cut(s) 106, 933
BtsCI GGATG 2 cut(s) 361, 709
BtsIMutI CAGTG 2 cut(s) 661, 810
Cac8I GCNNGC 4 cut(s) 127, 445, 627, 645
CciI TCATGA 1 cut(s) 882
CfoI GCGC 2 cut(s) 336, 385
Cfr10I RCCGGY 1 cut(s) 158
Cfr13I GGNCC 3 cut(s) 161, 218, 550
CseI GACGC 3 cut(s) 15, 107, 773
Csp6I GTAC 1 cut(s) 58
CspCI CAANNNNNGTGG 2 cut(s) 415, 450
CviAII CATG 8 cut(s) 40, 45, 139, 370, 444, 719, 883, 907
CviQI GTAC 1 cut(s) 58
DdeI CTNAG 4 cut(s) 154, 493, 861, 960
DinI GGCGCC 1 cut(s) 335
DpnI GATC 1 cut(s) 519
DpnII GATC 1 cut(s) 517
DriI GACNNNNNGTC 1 cut(s) 103
Eam1105I GACNNNNNGTC 1 cut(s) 103
EciI GGCGGA 1 cut(s) 415
Eco130I CCWWGG 1 cut(s) 44
Eco31I GGTCTC 1 cut(s) 782
Eco47I GGWCC 3 cut(s) 161, 218, 550
Eco57I CTGAAG 1 cut(s) 923
EcoRI GAATTC 1 cut(s) 878
EcoRII CCWGG 3 cut(s) 114, 166, 328
EcoT14I CCWWGG 1 cut(s) 44
EcoT22I ATGCAT 1 cut(s) 256
EgeI GGCGCC 1 cut(s) 335
EheI GGCGCC 1 cut(s) 335
ErhI CCWWGG 1 cut(s) 44
FaeI CATG 8 cut(s) 43, 48, 142, 373, 447, 722, 886, 910
FalI AAGNNNNNCTT 2 cut(s) 306, 338
FaqI GGGAC 1 cut(s) 231
FatI CATG 8 cut(s) 39, 44, 138, 369, 443, 718, 882, 906
FauI CCCGC 1 cut(s) 134
FbaI TGATCA 1 cut(s) 517
FblI GTMKAC 1 cut(s) 190
Fnu4HI GCNGC 1 cut(s) 785
FokI GGATG 2 cut(s) 368, 696
Fsp4HI GCNGC 1 cut(s) 785
FspBI CTAG 3 cut(s) 186, 507, 971
GlaI GCGC 2 cut(s) 335, 384
GluI GCNGC 1 cut(s) 785
GsuI CTGGAG 2 cut(s) 98, 399
HaeII RGCGCY 1 cut(s) 337
HaeIII GGCC 2 cut(s) 32, 64
HapII CCGG 2 cut(s) 159, 664
HgaI GACGC 3 cut(s) 15, 107, 773
HhaI GCGC 2 cut(s) 336, 385
Hin1I GRCGYC 2 cut(s) 99, 334
Hin1II CATG 8 cut(s) 43, 48, 142, 373, 447, 722, 886, 910
Hin6I GCGC 2 cut(s) 334, 383
HinP1I GCGC 2 cut(s) 334, 383
HincII GTYRAC 1 cut(s) 673
HindII GTYRAC 1 cut(s) 673
HindIII AAGCTT 2 cut(s) 390, 962
HinfI GANTC 2 cut(s) 660, 912
HpaII CCGG 2 cut(s) 159, 664
HphI GGTGA 3 cut(s) 292, 626, 798
Hpy166II GTNNAC 2 cut(s) 191, 673
Hpy188I TCNGA 4 cut(s) 259, 480, 500, 517
Hpy188III TCNNGA 7 cut(s) 378, 507, 521, 578, 587, 883, 977
Hpy8I GTNNAC 2 cut(s) 191, 673
Hpy99I CGWCG 5 cut(s) 10, 31, 89, 134, 767
HpyAV CCTTC 3 cut(s) 575, 743, 880
HpyCH4III ACNGT 1 cut(s) 656
HpyCH4V TGCA 6 cut(s) 203, 254, 443, 447, 643, 718
HpyF10VI GCNNNNNNNGC 1 cut(s) 389
HpyF3I CTNAG 4 cut(s) 154, 493, 861, 960
Hsp92I GRCGYC 2 cut(s) 99, 334
Hsp92II CATG 8 cut(s) 43, 48, 142, 373, 447, 722, 886, 910
HspAI GCGC 2 cut(s) 334, 383
KasI GGCGCC 1 cut(s) 333
Ksp22I TGATCA 1 cut(s) 517
Kzo9I GATC 1 cut(s) 517
LmnI GCTCC 2 cut(s) 117, 380
Lsp1109I GCAGC 1 cut(s) 796
LweI GCATC 1 cut(s) 263
MaeI CTAG 3 cut(s) 186, 507, 971
MaeIII GTNAC 4 cut(s) 316, 698, 737, 977
MalI GATC 1 cut(s) 519
MboI GATC 1 cut(s) 517
MboII GAAGA 6 cut(s) 3, 6, 12, 107, 929, 944
MluCI AATT 6 cut(s) 223, 342, 421, 755, 847, 878
Mly113I GGCGCC 1 cut(s) 334
MnlI CCTC 9 cut(s) 102, 174, 226, 276, 336, 390, 466, 615, 717
Mph1103I ATGCAT 1 cut(s) 256
MroXI GAANNNNTTC 1 cut(s) 564
MseI TTAA 2 cut(s) 294, 843
MspA1I CMGCKG 1 cut(s) 943
MspI CCGG 2 cut(s) 159, 664
MspR9I CCNGG 3 cut(s) 116, 168, 330
Mva1269I GAATGC 1 cut(s) 256
MvaI CCWGG 3 cut(s) 116, 168, 330
MvnI CGCG 3 cut(s) 26, 129, 430
MwoI GCNNNNNNNGC 1 cut(s) 389
NarI GGCGCC 1 cut(s) 334
NcoI CCATGG 1 cut(s) 44
NdeII GATC 1 cut(s) 517
NlaIII CATG 8 cut(s) 43, 48, 142, 373, 447, 722, 886, 910
NlaIV GGNNCC 4 cut(s) 113, 219, 335, 567
NmuCI GTSAC 2 cut(s) 698, 977
NsiI ATGCAT 1 cut(s) 256
NspI RCATGY 4 cut(s) 43, 142, 447, 722
PaeI GCATGC 1 cut(s) 447
PagI TCATGA 1 cut(s) 882
PcsI WCGNNNNNNNCGW 5 cut(s) 14, 23, 81, 90, 99
PctI GAATGC 1 cut(s) 256
PdmI GAANNNNTTC 1 cut(s) 564
PfeI GAWTC 2 cut(s) 660, 912
PflFI GACNNNGTC 1 cut(s) 83
PfoI TCCNGGA 1 cut(s) 166
PkrI GCNGC 1 cut(s) 786
PluTI GGCGCC 1 cut(s) 337
Psp6I CCWGG 3 cut(s) 114, 166, 328
PspGI CCWGG 3 cut(s) 114, 166, 328
PspN4I GGNNCC 4 cut(s) 113, 219, 335, 567
PspPI GGNCC 3 cut(s) 161, 218, 550
PsyI GACNNNGTC 1 cut(s) 83
PvuII CAGCTG 1 cut(s) 943
RsaI GTAC 1 cut(s) 59
RsaNI GTAC 1 cut(s) 58
SaqAI TTAA 2 cut(s) 294, 843
SatI GCNGC 1 cut(s) 785
Sau3AI GATC 1 cut(s) 517
Sau96I GGNCC 3 cut(s) 161, 218, 550
ScrFI CCNGG 3 cut(s) 116, 168, 330
SfaNI GCATC 1 cut(s) 263
SfoI GGCGCC 1 cut(s) 335
SinI GGWCC 3 cut(s) 161, 218, 550
SmlI CTYRAG 1 cut(s) 779
SmoI CTYRAG 1 cut(s) 779
SpeI ACTAGT 1 cut(s) 185
SphI GCATGC 1 cut(s) 447
Sse9I AATT 6 cut(s) 223, 342, 421, 755, 847, 878
SsiI CCGC 4 cut(s) 24, 127, 400, 430
SspDI GGCGCC 1 cut(s) 333
SspMI CTAG 3 cut(s) 186, 507, 971
StyD4I CCNGG 3 cut(s) 114, 166, 328
StyI CCWWGG 1 cut(s) 44
TaaI ACNGT 1 cut(s) 656
TaqI TCGA 2 cut(s) 107, 468
TasI AATT 6 cut(s) 223, 342, 421, 755, 847, 878
TatI WGTACW 1 cut(s) 57
TfiI GAWTC 2 cut(s) 660, 912
Tru1I TTAA 2 cut(s) 294, 843
Tru9I TTAA 2 cut(s) 294, 843
TscAI CASTG 2 cut(s) 661, 817
TseFI GTSAC 2 cut(s) 698, 977
TseI GCWGC 1 cut(s) 784
Tsp45I GTSAC 2 cut(s) 698, 977
TspDTI ATGAA 3 cut(s) 372, 871, 899
TspGWI ACGGA 1 cut(s) 824
TspRI CASTG 2 cut(s) 661, 817
Tth111I GACNNNGTC 1 cut(s) 83
VpaK11BI GGWCC 3 cut(s) 161, 218, 550
XapI RAATTY 3 cut(s) 421, 755, 878
XbaI TCTAGA 1 cut(s) 506
XceI RCATGY 4 cut(s) 43, 142, 447, 722
XmiI GTMKAC 1 cut(s) 190
XmnI GAANNNNTTC 1 cut(s) 564
XspI CTAG 3 cut(s) 186, 507, 971
Zsp2I ATGCAT 1 cut(s) 256
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.