MD04G1065200.v1.1

Replication factor C subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr04
OG0015060
Physical Location & Seq
Forward (+)
8753782 .. 8757499
3718 bp
Loading structure...
UTR
Exon/CDS
Intron
MD04G1065200.v1.1.491

Sequence Viewer

Length: 993 bp
ATGGCGTCGTCTTCTTCTTCGTCAGCCTACGACATGCCGTGGGTGGAGAAGTACAGGCCCACCAAGGTCGCCGACATTGTGGGCAATGAAGACGCCGTGTCCAGAATCCAGGTCATCGCTCGCGACGGCAACATGCCCAACCTCATCTTAGCCGGTCCTCCTGGAACTGGTAAGACCACTAGCATACTGGCTCTTGCACATGAGCTTTTGGGACCAAACTATAAGGAGGCTGTTTTAGAGCTGAATGCATCAGATGACAGGGGAATCGATGTTGTGAGGAACAAAATTAAAATGTTTGCTCAAAAGAAAGTTACACTGCCTTCCGGACGCCATAAAGTTGTCATCTTGGATGAAGCTGACAGCATGACATCTGGAGCACAACAAGCTCTGAGGCGAACAATGGAAATATATTCAAATTCCACTCGTTTCGCTCTTGCGTGCAATACATCTTCCAAAATCATTGAGCCTATTCAGAGTAGATGTGCCCTTGTCCGGTTTTCTAGATTGACTGATGAGGAGATACTTGGTCGCCTAATGATAGTGGTTCAAGCTGAGAAGGTTCCATATGTTCCAGAAGGTCTTGAAGCGATTATTTTCACCGCTGATGGTGATATGAGGCAGGCACTGAATAACTTGCAAGCTACAAACAGTGGATTCCGGTTTGTGAACCAAGAAAATGTTTTCAAGGTCTGTGACCAGCCTCATCCGTTGCATGTAAAGAATATGGTGCGCAACATACTGGAAGGGAAATTTGATGATGCTTGTTCGGGTCTCAAGCAGCTCTACGATCTGGGTTACTCCCCAACGGACATAATCACAACTTTTTTCCGTATCATAAAAAACTATGATATGGCTGAGTTTTTGAAACTGGAGTTCATGAAGGAAACTGGATTTGCTCACATGAGAATCTGTGATGGAGTTGGCTCGTACCTTCAGATGTGTGGTCTTCTGGCTAAGCTTTCCCTAGTCCGTGAAACCGCGAAGGAAACATAA
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

331

Amino Acids

36.68

Weight (kDa)

6.96

Isoelectric Point (pI)

40.47

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Rad17 PF03215 13 - 80 1e-05 Rad17 P-loop domain
nSTAND_NTPase5 PF25199 32 - 150 2.2e-06 Novel STAND NTPase 5
AAA_14 PF13173 47 - 147 1.5e-06 AAA domain
AAA PF00004 48 - 165 5.3e-14 ATPase family associated with various cellular activities (AAA)
DNA_pol3_delta2 PF13177 88 - 169 1.5e-08 DNA polymerase III, delta subunit
Rep_fac_C PF08542 234 - 319 6.5e-24 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)
Acc16I TGCGCA 1 cut(s) 731
AccII CGCG 2 cut(s) 123, 980
AccIII TCCGGA 1 cut(s) 323
AciI CCGC 2 cut(s) 600, 978
AcsI RAATTY 2 cut(s) 415, 749
AcuI CTGAAG 1 cut(s) 917
AcyI GRCGYC 3 cut(s) 5, 93, 328
AfaI GTAC 2 cut(s) 53, 929
AfiI CCNNNNNNNGG 2 cut(s) 167, 492
AgsI TTSAA 5 cut(s) 414, 548, 584, 685, 865
AhdI GACNNNNNGTC 1 cut(s) 97
AjnI CCWGG 2 cut(s) 108, 160
AluBI AGCT 8 cut(s) 205, 241, 356, 386, 551, 641, 781, 958
AluI AGCT 8 cut(s) 205, 241, 356, 386, 551, 641, 781, 958
Alw21I GWGCWC 1 cut(s) 379
Alw26I GTCTC 1 cut(s) 776
AlwNI CAGNNNCTG 1 cut(s) 625
Aor13HI TCCGGA 1 cut(s) 323
AoxI GGCC 1 cut(s) 56
ApeKI GCWGC 1 cut(s) 778
ApoI RAATTY 2 cut(s) 415, 749
AspLEI GCGC 1 cut(s) 732
AspS9I GGNCC 3 cut(s) 57, 155, 212
AsuHPI GGTGA 2 cut(s) 589, 620
AvaII GGWCC 2 cut(s) 155, 212
BaeGI GKGCMC 1 cut(s) 487
BbsI GAAGAC 3 cut(s) 3, 96, 938
Bbv12I GWGCWC 1 cut(s) 379
BbvI GCAGC 1 cut(s) 790
BccI CCATC 2 cut(s) 599, 908
BceAI ACGGC 3 cut(s) 22, 80, 142
BciT130I CCWGG 2 cut(s) 110, 162
BcoDI GTCTC 1 cut(s) 776
BfaI CTAG 3 cut(s) 180, 501, 965
BisI GCNGC 1 cut(s) 779
BlpI GCTNAGC 1 cut(s) 954
BlsI GCNGC 1 cut(s) 780
Bme1390I CCNGG 2 cut(s) 110, 162
Bme18I GGWCC 2 cut(s) 155, 212
BmeRI GACNNNNNGTC 1 cut(s) 97
BmgT120I GGNCC 3 cut(s) 57, 155, 212
BmiI GGNNCC 2 cut(s) 213, 561
BmrFI CCNGG 2 cut(s) 110, 162
BmsI GCATC 2 cut(s) 257, 748
BpiI GAAGAC 3 cut(s) 3, 96, 938
BpmI CTGGAG 2 cut(s) 393, 890
Bpu1102I GCTNAGC 1 cut(s) 954
BpuEI CTTGAG 1 cut(s) 758
Bsa29I ATCGAT 1 cut(s) 267
BsaHI GRCGYC 3 cut(s) 5, 93, 328
BsaI GGTCTC 1 cut(s) 776
BsaJI CCNNGG 2 cut(s) 38, 63
BsaWI WCCGGW 3 cut(s) 323, 492, 657
Bsc4I CCNNNNNNNGG 2 cut(s) 167, 492
Bse118I RCCGGY 1 cut(s) 152
Bse1I ACTGG 5 cut(s) 172, 192, 744, 873, 892
Bse3DI GCAATG 1 cut(s) 91
BseAI TCCGGA 1 cut(s) 323
BseBI CCWGG 2 cut(s) 110, 162
BseCI ATCGAT 1 cut(s) 267
BseDI CCNNGG 2 cut(s) 38, 63
BseGI GGATG 2 cut(s) 355, 703
BseLI CCNNNNNNNGG 2 cut(s) 167, 492
BseMI GCAATG 1 cut(s) 91
BseMII CTCAG 3 cut(s) 380, 543, 846
BseNI ACTGG 5 cut(s) 172, 192, 744, 873, 892
BseRI GAGGAG 1 cut(s) 530
BseSI GKGCMC 1 cut(s) 487
BseXI GCAGC 1 cut(s) 790
Bsh1236I CGCG 2 cut(s) 123, 980
BshFI GGCC 1 cut(s) 58
BshVI ATCGAT 1 cut(s) 267
BsiHKAI GWGCWC 1 cut(s) 379
BsiSI CCGG 4 cut(s) 153, 324, 493, 658
BslFI GGGAC 1 cut(s) 225
BslI CCNNNNNNNGG 2 cut(s) 167, 492
BsmAI GTCTC 1 cut(s) 776
BsmFI GGGAC 1 cut(s) 225
BsmI GAATGC 1 cut(s) 250
BsnI GGCC 1 cut(s) 58
Bso31I GGTCTC 1 cut(s) 776
Bsp1286I GDGCHC 2 cut(s) 379, 487
Bsp13I TCCGGA 1 cut(s) 323
Bsp143I GATC 1 cut(s) 787
Bsp1720I GCTNAGC 1 cut(s) 954
Bsp68I TCGCGA 1 cut(s) 123
BspACI CCGC 2 cut(s) 600, 978
BspANI GGCC 1 cut(s) 58
BspCNI CTCAG 3 cut(s) 381, 544, 847
BspDI ATCGAT 1 cut(s) 267
BspEI TCCGGA 1 cut(s) 323
BspFNI CGCG 2 cut(s) 123, 980
BspHI TCATGA 1 cut(s) 876
BspLI GGNNCC 2 cut(s) 213, 561
BspTNI GGTCTC 1 cut(s) 776
BsrDI GCAATG 1 cut(s) 91
BsrFI RCCGGY 1 cut(s) 152
BsrI ACTGG 5 cut(s) 172, 192, 744, 873, 892
BssAI RCCGGY 1 cut(s) 152
BssECI CCNNGG 2 cut(s) 38, 63
BssMI GATC 1 cut(s) 787
BssNI GRCGYC 3 cut(s) 5, 93, 328
BssT1I CCWWGG 1 cut(s) 63
Bst2UI CCWGG 2 cut(s) 110, 162
Bst4CI ACNGT 1 cut(s) 650
BstACI GRCGYC 3 cut(s) 5, 93, 328
BstC8I GCNNGC 4 cut(s) 121, 439, 621, 639
BstDEI CTNAG 5 cut(s) 148, 389, 552, 855, 954
BstDSI CCRYGG 1 cut(s) 38
BstF5I GGATG 2 cut(s) 355, 703
BstFNI CGCG 2 cut(s) 123, 980
BstHHI GCGC 1 cut(s) 732
BstKTI GATC 1 cut(s) 790
BstMAI GTCTC 1 cut(s) 776
BstMBI GATC 1 cut(s) 787
BstMWI GCNNNNNNNGC 1 cut(s) 383
BstNI CCWGG 2 cut(s) 110, 162
BstNSI RCATGY 3 cut(s) 37, 136, 716
BstSCI CCNGG 2 cut(s) 108, 160
BstSLI GKGCMC 1 cut(s) 487
BstUI CGCG 2 cut(s) 123, 980
BstV1I GCAGC 1 cut(s) 790
BstV2I GAAGAC 3 cut(s) 3, 96, 938
Bsu15I ATCGAT 1 cut(s) 267
BsuRI GGCC 1 cut(s) 58
BsuTUI ATCGAT 1 cut(s) 267
BtgI CCRYGG 1 cut(s) 38
BtgZI GCGATG 1 cut(s) 100
BtsCI GGATG 2 cut(s) 355, 703
BtsI GCAGTG 1 cut(s) 314
BtsIMutI CAGTG 3 cut(s) 314, 623, 655
BtuMI TCGCGA 1 cut(s) 123
Cac8I GCNNGC 4 cut(s) 121, 439, 621, 639
CaiI CAGNNNCTG 1 cut(s) 625
CciI TCATGA 1 cut(s) 876
CfoI GCGC 1 cut(s) 732
Cfr10I RCCGGY 1 cut(s) 152
Cfr13I GGNCC 3 cut(s) 57, 155, 212
ClaI ATCGAT 1 cut(s) 267
CseI GACGC 2 cut(s) 101, 336
Csp6I GTAC 2 cut(s) 52, 928
CviAII CATG 7 cut(s) 34, 133, 200, 364, 713, 877, 901
CviQI GTAC 2 cut(s) 52, 928
DdeI CTNAG 5 cut(s) 148, 389, 552, 855, 954
DpnI GATC 1 cut(s) 789
DpnII GATC 1 cut(s) 787
DriI GACNNNNNGTC 1 cut(s) 97
Eam1105I GACNNNNNGTC 1 cut(s) 97
Eco130I CCWWGG 1 cut(s) 63
Eco31I GGTCTC 1 cut(s) 776
Eco47I GGWCC 2 cut(s) 155, 212
Eco57I CTGAAG 1 cut(s) 917
EcoRII CCWGG 2 cut(s) 108, 160
EcoT14I CCWWGG 1 cut(s) 63
EcoT22I ATGCAT 1 cut(s) 250
ErhI CCWWGG 1 cut(s) 63
FaeI CATG 7 cut(s) 37, 136, 203, 367, 716, 880, 904
FaqI GGGAC 1 cut(s) 225
FatI CATG 7 cut(s) 33, 132, 199, 363, 712, 876, 900
FauNDI CATATG 1 cut(s) 565
Fnu4HI GCNGC 1 cut(s) 779
FokI GGATG 2 cut(s) 362, 690
Fsp4HI GCNGC 1 cut(s) 779
FspBI CTAG 3 cut(s) 180, 501, 965
FspI TGCGCA 1 cut(s) 731
GlaI GCGC 1 cut(s) 731
GluI GCNGC 1 cut(s) 779
GsuI CTGGAG 2 cut(s) 393, 890
HaeIII GGCC 1 cut(s) 58
HapII CCGG 4 cut(s) 153, 324, 493, 658
HgaI GACGC 2 cut(s) 101, 336
HhaI GCGC 1 cut(s) 732
Hin1I GRCGYC 3 cut(s) 5, 93, 328
Hin1II CATG 7 cut(s) 37, 136, 203, 367, 716, 880, 904
Hin6I GCGC 1 cut(s) 730
HinP1I GCGC 1 cut(s) 730
HindIII AAGCTT 1 cut(s) 956
HinfI GANTC 4 cut(s) 105, 264, 654, 906
HpaII CCGG 4 cut(s) 153, 324, 493, 658
HphI GGTGA 2 cut(s) 589, 620
Hpy166II GTNNAC 1 cut(s) 667
Hpy188I TCNGA 4 cut(s) 253, 390, 474, 936
Hpy188III TCNNGA 8 cut(s) 102, 122, 324, 372, 501, 572, 581, 877
Hpy8I GTNNAC 1 cut(s) 667
Hpy99I CGWCG 2 cut(s) 10, 128
HpyAV CCTTC 7 cut(s) 330, 550, 569, 737, 874, 941, 976
HpyCH4III ACNGT 1 cut(s) 650
HpyCH4V TGCA 5 cut(s) 197, 248, 441, 637, 712
HpyF10VI GCNNNNNNNGC 1 cut(s) 383
HpyF3I CTNAG 5 cut(s) 148, 389, 552, 855, 954
Hsp92I GRCGYC 3 cut(s) 5, 93, 328
Hsp92II CATG 7 cut(s) 37, 136, 203, 367, 716, 880, 904
HspAI GCGC 1 cut(s) 730
Kpn2I TCCGGA 1 cut(s) 323
Kzo9I GATC 1 cut(s) 787
LmnI GCTCC 1 cut(s) 374
Lsp1109I GCAGC 1 cut(s) 790
LweI GCATC 2 cut(s) 257, 748
MaeI CTAG 3 cut(s) 180, 501, 965
MaeIII GTNAC 3 cut(s) 310, 692, 794
MalI GATC 1 cut(s) 789
MboI GATC 1 cut(s) 787
MboII GAAGA 6 cut(s) 3, 6, 9, 101, 441, 938
MhlI GDGCHC 2 cut(s) 379, 487
MluCI AATT 3 cut(s) 285, 415, 749
MnlI CCTC 8 cut(s) 152, 168, 220, 270, 384, 508, 609, 711
Mph1103I ATGCAT 1 cut(s) 250
MroI TCCGGA 1 cut(s) 323
MseI TTAA 1 cut(s) 288
MspA1I CMGCKG 1 cut(s) 602
MspI CCGG 4 cut(s) 153, 324, 493, 658
MspR9I CCNGG 2 cut(s) 110, 162
Mva1269I GAATGC 1 cut(s) 250
MvaI CCWGG 2 cut(s) 110, 162
MvnI CGCG 2 cut(s) 123, 980
MwoI GCNNNNNNNGC 1 cut(s) 383
NdeI CATATG 1 cut(s) 565
NdeII GATC 1 cut(s) 787
NlaIII CATG 7 cut(s) 37, 136, 203, 367, 716, 880, 904
NlaIV GGNNCC 2 cut(s) 213, 561
NmuCI GTSAC 1 cut(s) 692
NruI TCGCGA 1 cut(s) 123
NsbI TGCGCA 1 cut(s) 731
NsiI ATGCAT 1 cut(s) 250
NspI RCATGY 3 cut(s) 37, 136, 716
PagI TCATGA 1 cut(s) 876
PctI GAATGC 1 cut(s) 250
PfeI GAWTC 4 cut(s) 105, 264, 654, 906
PfoI TCCNGGA 1 cut(s) 160
PkrI GCNGC 1 cut(s) 780
Psp6I CCWGG 2 cut(s) 108, 160
PspGI CCWGG 2 cut(s) 108, 160
PspN4I GGNNCC 2 cut(s) 213, 561
PspPI GGNCC 3 cut(s) 57, 155, 212
PstNI CAGNNNCTG 1 cut(s) 625
RruI TCGCGA 1 cut(s) 123
RsaI GTAC 2 cut(s) 53, 929
RsaNI GTAC 2 cut(s) 52, 928
SaqAI TTAA 1 cut(s) 288
SatI GCNGC 1 cut(s) 779
Sau3AI GATC 1 cut(s) 787
Sau96I GGNCC 3 cut(s) 57, 155, 212
ScrFI CCNGG 2 cut(s) 110, 162
SduI GDGCHC 2 cut(s) 379, 487
SfaNI GCATC 2 cut(s) 257, 748
SinI GGWCC 2 cut(s) 155, 212
SmlI CTYRAG 1 cut(s) 773
SmoI CTYRAG 1 cut(s) 773
Sse9I AATT 3 cut(s) 285, 415, 749
SsiI CCGC 2 cut(s) 600, 978
SspMI CTAG 3 cut(s) 180, 501, 965
StyD4I CCNGG 2 cut(s) 108, 160
StyI CCWWGG 1 cut(s) 63
TaaI ACNGT 1 cut(s) 650
TaqI TCGA 1 cut(s) 267
TasI AATT 3 cut(s) 285, 415, 749
TatI WGTACW 1 cut(s) 51
TfiI GAWTC 4 cut(s) 105, 264, 654, 906
Tru1I TTAA 1 cut(s) 288
Tru9I TTAA 1 cut(s) 288
TscAI CASTG 3 cut(s) 321, 630, 655
TseFI GTSAC 1 cut(s) 692
TseI GCWGC 1 cut(s) 778
Tsp45I GTSAC 1 cut(s) 692
TspDTI ATGAA 4 cut(s) 102, 366, 865, 893
TspGWI ACGGA 4 cut(s) 696, 818, 821, 959
TspRI CASTG 3 cut(s) 321, 630, 655
VpaK11BI GGWCC 2 cut(s) 155, 212
XapI RAATTY 2 cut(s) 415, 749
XbaI TCTAGA 1 cut(s) 500
XceI RCATGY 3 cut(s) 37, 136, 716
XcmI CCANNNNNNNNNTGG 1 cut(s) 184
XspI CTAG 3 cut(s) 180, 501, 965
Zsp2I ATGCAT 1 cut(s) 250
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.