Rorug06G0007300

Transcription initiation factor TFIID

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_rugosa
GWHBQTZ00000006
OG0003127
Physical Location & Seq
Forward (+)
1067266 .. 1068601
1336 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug06G0007300.1

Sequence Viewer

Length: 1173 bp
ATGTGCTCGACACCACTCTCTTCCACGCATGTGCTCGACGCCACTCTCTTCCACGCATGTGCTCGACACCACTCCCTCCAACAAGGGCTCTCTCTGCACCATTACATGCTTGCCCACAACCCCATTACACCTCCCGACCTCTTTGTCTCCAACCACCTCATCAACTTGTACGCCAAATTTGGCTACTTAGACCATGCCCGCCATCTGTTCGATGAAATGCCTAGAAAAAACCTCGTCACCTGGACCGCTCTTATTTCCTGTTACGCACAGCGGAGTAGAGCTGAAGCTTGTTTTCGTTTATTTGCTGCCATGTTGCTGCATCACCTCCCGAATGAGTTTGCATTTTCCAGCGTGCTAAGTTCGTGTGCCGATAGTGATGGTGGATATGGTCGGCAGCTACACGCCCTCGCTTTGAAAATGTCTTTGGATGCTTGCGTTTACGTTGCGAATGCTCTCATTACCATGTATAGCAAGGTGTGTGATCATGGAGCGGGACGAGTTGGTGAGGCTGAGAAGCTTGTAAGTAGAATGGCAATGGAGCCCGATTCCGTAGTTTGGAGTGCACTCCTTGGATCATGTAGGAAGCATGGAAATACACAGTTGGCCAAGTTAGCAGCTGATAGACTGAAGGAGTTGGCTCCAGATAGTTCATTAGTTTATGTACAAATGTCAAACATATATAGCTCTGATGGTAACTTTGGTGAAGCGGGCCTAATTAGGAAGGAAATGAAAGGGTCTCGAGTGAAAAAGGAACCTGGATTAAGCTGGATTGAGATCGGAAATCAGGTGCATGAATTCTCCTCTGGAGGCCGACTCCATCCAGAAAGGAATCTTATAAGCAGAAAACTAAAAGAACTGATTCGACGGTTAAGGGAAATTGGTTATGTTCCAGATACAAGCTCATCCTTGCATGATGTGGAAGAGGAGCACAAAGAGGAGCAATTGTACCATCATAGTGAGAAGCTAGCTTTAGTGTTTGCCATTATGAATGAAAGCGGTTTACATTGCGGTAGGACTGCTATAAAAATAATGAAGAATATCAGAGTATGCTTGGATTGCCACAACTTCATGAAGTTAGCATCAAATCTACTTCAAAAGGATATTGTTGTGAGAGACTCAAACCGTTTCCACCACTTTAAAGATGGCATATGTTCTTGCAATGATTACTGGTAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0000428 GO:0000988 GO:0000989 GO:0001067 GO:0001076 GO:0001129 GO:0001132 GO:0003674 GO:0003676 GO:0003677 GO:0003682 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005667 GO:0005669 GO:0005911 GO:0006139 GO:0006351 GO:0006352 GO:0006355 GO:0006357 GO:0006366 GO:0006367 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009506 GO:0009889 GO:0009891 GO:0009893 GO:0009987 GO:0010467 GO:0010468 GO:0010556 GO:0010557 GO:0010604 GO:0010628 GO:0016043 GO:0016070 GO:0016591 GO:0018130 GO:0019219 GO:0019222 GO:0019438 GO:0022607 GO:0030054 GO:0030880 GO:0031323 GO:0031325 GO:0031326 GO:0031328 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0034622 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0043565 GO:0043933 GO:0044085 GO:0044212 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044464 GO:0044798 GO:0045893 GO:0045935 GO:0045944 GO:0046483 GO:0048518 GO:0048522 GO:0050789 GO:0050794 GO:0051123 GO:0051171 GO:0051173 GO:0051252 GO:0051254 GO:0055029 GO:0055044 GO:0060255 GO:0061695 GO:0065003 GO:0065004 GO:0065007 GO:0070013 GO:0070897 GO:0071704 GO:0071824 GO:0071840 GO:0080090 GO:0090304 GO:0090575 GO:0097159 GO:0097659 GO:0140110 GO:1901360 GO:1901362 GO:1901363 GO:1901576 GO:1902494 GO:1902680 GO:1903506 GO:1903508 GO:1990234 GO:2000112 GO:2001141
KEGG Pathways
Metabolic & Signaling
ko03022 map03022
Pfam Domains
Protein Families
Peptidase_M1

Protein Analysis

390

Amino Acids

43.93

Weight (kDa)

8.18

Isoelectric Point (pI)

44.34

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PPR_2 PF13041 77 - 123 1.5e-06 PPR repeat family
E_motif PF20431 196 - 258 3.5e-15 E motif
DYW_deaminase PF14432 294 - 390 1.2e-36 DYW family of nucleic acid deaminases
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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 836
AasI GACNNNNNNGTC 1 cut(s) 143
AccBSI CCGCTC 2 cut(s) 248, 491
AciI CCGC 7 cut(s) 199, 246, 271, 491, 707, 996, 1008
AclWI GGATC 1 cut(s) 580
AcoI YGGCCR 1 cut(s) 603
AcsI RAATTY 2 cut(s) 176, 794
AcuI CTGAAG 2 cut(s) 303, 647
AcyI GRCGYC 1 cut(s) 39
AfaI GTAC 3 cut(s) 170, 663, 947
AfiI CCNNNNNNNGG 1 cut(s) 555
AgsI TTSAA 2 cut(s) 415, 1094
AjnI CCWGG 2 cut(s) 239, 754
AjuI GAANNNNNNNTTGG 2 cut(s) 407, 439
AleI CACNNNNGTG 2 cut(s) 29, 57
Alw21I GWGCWC 5 cut(s) 8, 36, 64, 565, 930
Alw26I GTCTC 3 cut(s) 151, 741, 1107
Alw44I GTGCAC 1 cut(s) 561
AlwI GGATC 1 cut(s) 580
Ama87I CYCGRG 1 cut(s) 738
AoxI GGCC 3 cut(s) 603, 709, 808
ApaLI GTGCAC 1 cut(s) 561
ApeKI GCWGC 4 cut(s) 305, 316, 394, 614
ApoI RAATTY 2 cut(s) 176, 794
Asp700I GAANNNNTTC 1 cut(s) 858
AspS9I GGNCC 2 cut(s) 243, 709
AsuHPI GGTGA 4 cut(s) 229, 314, 515, 713
AsuNHI GCTAGC 1 cut(s) 964
AvaI CYCGRG 1 cut(s) 738
AvaII GGWCC 1 cut(s) 243
BaeGI GKGCMC 1 cut(s) 565
BalI TGGCCA 1 cut(s) 605
BanII GRGCYC 2 cut(s) 90, 543
Bbv12I GWGCWC 5 cut(s) 8, 36, 64, 565, 930
BbvI GCAGC 4 cut(s) 292, 303, 406, 626
BccI CCATC 6 cut(s) 210, 371, 683, 825, 957, 1136
BciT130I CCWGG 2 cut(s) 241, 756
BclI TGATCA 1 cut(s) 481
BcoDI GTCTC 3 cut(s) 151, 741, 1107
BfaI CTAG 2 cut(s) 222, 965
BisI GCNGC 4 cut(s) 306, 317, 395, 615
BlsI GCNGC 4 cut(s) 307, 318, 396, 616
Bme1390I CCNGG 2 cut(s) 241, 756
Bme18I GGWCC 1 cut(s) 243
BmeT110I CYCGRG 1 cut(s) 738
BmgT120I GGNCC 2 cut(s) 243, 709
BmiI GGNNCC 3 cut(s) 540, 639, 753
BmrFI CCNGG 2 cut(s) 241, 756
BmsI GCATC 3 cut(s) 328, 418, 1088
BmtI GCTAGC 1 cut(s) 968
BplI GAGNNNNNCTC 2 cut(s) 798, 830
BpmI CTGGAG 2 cut(s) 624, 825
BsaBI GATNNNNATC 1 cut(s) 773
BsaHI GRCGYC 1 cut(s) 39
BsaI GGTCTC 1 cut(s) 741
BsaJI CCNNGG 1 cut(s) 568
BsaXI ACNNNNNCTCC 2 cut(s) 929, 959
Bsc4I CCNNNNNNNGG 1 cut(s) 555
Bse1I ACTGG 1 cut(s) 1172
Bse3DI GCAATG 3 cut(s) 540, 1003, 1165
Bse8I GATNNNNATC 1 cut(s) 773
BseBI CCWGG 2 cut(s) 241, 756
BseDI CCNNGG 1 cut(s) 568
BseGI GGATG 3 cut(s) 433, 817, 902
BseJI GATNNNNATC 1 cut(s) 773
BseLI CCNNNNNNNGG 1 cut(s) 555
BseMI GCAATG 3 cut(s) 540, 1003, 1165
BseMII CTCAG 1 cut(s) 501
BseNI ACTGG 1 cut(s) 1172
BseRI GAGGAG 3 cut(s) 790, 938, 950
BseSI GKGCMC 1 cut(s) 565
BseXI GCAGC 4 cut(s) 292, 303, 406, 626
BsgI GTGCAG 1 cut(s) 80
BshFI GGCC 3 cut(s) 605, 711, 810
BsiHKAI GWGCWC 5 cut(s) 8, 36, 64, 565, 930
BsiHKCI CYCGRG 1 cut(s) 738
BslFI GGGAC 1 cut(s) 507
BslI CCNNNNNNNGG 1 cut(s) 555
BsmAI GTCTC 3 cut(s) 151, 741, 1107
BsmFI GGGAC 1 cut(s) 507
BsmI GAATGC 1 cut(s) 454
BsnI GGCC 3 cut(s) 605, 711, 810
Bso31I GGTCTC 1 cut(s) 741
BsoBI CYCGRG 1 cut(s) 738
Bsp1286I GDGCHC 7 cut(s) 8, 36, 64, 90, 543, 565, 930
Bsp1407I TGTACA 1 cut(s) 661
Bsp143I GATC 3 cut(s) 481, 572, 774
BspACI CCGC 7 cut(s) 199, 246, 271, 491, 707, 996, 1008
BspANI GGCC 3 cut(s) 605, 711, 810
BspCNI CTCAG 1 cut(s) 502
BspHI TCATGA 1 cut(s) 1068
BspLI GGNNCC 3 cut(s) 540, 639, 753
BspOI GCTAGC 1 cut(s) 968
BspPI GGATC 1 cut(s) 580
BspTNI GGTCTC 1 cut(s) 741
BsrBI CCGCTC 2 cut(s) 248, 491
BsrDI GCAATG 3 cut(s) 540, 1003, 1165
BsrGI TGTACA 1 cut(s) 661
BsrI ACTGG 1 cut(s) 1172
BssECI CCNNGG 1 cut(s) 568
BssMI GATC 3 cut(s) 481, 572, 774
BssNI GRCGYC 1 cut(s) 39
BssT1I CCWWGG 1 cut(s) 568
Bst2UI CCWGG 2 cut(s) 241, 756
Bst4CI ACNGT 3 cut(s) 600, 867, 1124
Bst6I CTCTTC 3 cut(s) 25, 53, 915
BstACI GRCGYC 1 cut(s) 39
BstAUI TGTACA 1 cut(s) 661
BstC8I GCNNGC 6 cut(s) 111, 199, 353, 433, 709, 966
BstDEI CTNAG 3 cut(s) 187, 356, 510
BstF5I GGATG 3 cut(s) 433, 817, 902
BstKTI GATC 3 cut(s) 484, 575, 777
BstMAI GTCTC 3 cut(s) 151, 741, 1107
BstMBI GATC 3 cut(s) 481, 572, 774
BstMWI GCNNNNNNNGC 3 cut(s) 94, 611, 1056
BstNI CCWGG 2 cut(s) 241, 756
BstNSI RCATGY 3 cut(s) 32, 60, 109
BstSCI CCNGG 2 cut(s) 239, 754
BstSLI GKGCMC 1 cut(s) 565
BstV1I GCAGC 4 cut(s) 292, 303, 406, 626
BsuRI GGCC 3 cut(s) 605, 711, 810
BtsCI GGATG 3 cut(s) 433, 817, 902
Cac8I GCNNGC 6 cut(s) 111, 199, 353, 433, 709, 966
CciI TCATGA 1 cut(s) 1068
Cfr13I GGNCC 2 cut(s) 243, 709
CseI GACGC 1 cut(s) 47
Csp6I GTAC 3 cut(s) 169, 662, 946
CviQI GTAC 3 cut(s) 169, 662, 946
DdeI CTNAG 3 cut(s) 187, 356, 510
DpnI GATC 3 cut(s) 483, 574, 776
DpnII GATC 3 cut(s) 481, 572, 774
DraI TTTAAA 1 cut(s) 1138
DrdI GACNNNNNNGTC 1 cut(s) 143
DseDI GACNNNNNNGTC 1 cut(s) 143
EaeI YGGCCR 1 cut(s) 603
Eam1104I CTCTTC 3 cut(s) 25, 53, 915
EarI CTCTTC 3 cut(s) 25, 53, 915
Eco130I CCWWGG 1 cut(s) 568
Eco24I GRGCYC 2 cut(s) 90, 543
Eco31I GGTCTC 1 cut(s) 741
Eco47I GGWCC 1 cut(s) 243
Eco57I CTGAAG 2 cut(s) 303, 647
Eco88I CYCGRG 1 cut(s) 738
EcoRI GAATTC 1 cut(s) 794
EcoRII CCWGG 2 cut(s) 239, 754
EcoT14I CCWWGG 1 cut(s) 568
EcoT38I GRGCYC 2 cut(s) 90, 543
ErhI CCWWGG 1 cut(s) 568
FaqI GGGAC 1 cut(s) 507
FauI CCCGC 3 cut(s) 206, 484, 700
FauNDI CATATG 1 cut(s) 1148
FbaI TGATCA 1 cut(s) 481
Fnu4HI GCNGC 4 cut(s) 306, 317, 395, 615
FokI GGATG 3 cut(s) 440, 804, 889
FriOI GRGCYC 2 cut(s) 90, 543
Fsp4HI GCNGC 4 cut(s) 306, 317, 395, 615
FspBI CTAG 2 cut(s) 222, 965
GluI GCNGC 4 cut(s) 306, 317, 395, 615
GsuI CTGGAG 2 cut(s) 624, 825
HaeIII GGCC 3 cut(s) 605, 711, 810
HgaI GACGC 1 cut(s) 47
Hin1I GRCGYC 1 cut(s) 39
HindIII AAGCTT 2 cut(s) 285, 515
HinfI GANTC 5 cut(s) 545, 813, 829, 859, 1115
HphI GGTGA 4 cut(s) 229, 314, 515, 713
Hpy166II GTNNAC 3 cut(s) 439, 563, 1001
Hpy188I TCNGA 3 cut(s) 688, 779, 1043
Hpy188III TCNNGA 8 cut(s) 134, 328, 641, 738, 804, 821, 890, 1069
Hpy8I GTNNAC 3 cut(s) 439, 563, 1001
Hpy99I CGWCG 2 cut(s) 41, 867
HpyAV CCTTC 2 cut(s) 622, 715
HpyCH4III ACNGT 3 cut(s) 600, 867, 1124
HpyCH4IV ACGT 1 cut(s) 441
HpyCH4V TGCA 7 cut(s) 97, 319, 341, 563, 790, 910, 1158
HpyF10VI GCNNNNNNNGC 3 cut(s) 94, 611, 1056
HpyF3I CTNAG 3 cut(s) 187, 356, 510
HpySE526I ACGT 1 cut(s) 441
Hsp92I GRCGYC 1 cut(s) 39
Ksp22I TGATCA 1 cut(s) 481
Kzo9I GATC 3 cut(s) 481, 572, 774
LmnI GCTCC 5 cut(s) 488, 538, 643, 925, 937
Lsp1109I GCAGC 4 cut(s) 292, 303, 406, 626
LweI GCATC 3 cut(s) 328, 418, 1088
MaeI CTAG 2 cut(s) 222, 965
MaeII ACGT 1 cut(s) 441
MaeIII GTNAC 3 cut(s) 235, 260, 692
MalI GATC 3 cut(s) 483, 574, 776
MbiI CCGCTC 2 cut(s) 248, 491
MboI GATC 3 cut(s) 481, 572, 774
MboII GAAGA 4 cut(s) 12, 40, 932, 1045
MfeI CAATTG 1 cut(s) 941
MhlI GDGCHC 7 cut(s) 8, 36, 64, 90, 543, 565, 930
MlsI TGGCCA 1 cut(s) 605
MluCI AATT 5 cut(s) 176, 714, 794, 876, 941
MluNI TGGCCA 1 cut(s) 605
MlyI GAGTC 2 cut(s) 807, 1109
MmeI TCCRAC 2 cut(s) 103, 174
Mox20I TGGCCA 1 cut(s) 605
MroXI GAANNNNTTC 1 cut(s) 858
MscI TGGCCA 1 cut(s) 605
MseI TTAA 3 cut(s) 761, 869, 1137
MslI CAYNNNNRTG 4 cut(s) 29, 57, 461, 954
Msp20I TGGCCA 1 cut(s) 605
MspA1I CMGCKG 2 cut(s) 271, 617
MspR9I CCNGG 2 cut(s) 241, 756
MunI CAATTG 1 cut(s) 941
Mva1269I GAATGC 1 cut(s) 454
MvaI CCWGG 2 cut(s) 241, 756
MwoI GCNNNNNNNGC 3 cut(s) 94, 611, 1056
NdeI CATATG 1 cut(s) 1148
NdeII GATC 3 cut(s) 481, 572, 774
NheI GCTAGC 1 cut(s) 964
NlaIV GGNNCC 3 cut(s) 540, 639, 753
NmuCI GTSAC 1 cut(s) 235
NspI RCATGY 3 cut(s) 32, 60, 109
OliI CACNNNNGTG 2 cut(s) 29, 57
PaeR7I CTCGAG 1 cut(s) 738
PagI TCATGA 1 cut(s) 1068
PctI GAATGC 1 cut(s) 454
PdmI GAANNNNTTC 1 cut(s) 858
PfeI GAWTC 3 cut(s) 545, 829, 859
PkrI GCNGC 4 cut(s) 307, 318, 396, 616
PleI GAGTC 2 cut(s) 807, 1109
PpsI GAGTC 2 cut(s) 807, 1109
PsiI TTATAA 1 cut(s) 836
Psp6I CCWGG 2 cut(s) 239, 754
PspGI CCWGG 2 cut(s) 239, 754
PspN4I GGNNCC 3 cut(s) 540, 639, 753
PspPI GGNCC 2 cut(s) 243, 709
PvuII CAGCTG 1 cut(s) 617
RsaI GTAC 3 cut(s) 170, 663, 947
RsaNI GTAC 3 cut(s) 169, 662, 946
RseI CAYNNNNRTG 4 cut(s) 29, 57, 461, 954
SaqAI TTAA 3 cut(s) 761, 869, 1137
SatI GCNGC 4 cut(s) 306, 317, 395, 615
Sau3AI GATC 3 cut(s) 481, 572, 774
Sau96I GGNCC 2 cut(s) 243, 709
SchI GAGTC 2 cut(s) 807, 1109
ScrFI CCNGG 2 cut(s) 241, 756
SduI GDGCHC 7 cut(s) 8, 36, 64, 90, 543, 565, 930
SfaNI GCATC 3 cut(s) 328, 418, 1088
Sfr274I CTCGAG 1 cut(s) 738
SinI GGWCC 1 cut(s) 243
SlaI CTCGAG 1 cut(s) 738
SmiMI CAYNNNNRTG 4 cut(s) 29, 57, 461, 954
SmlI CTYRAG 1 cut(s) 738
SmoI CTYRAG 1 cut(s) 738
Sse9I AATT 5 cut(s) 176, 714, 794, 876, 941
SsiI CCGC 7 cut(s) 199, 246, 271, 491, 707, 996, 1008
SspMI CTAG 2 cut(s) 222, 965
StyD4I CCNGG 2 cut(s) 239, 754
StyI CCWWGG 1 cut(s) 568
TaaI ACNGT 3 cut(s) 600, 867, 1124
TaiI ACGT 1 cut(s) 444
TaqI TCGA 6 cut(s) 8, 36, 64, 210, 739, 862
TasI AATT 5 cut(s) 176, 714, 794, 876, 941
TatI WGTACW 1 cut(s) 661
TfiI GAWTC 3 cut(s) 545, 829, 859
Tru1I TTAA 3 cut(s) 761, 869, 1137
Tru9I TTAA 3 cut(s) 761, 869, 1137
TseFI GTSAC 1 cut(s) 235
TseI GCWGC 4 cut(s) 305, 316, 394, 614
Tsp45I GTSAC 1 cut(s) 235
TspDTI ATGAA 9 cut(s) 228, 639, 743, 807, 1001, 1005, 1046, 1057, 1085
TspGWI ACGGA 1 cut(s) 538
VneI GTGCAC 1 cut(s) 561
VpaK11BI GGWCC 1 cut(s) 243
XapI RAATTY 2 cut(s) 176, 794
XceI RCATGY 3 cut(s) 32, 60, 109
XcmI CCANNNNNNNNNTGG 1 cut(s) 1139
XhoI CTCGAG 1 cut(s) 738
XmnI GAANNNNTTC 1 cut(s) 858
XspI CTAG 2 cut(s) 222, 965
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.