Rorug04G0148900

RNA polymerase-associated protein CTR9 homolog

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_rugosa
GWHBQTZ00000004
OG0002125
Physical Location & Seq
Reverse (-)
26195810 .. 26200559
4750 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug04G0148900.1

Sequence Viewer

Length: 810 bp
ATGTACAATAATGTGGGAGCCCAGCCTGGTGTGCCGAGACCACCTGCAAATCCCCAGCCTAATCCGTTTGGAAATACGTTTTATGGTGCTGGTTCAGGACTTATCCGAGGTGGATTGGGTGCCTATGGAGAGAAAATTCTAGGATCAAGCTCTGAGTATGTACAAAGCAACATTAGTAGATATTTCTCTGATCCTCAGTATTACTTCCAAGTGAATGATCAGTATGTGAGGAACAAATTGAAGGTGGTTCTATTTCCATTTCTGCACAGGGGTCATTGGACACGGATAACTGAGCCCGTAGGAGGCAGACTTTCTTATAAACCCCCAATATACGATATCAATGCACCCGACCTATACATTCCCTTTATGGCATTTGGTACCTATGTGGTTTTGGCTGGCTTCTCATTGGGTCGTCATGGGAAGTTCAGCCCTGAGGCTCTAAACTGGTTATTTATCAAGGGATTGCTTGGCTGGTTTGTGCAAGTTATAATTCTGAAAATCACGTTGTTTTCATTGGGTGGTGGTGAGGCGCCCTTGCTAGATATGGTGGCATATGCAGGTTATACTTTCACTGGGTTATGCTTGGCTGTGCTTGGACGGATTATGTGGAATTATTCGTACTATTTTTTGATGCCTTGGACCTGTTTATGCATGGGAGTCTTCTTGGTGAAGACTATGAAGAGAGTCCTCTTTGCAGAGGTGAGGAGTTATGATTCAAGCAAGCACCATTATCTCCTGCTCTTCATTGCTTTGGCTCAGTTCCCAGTTTTTACTTGGCTTGGTAACATTAGTGTTAATTGGCTGATATAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0000122 GO:0000428 GO:0000785 GO:0000993 GO:0001098 GO:0001099 GO:0003674 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005694 GO:0006325 GO:0006355 GO:0006357 GO:0006464 GO:0006479 GO:0006807 GO:0006996 GO:0008023 GO:0008150 GO:0008152 GO:0008213 GO:0009889 GO:0009890 GO:0009891 GO:0009892 GO:0009893 GO:0009909 GO:0009910 GO:0009987 GO:0010468 GO:0010556 GO:0010557 GO:0010558 GO:0010604 GO:0010605 GO:0010628 GO:0010629 GO:0010638 GO:0016020 GO:0016043 GO:0016569 GO:0016570 GO:0016571 GO:0016591 GO:0016593 GO:0018022 GO:0018023 GO:0018193 GO:0018205 GO:0019219 GO:0019222 GO:0019538 GO:0019899 GO:0030880 GO:0031056 GO:0031058 GO:0031060 GO:0031062 GO:0031323 GO:0031324 GO:0031325 GO:0031326 GO:0031327 GO:0031328 GO:0031399 GO:0031401 GO:0031974 GO:0031981 GO:0032259 GO:0032268 GO:0032270 GO:0032784 GO:0032786 GO:0032968 GO:0032991 GO:0033043 GO:0033044 GO:0034243 GO:0034968 GO:0035327 GO:0036211 GO:0043170 GO:0043175 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043412 GO:0043414 GO:0044237 GO:0044238 GO:0044260 GO:0044267 GO:0044422 GO:0044424 GO:0044427 GO:0044428 GO:0044446 GO:0044451 GO:0044464 GO:0044877 GO:0045892 GO:0045893 GO:0045934 GO:0045935 GO:0045944 GO:0048518 GO:0048519 GO:0048522 GO:0048523 GO:0048580 GO:0048581 GO:0048831 GO:0050789 GO:0050793 GO:0050794 GO:0051093 GO:0051128 GO:0051130 GO:0051171 GO:0051172 GO:0051173 GO:0051239 GO:0051241 GO:0051246 GO:0051247 GO:0051252 GO:0051253 GO:0051254 GO:0051276 GO:0051568 GO:0051569 GO:0051571 GO:0055029 GO:0060255 GO:0061695 GO:0065007 GO:0070013 GO:0070063 GO:0071704 GO:0071840 GO:0080090 GO:0080182 GO:1901564 GO:1902275 GO:1902494 GO:1902679 GO:1902680 GO:1903506 GO:1903507 GO:1903508 GO:1905269 GO:1990234 GO:2000026 GO:2000112 GO:2000113 GO:2000241 GO:2000242 GO:2001141 GO:2001252
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
TPR_1 TPR_16 TPR_2 TPR_6 TPR_8

Protein Analysis

269

Amino Acids

30.37

Weight (kDa)

9.4

Isoelectric Point (pI)

44.71

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
YIF1 PF03878 41 - 260 2e-56 YIF1
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 2 cut(s) 318, 488
AarI CACCTGC 1 cut(s) 52
Acc36I ACCTGC 2 cut(s) 52, 548
Acc65I GGTACC 1 cut(s) 377
AccB1I GGYRCC 3 cut(s) 119, 377, 529
AclWI GGATC 2 cut(s) 151, 185
AcsI RAATTY 1 cut(s) 135
AcyI GRCGYC 1 cut(s) 530
AfaI GTAC 4 cut(s) 5, 162, 379, 620
AfiI CCNNNNNNNGG 1 cut(s) 302
AgsI TTSAA 2 cut(s) 241, 717
AjnI CCWGG 1 cut(s) 25
AluBI AGCT 1 cut(s) 150
AluI AGCT 1 cut(s) 150
Alw26I GTCTC 1 cut(s) 31
AlwI GGATC 2 cut(s) 151, 185
ApoI RAATTY 1 cut(s) 135
Asp718I GGTACC 1 cut(s) 377
AspLEI GCGC 1 cut(s) 532
AspS9I GGNCC 1 cut(s) 639
AsuHPI GGTGA 3 cut(s) 536, 679, 712
AvaII GGWCC 1 cut(s) 639
AxyI CCTNAGG 1 cut(s) 432
BaeI ACNNNNGTAYC 2 cut(s) 369, 402
BanI GGYRCC 3 cut(s) 119, 377, 529
BanII GRGCYC 2 cut(s) 22, 297
BbsI GAAGAC 2 cut(s) 652, 677
BcgI CGANNNNNNTGC 2 cut(s) 323, 357
BciT130I CCWGG 1 cut(s) 27
BclI TGATCA 1 cut(s) 217
BcoDI GTCTC 1 cut(s) 31
BfaI CTAG 2 cut(s) 140, 539
BfoI RGCGCY 1 cut(s) 533
BfuAI ACCTGC 2 cut(s) 52, 548
Bme1390I CCNGG 1 cut(s) 27
Bme18I GGWCC 1 cut(s) 639
BmgT120I GGNCC 1 cut(s) 639
BmiI GGNNCC 4 cut(s) 19, 121, 379, 531
BmrFI CCNGG 1 cut(s) 27
BmrI ACTGGG 2 cut(s) 582, 758
BmsI GCATC 1 cut(s) 621
BmuI ACTGGG 2 cut(s) 582, 758
BpiI GAAGAC 2 cut(s) 652, 677
BsaHI GRCGYC 1 cut(s) 530
BsaI GGTCTC 1 cut(s) 31
BsaJI CCNNGG 2 cut(s) 106, 635
Bsc4I CCNNNNNNNGG 1 cut(s) 302
Bse1I ACTGG 3 cut(s) 449, 577, 764
Bse21I CCTNAGG 1 cut(s) 432
Bse3DI GCAATG 1 cut(s) 744
BseBI CCWGG 1 cut(s) 27
BseDI CCNNGG 2 cut(s) 106, 635
BseLI CCNNNNNNNGG 1 cut(s) 302
BseMI GCAATG 1 cut(s) 744
BseMII CTCAG 5 cut(s) 144, 209, 282, 423, 770
BseNI ACTGG 3 cut(s) 449, 577, 764
BseRI GAGGAG 1 cut(s) 718
BseYI CCCAGC 2 cut(s) 21, 54
BsgI GTGCAG 1 cut(s) 248
BshNI GGYRCC 3 cut(s) 119, 377, 529
BslI CCNNNNNNNGG 1 cut(s) 302
BsmAI GTCTC 1 cut(s) 31
Bso31I GGTCTC 1 cut(s) 31
Bsp1286I GDGCHC 2 cut(s) 22, 297
Bsp1407I TGTACA 2 cut(s) 3, 160
Bsp143I GATC 3 cut(s) 143, 190, 217
BspCNI CTCAG 5 cut(s) 145, 208, 283, 424, 769
BspLI GGNNCC 4 cut(s) 19, 121, 379, 531
BspMI ACCTGC 2 cut(s) 52, 548
BspPI GGATC 2 cut(s) 151, 185
BspQI GCTCTTC 1 cut(s) 746
BspT107I GGYRCC 3 cut(s) 119, 377, 529
BspTNI GGTCTC 1 cut(s) 31
BsrDI GCAATG 1 cut(s) 744
BsrGI TGTACA 2 cut(s) 3, 160
BsrI ACTGG 3 cut(s) 449, 577, 764
BssECI CCNNGG 2 cut(s) 106, 635
BssMI GATC 3 cut(s) 143, 190, 217
BssNI GRCGYC 1 cut(s) 530
BssT1I CCWWGG 1 cut(s) 635
Bst2UI CCWGG 1 cut(s) 27
Bst6I CTCTTC 2 cut(s) 674, 746
BstACI GRCGYC 1 cut(s) 530
BstAUI TGTACA 2 cut(s) 3, 160
BstC8I GCNNGC 2 cut(s) 397, 722
BstDEI CTNAG 5 cut(s) 153, 195, 291, 432, 756
BstH2I RGCGCY 1 cut(s) 533
BstHHI GCGC 1 cut(s) 532
BstKTI GATC 3 cut(s) 146, 193, 220
BstMAI GTCTC 1 cut(s) 31
BstMBI GATC 3 cut(s) 143, 190, 217
BstMWI GCNNNNNNNGC 1 cut(s) 31
BstNI CCWGG 1 cut(s) 27
BstSCI CCNGG 1 cut(s) 25
BstV2I GAAGAC 2 cut(s) 652, 677
Bsu36I CCTNAGG 1 cut(s) 432
BtsIMutI CAGTG 1 cut(s) 570
BveI ACCTGC 2 cut(s) 52, 548
Cac8I GCNNGC 2 cut(s) 397, 722
CfoI GCGC 1 cut(s) 532
Cfr13I GGNCC 1 cut(s) 639
Csp6I GTAC 4 cut(s) 4, 161, 378, 619
CviAII CATG 2 cut(s) 416, 652
CviQI GTAC 4 cut(s) 4, 161, 378, 619
DdeI CTNAG 5 cut(s) 153, 195, 291, 432, 756
DinI GGCGCC 1 cut(s) 531
DpnI GATC 3 cut(s) 145, 192, 219
DpnII GATC 3 cut(s) 143, 190, 217
Eam1104I CTCTTC 2 cut(s) 674, 746
EarI CTCTTC 2 cut(s) 674, 746
Eco130I CCWWGG 1 cut(s) 635
Eco24I GRGCYC 2 cut(s) 22, 297
Eco31I GGTCTC 1 cut(s) 31
Eco32I GATATC 1 cut(s) 337
Eco47I GGWCC 1 cut(s) 639
Eco81I CCTNAGG 1 cut(s) 432
EcoRII CCWGG 1 cut(s) 25
EcoRV GATATC 1 cut(s) 337
EcoT14I CCWWGG 1 cut(s) 635
EcoT22I ATGCAT 1 cut(s) 653
EcoT38I GRGCYC 2 cut(s) 22, 297
EgeI GGCGCC 1 cut(s) 531
EheI GGCGCC 1 cut(s) 531
ErhI CCWWGG 1 cut(s) 635
FaeI CATG 2 cut(s) 419, 655
FatI CATG 2 cut(s) 415, 651
FauNDI CATATG 1 cut(s) 553
FbaI TGATCA 1 cut(s) 217
FriOI GRGCYC 2 cut(s) 22, 297
FspBI CTAG 2 cut(s) 140, 539
GlaI GCGC 1 cut(s) 531
GsaI CCCAGC 2 cut(s) 25, 58
HaeII RGCGCY 1 cut(s) 533
HhaI GCGC 1 cut(s) 532
Hin1I GRCGYC 1 cut(s) 530
Hin1II CATG 2 cut(s) 419, 655
Hin6I GCGC 1 cut(s) 530
HinP1I GCGC 1 cut(s) 530
HinfI GANTC 3 cut(s) 657, 684, 713
HphI GGTGA 3 cut(s) 536, 679, 712
Hpy188I TCNGA 4 cut(s) 107, 154, 190, 495
Hpy188III TCNNGA 1 cut(s) 96
HpyAV CCTTC 1 cut(s) 235
HpyCH4IV ACGT 2 cut(s) 77, 503
HpyCH4V TGCA 7 cut(s) 47, 265, 344, 481, 557, 651, 695
HpyF10VI GCNNNNNNNGC 1 cut(s) 31
HpyF3I CTNAG 5 cut(s) 153, 195, 291, 432, 756
HpySE526I ACGT 2 cut(s) 77, 503
Hsp92I GRCGYC 1 cut(s) 530
Hsp92II CATG 2 cut(s) 419, 655
HspAI GCGC 1 cut(s) 530
KasI GGCGCC 1 cut(s) 529
KpnI GGTACC 1 cut(s) 381
Ksp22I TGATCA 1 cut(s) 217
Kzo9I GATC 3 cut(s) 143, 190, 217
LguI GCTCTTC 1 cut(s) 746
LmnI GCTCC 1 cut(s) 17
LweI GCATC 1 cut(s) 621
MaeI CTAG 2 cut(s) 140, 539
MaeII ACGT 2 cut(s) 77, 503
MaeIII GTNAC 1 cut(s) 782
MalI GATC 3 cut(s) 145, 192, 219
MboI GATC 3 cut(s) 143, 190, 217
MboII GAAGA 4 cut(s) 652, 682, 691, 733
MhlI GDGCHC 2 cut(s) 22, 297
MluCI AATT 5 cut(s) 135, 236, 489, 610, 796
Mly113I GGCGCC 1 cut(s) 530
MlyI GAGTC 2 cut(s) 666, 693
MnlI CCTC 9 cut(s) 101, 204, 222, 296, 427, 520, 691, 696, 698
Mph1103I ATGCAT 1 cut(s) 653
MseI TTAA 1 cut(s) 795
MspR9I CCNGG 1 cut(s) 27
MvaI CCWGG 1 cut(s) 27
MwoI GCNNNNNNNGC 1 cut(s) 31
NarI GGCGCC 1 cut(s) 530
NdeI CATATG 1 cut(s) 553
NdeII GATC 3 cut(s) 143, 190, 217
NlaIII CATG 2 cut(s) 419, 655
NlaIV GGNNCC 4 cut(s) 19, 121, 379, 531
NmeAIII GCCGAG 1 cut(s) 60
NsiI ATGCAT 1 cut(s) 653
PaqCI CACCTGC 1 cut(s) 52
PciSI GCTCTTC 1 cut(s) 746
PfeI GAWTC 1 cut(s) 713
PleI GAGTC 2 cut(s) 665, 692
PluTI GGCGCC 1 cut(s) 533
PpsI GAGTC 2 cut(s) 665, 692
PsiI TTATAA 2 cut(s) 318, 488
Psp6I CCWGG 1 cut(s) 25
PspFI CCCAGC 2 cut(s) 21, 54
PspGI CCWGG 1 cut(s) 25
PspN4I GGNNCC 4 cut(s) 19, 121, 379, 531
PspPI GGNCC 1 cut(s) 639
RsaI GTAC 4 cut(s) 5, 162, 379, 620
RsaNI GTAC 4 cut(s) 4, 161, 378, 619
SapI GCTCTTC 1 cut(s) 746
SaqAI TTAA 1 cut(s) 795
Sau3AI GATC 3 cut(s) 143, 190, 217
Sau96I GGNCC 1 cut(s) 639
SchI GAGTC 2 cut(s) 666, 693
ScrFI CCNGG 1 cut(s) 27
SduI GDGCHC 2 cut(s) 22, 297
SfaNI GCATC 1 cut(s) 621
SfoI GGCGCC 1 cut(s) 531
SinI GGWCC 1 cut(s) 639
Sse9I AATT 5 cut(s) 135, 236, 489, 610, 796
SspDI GGCGCC 1 cut(s) 529
SspMI CTAG 2 cut(s) 140, 539
StyD4I CCNGG 1 cut(s) 25
StyI CCWWGG 1 cut(s) 635
TaiI ACGT 2 cut(s) 80, 506
TasI AATT 5 cut(s) 135, 236, 489, 610, 796
TatI WGTACW 2 cut(s) 3, 160
TfiI GAWTC 1 cut(s) 713
Tru1I TTAA 1 cut(s) 795
Tru9I TTAA 1 cut(s) 795
TscAI CASTG 1 cut(s) 577
TspDTI ATGAA 3 cut(s) 501, 692, 733
TspGWI ACGGA 3 cut(s) 54, 298, 613
TspRI CASTG 1 cut(s) 577
VpaK11BI GGWCC 1 cut(s) 639
XapI RAATTY 1 cut(s) 135
XcmI CCANNNNNNNNNTGG 1 cut(s) 771
XspI CTAG 2 cut(s) 140, 539
Zsp2I ATGCAT 1 cut(s) 653
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.