RchiOBHm_Chr3g0496641

DNA-directed 5'-3' RNA polymerase activity

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
3
OG0000089
Physical Location & Seq
Forward (+)
47855305 .. 47857031
1727 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ45895

Sequence Viewer

Length: 540 bp
ATGCTTTCTCAATCACAAGAGATTGAACGATTGAAAGAAGTGGTTGCCACTCTTTTAGCAAGATCAGAGAAAGAAGGGAATAACCACAATGAAAATCCTAGTGTTCAACATCATAGCAGTGATGGAGTACAAAGCAACCAAAATATTGCAAGTGTTCGAGGTTCTGACAGTGGGAGGCCACAAAGCAAGCAAAGCAACCAAAAGAAAACTTCAAGTATTCAATATTCTGCTGATCATGGGTCACAAAGCAAAGACAAAGAAGGTAAAAGGACCAAAGTTACAAAGGATGATCAGAATAGAATCGAATTGTTAAGTTGGTTTGAGAAGGAAGAACAGGTTGTTGCAATTGCAAAACTTGAGTCAAAAGATCCAAATGTAAAGGTCCATCATGTGCCCCTTGGTCATGAATGCTGGAAAGTTTGGGTGCTTGATGTTTTTGAGGATATAGCTTTATATCGACCAACTAGGGAGTTTGGAACACTGAGTATGGCTCAAGGAAGTACAATTGCATGGCCTATCAAGTACATCAAACAAGTTTAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0000375 GO:0000377 GO:0000398 GO:0000418 GO:0000419 GO:0000428 GO:0003674 GO:0003824 GO:0003899 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005665 GO:0005666 GO:0005730 GO:0005736 GO:0005737 GO:0005829 GO:0006139 GO:0006259 GO:0006281 GO:0006283 GO:0006289 GO:0006351 GO:0006352 GO:0006353 GO:0006354 GO:0006355 GO:0006356 GO:0006360 GO:0006361 GO:0006363 GO:0006366 GO:0006367 GO:0006368 GO:0006370 GO:0006383 GO:0006396 GO:0006397 GO:0006399 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0007154 GO:0007165 GO:0007166 GO:0007167 GO:0007169 GO:0008150 GO:0008152 GO:0008270 GO:0008380 GO:0008543 GO:0009058 GO:0009059 GO:0009301 GO:0009304 GO:0009452 GO:0009719 GO:0009889 GO:0009893 GO:0009987 GO:0010033 GO:0010467 GO:0010468 GO:0010556 GO:0010604 GO:0010628 GO:0016070 GO:0016071 GO:0016073 GO:0016591 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019219 GO:0019222 GO:0019438 GO:0023052 GO:0030880 GO:0031323 GO:0031326 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0033554 GO:0034062 GO:0034641 GO:0034645 GO:0034654 GO:0034660 GO:0036260 GO:0040029 GO:0042221 GO:0042795 GO:0042797 GO:0043167 GO:0043169 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044344 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044451 GO:0044452 GO:0044464 GO:0045815 GO:0046483 GO:0046872 GO:0046914 GO:0048518 GO:0050789 GO:0050794 GO:0050896 GO:0051171 GO:0051252 GO:0051716 GO:0055029 GO:0060147 GO:0060255 GO:0060964 GO:0060966 GO:0060968 GO:0061695 GO:0065007 GO:0070013 GO:0070848 GO:0070887 GO:0071310 GO:0071363 GO:0071495 GO:0071704 GO:0071774 GO:0080090 GO:0090304 GO:0097659 GO:0097747 GO:0098781 GO:0140098 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1903506 GO:1990234 GO:2000112 GO:2001141
KEGG Pathways
Metabolic & Signaling
ko00230 ko00240 ko01100 ko03010 ko03020 ko04623 ko05016 ko05169 ko05202 map00230 map00240 map01100 map03010 map03020 map04623 map05016 map05169 map05202
Pfam Domains
Protein Families
RNA_pol_N

Protein Analysis

179

Amino Acids

20.26

Weight (kDa)

7.87

Isoelectric Point (pI)

51.34

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
DUF8039 PF26133 103 - 177 1.3e-07 Domain of unknown function (DUF8039)
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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Orthologous Genes (Group: OG0000089)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G42700
fragaria_vesca FvH4_1g29233 FvH4_1g29373 FvH4_2g07142 FvH4_2g08144 FvH4_3g21852 FvH4_3g29221 FvH4_3g32731 FvH4_3g45091 FvH4_4g01311 FvH4_4g03220 FvH4_4g06631 FvH4_4g10040 FvH4_4g10363 FvH4_4g12371 FvH4_4g15323 FvH4_4g15580 FvH4_4g16173 FvH4_5g18843 FvH4_5g23172 FvH4_5g27660 FvH4_5g37213 FvH4_6g17382 FvH4_6g20172 FvH4_6g20173 FvH4_6g21082 FvH4_6g35541
malus_domestica MD02G1251500.v1.1 MD02G1252300.v1.1
pyrus_communis pycom01g02580 pycom01g08340 pycom01g08610 pycom11g01520 pycom12g04790
rosa_chinensis RchiOBHm_Chr0c16g0499821 RchiOBHm_Chr0c16g0499871 RchiOBHm_Chr0c28g0501051 RchiOBHm_Chr1g0313071 RchiOBHm_Chr1g0315701 RchiOBHm_Chr1g0318841 RchiOBHm_Chr1g0326261 RchiOBHm_Chr1g0357501 RchiOBHm_Chr2g0133581 RchiOBHm_Chr2g0134701 RchiOBHm_Chr2g0152521 RchiOBHm_Chr3g0455961 RchiOBHm_Chr3g0458231 RchiOBHm_Chr3g0460621 RchiOBHm_Chr3g0492791 RchiOBHm_Chr3g0492801 RchiOBHm_Chr3g0496631 RchiOBHm_Chr3g0496641 RchiOBHm_Chr4g0386541 RchiOBHm_Chr4g0415851 RchiOBHm_Chr4g0420561 RchiOBHm_Chr4g0422721 RchiOBHm_Chr4g0433611 RchiOBHm_Chr4g0444771 RchiOBHm_Chr5g0033771 RchiOBHm_Chr5g0059371 RchiOBHm_Chr5g0060161 RchiOBHm_Chr5g0064791 RchiOBHm_Chr5g0064801 RchiOBHm_Chr6g0269851 RchiOBHm_Chr6g0280321 RchiOBHm_Chr6g0287111 RchiOBHm_Chr7g0177401 RchiOBHm_Chr7g0200581 RchiOBHm_Chr7g0200591 RchiOBHm_Chr7g0231331
rosa_laevigata RLG00000001052 RLG00000001162 RLG00000002271 RLG00000002679 RLG00000007743 RLG00000009828 RLG00000009891 RLG00000009895 RLG00000009898 RLG00000017129 RLG00000018019 RLG00000018832 RLG00000018849 RLG00000019409 RLG00000019469 RLG00000019633 RLG00000019682 RLG00000020304 RLG00000024132 RLG00000027333 RLG00000028566 RLG00000031685 RLG00000031699 RLG00000034060 RLG00000034663 RLG00000035858 RLG00000036314
rosa_multiflora Rmu_sc0000178.1_g000001 Rmu_sc0000847.1_g000010 Rmu_sc0000861.1_g000033 Rmu_sc0001043.1_g000008 Rmu_sc0001499.1_g000050 Rmu_sc0001572.1_g000045 Rmu_sc0001768.1_g000043 Rmu_sc0001824.1_g000038 Rmu_sc0002037.1_g000022 Rmu_sc0002042.1_g000011 Rmu_sc0002322.1_g000001 Rmu_sc0002401.1_g000002 Rmu_sc0002438.1_g000018 Rmu_sc0002648.1_g000010 Rmu_sc0002784.1_g000047 Rmu_sc0003776.1_g000004 Rmu_sc0003780.1_g000005 Rmu_sc0004140.1_g000039 Rmu_sc0004596.1_g000033 Rmu_sc0004866.1_g000040 Rmu_sc0004964.1_g000011 Rmu_sc0005065.1_g000039 Rmu_sc0005137.1_g000032 Rmu_sc0005294.1_g000031 Rmu_sc0005426.1_g000005 Rmu_sc0005789.1_g000017 Rmu_sc0007891.1_g000008 Rmu_sc0008554.1_g000002 Rmu_sc0011363.1_g000002 Rmu_sc0020081.1_g000001 Rmu_ssc0000079.1_g000015
rosa_roxburghii Rroxscaffold_1G00010060 Rroxscaffold_1G00013840 Rroxscaffold_1G00031540 Rroxscaffold_1G00039640 Rroxscaffold_1G00048530 Rroxscaffold_2G00093720 Rroxscaffold_2G00093730 Rroxscaffold_2G00109830 Rroxscaffold_2G00109890 Rroxscaffold_2G00149920 Rroxscaffold_3G00274720 Rroxscaffold_4G00300310 Rroxscaffold_5G00347510 Rroxscaffold_5G00360920 Rroxscaffold_5G00362090 Rroxscaffold_5G00368170 Rroxscaffold_6G00391580 Rroxscaffold_7G00181720 Rroxscaffold_7G00209870
rosa_rugosa Rorug01G0071800 Rorug01G0071900 Rorug01G0072000 Rorug01G0072100 Rorug01G0084700 Rorug01G0104500 Rorug01G0104500 Rorug01G0134900.1 Rorug01G0135000.1 Rorug01G0183500 Rorug01G0256500 Rorug01G0312300 Rorug01G0312400 Rorug01G0351500 Rorug01G0384100 Rorug02G0039300 Rorug02G0319100 Rorug02G0319200 Rorug02G0319300 Rorug02G0461700 Rorug02G0531700 Rorug02G0617600 Rorug03G0155300 Rorug03G0190400 Rorug03G0248900 Rorug03G0249000 Rorug05G0141900 Rorug05G0325500 Rorug05G0325600 Rorug05G0369600 Rorug05G0490000 Rorug05G0490100.1 Rorug06G0009300 Rorug06G0035500 Rorug06G0082200 Rorug06G0133600 Rorug06G0133700 Rorug06G0149500 Rorug06G0149600 Rorug06G0149700 Rorug06G0351300 Rorug06G0443300 Rorug06G0443400 Rorug06G0443500 Rorug06G0443500 Rorug06G0443500 Rorug06G0480000 Rorug07G0260700 Rorug07G0260800 Rorug07G0289600 Rorug07G0289700 Rorug07G0319200 Rorug07G0319300
rosa_samantha Rh1AG098300 Rh1BG003900 Rh1BG262700 Rh1CG054000 Rh1CG054100 Rh1CG054200 Rh1CG232800 Rh1DG058300 Rh1DG058400 Rh1DG058500 Rh1DG085300 Rh1DG137700 Rh2AG234800 Rh2BG248300 Rh2CG045400 Rh2CG239300 Rh2CG239400 Rh2CG326600 Rh2CG349000 Rh2CG355400 Rh2CG402000 Rh2DG001000 Rh2DG242300 Rh3AG001600 Rh3AG306500 Rh3BG373600 Rh3CG001300 Rh3CG365600 Rh4AG013600 Rh4AG178000 Rh4AG198400 Rh4AG198600 Rh4AG416100 Rh4AG416300 Rh4BG029700 Rh4BG138600 Rh4BG150700 Rh4BG196400 Rh4BG427400 Rh4BG427600 Rh4CG442400 Rh4CG442500 Rh4DG171400 Rh4DG171500 Rh4DG171600 Rh4DG196200 Rh4DG423300 Rh4DG423400 Rh5AG490200 Rh5CG422300 Rh5CG428400 Rh5CG513400 Rh5CG519500 Rh5CG579300 Rh6AG225400 Rh6BG053200 Rh6BG195500 Rh6BG245600 Rh6DG161700 Rh6DG238400 Rh7AG348200 Rh7AG396700 Rh7AG396800 Rh7AG410600 Rh7BG445300 Rh7CG255900 Rh7CG365800 Rh7CG415100 Rh7CG415200 Rh7DG191000 Rh7DG191100 Rh7DG362700
rosa_wichuraiana Rw1G003060 Rw2G017950 Rw2G019900 Rw2G038280 Rw2G048340 Rw3G026970 Rw4G006460 Rw4G009350 Rw4G016820 Rw5G034510 Rw5G049530 Rw6G004160 Rw7G032270

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AclWI GGATC 1 cut(s) 362
AfaI GTAC 3 cut(s) 129, 502, 524
AgsI TTSAA 5 cut(s) 26, 34, 107, 213, 221
AluBI AGCT 1 cut(s) 449
AluI AGCT 1 cut(s) 449
AlwI GGATC 1 cut(s) 362
AoxI GGCC 2 cut(s) 176, 512
ArsI GACNNNNNNTTYG 2 cut(s) 344, 376
AspS9I GGNCC 2 cut(s) 270, 382
AvaII GGWCC 2 cut(s) 270, 382
BaeGI GKGCMC 1 cut(s) 396
BccI CCATC 2 cut(s) 116, 393
BclI TGATCA 2 cut(s) 232, 289
BfaI CTAG 2 cut(s) 99, 465
Bme18I GGWCC 2 cut(s) 270, 382
BmgT120I GGNCC 2 cut(s) 270, 382
BplI GAGNNNNNCTC 2 cut(s) 475, 507
BpuEI CTTGAG 2 cut(s) 377, 477
BsaJI CCNNGG 1 cut(s) 397
BseDI CCNNGG 1 cut(s) 397
BseGI GGATG 1 cut(s) 292
BseMII CTCAG 1 cut(s) 473
BseSI GKGCMC 1 cut(s) 396
BshFI GGCC 2 cut(s) 178, 514
BsmI GAATGC 1 cut(s) 413
BsnI GGCC 2 cut(s) 178, 514
Bsp1286I GDGCHC 1 cut(s) 396
Bsp143I GATC 4 cut(s) 62, 232, 289, 367
BspANI GGCC 2 cut(s) 178, 514
BspCNI CTCAG 1 cut(s) 474
BspHI TCATGA 1 cut(s) 403
BspPI GGATC 1 cut(s) 362
BssECI CCNNGG 1 cut(s) 397
BssMI GATC 4 cut(s) 62, 232, 289, 367
BssT1I CCWWGG 1 cut(s) 397
Bst4CI ACNGT 1 cut(s) 170
BstC8I GCNNGC 1 cut(s) 188
BstDEI CTNAG 1 cut(s) 482
BstF5I GGATG 1 cut(s) 292
BstKTI GATC 4 cut(s) 65, 235, 292, 370
BstMBI GATC 4 cut(s) 62, 232, 289, 367
BstMWI GCNNNNNNNGC 1 cut(s) 192
BstSLI GKGCMC 1 cut(s) 396
BstX2I RGATCY 1 cut(s) 367
BstYI RGATCY 1 cut(s) 367
BsuRI GGCC 2 cut(s) 178, 514
BtsCI GGATG 1 cut(s) 292
BtsI GCAGTG 1 cut(s) 124
BtsIMutI CAGTG 3 cut(s) 124, 175, 479
Cac8I GCNNGC 1 cut(s) 188
CciI TCATGA 1 cut(s) 403
Cfr13I GGNCC 2 cut(s) 270, 382
Csp6I GTAC 3 cut(s) 128, 501, 523
CviAII CATG 4 cut(s) 236, 389, 404, 510
CviJI RGCY 4 cut(s) 178, 449, 491, 514
CviKI_1 RGCY 4 cut(s) 178, 449, 491, 514
CviQI GTAC 3 cut(s) 128, 501, 523
DdeI CTNAG 1 cut(s) 482
DpnI GATC 4 cut(s) 64, 234, 291, 369
DpnII GATC 4 cut(s) 62, 232, 289, 367
Eco130I CCWWGG 1 cut(s) 397
Eco47I GGWCC 2 cut(s) 270, 382
EcoT14I CCWWGG 1 cut(s) 397
ErhI CCWWGG 1 cut(s) 397
FaeI CATG 4 cut(s) 239, 392, 407, 513
FaiI YATR 8 cut(s) 114, 237, 390, 405, 446, 454, 488, 511
FatI CATG 4 cut(s) 235, 388, 403, 509
FbaI TGATCA 2 cut(s) 232, 289
FokI GGATG 1 cut(s) 299
FspBI CTAG 2 cut(s) 99, 465
HaeIII GGCC 2 cut(s) 178, 514
Hin1II CATG 4 cut(s) 239, 392, 407, 513
HinfI GANTC 2 cut(s) 300, 359
Hpy188I TCNGA 3 cut(s) 67, 166, 294
Hpy188III TCNNGA 1 cut(s) 404
HpyAV CCTTC 3 cut(s) 68, 254, 319
HpyCH4III ACNGT 1 cut(s) 170
HpyCH4V TGCA 4 cut(s) 149, 344, 350, 509
HpyF10VI GCNNNNNNNGC 1 cut(s) 192
HpyF3I CTNAG 1 cut(s) 482
Hsp92II CATG 4 cut(s) 239, 392, 407, 513
Ksp22I TGATCA 2 cut(s) 232, 289
Kzo9I GATC 4 cut(s) 62, 232, 289, 367
LpnPI CCDG 2 cut(s) 320, 397
MaeI CTAG 2 cut(s) 99, 465
MaeIII GTNAC 2 cut(s) 240, 277
MalI GATC 4 cut(s) 64, 234, 291, 369
MboI GATC 4 cut(s) 62, 232, 289, 367
MboII GAAGA 1 cut(s) 341
MfeI CAATTG 2 cut(s) 345, 504
MflI RGATCY 1 cut(s) 367
MhlI GDGCHC 1 cut(s) 396
MluCI AATT 3 cut(s) 305, 345, 504
MlyI GAGTC 1 cut(s) 368
MnlI CCTC 3 cut(s) 152, 168, 433
MseI TTAA 1 cut(s) 311
MslI CAYNNNNRTG 1 cut(s) 117
MunI CAATTG 2 cut(s) 345, 504
Mva1269I GAATGC 1 cut(s) 413
MwoI GCNNNNNNNGC 1 cut(s) 192
NdeII GATC 4 cut(s) 62, 232, 289, 367
NlaIII CATG 4 cut(s) 239, 392, 407, 513
NmuCI GTSAC 1 cut(s) 240
PagI TCATGA 1 cut(s) 403
PctI GAATGC 1 cut(s) 413
PfeI GAWTC 1 cut(s) 300
PleI GAGTC 1 cut(s) 367
PpsI GAGTC 1 cut(s) 367
PspPI GGNCC 2 cut(s) 270, 382
PsuI RGATCY 1 cut(s) 367
RsaI GTAC 3 cut(s) 129, 502, 524
RsaNI GTAC 3 cut(s) 128, 501, 523
RseI CAYNNNNRTG 1 cut(s) 117
SaqAI TTAA 1 cut(s) 311
Sau3AI GATC 4 cut(s) 62, 232, 289, 367
Sau96I GGNCC 2 cut(s) 270, 382
SchI GAGTC 1 cut(s) 368
SduI GDGCHC 1 cut(s) 396
SetI ASST 5 cut(s) 163, 265, 339, 384, 451
SinI GGWCC 2 cut(s) 270, 382
SmiMI CAYNNNNRTG 1 cut(s) 117
SmlI CTYRAG 2 cut(s) 356, 492
SmoI CTYRAG 2 cut(s) 356, 492
Sse9I AATT 3 cut(s) 305, 345, 504
SspI AATATT 2 cut(s) 145, 224
SspMI CTAG 2 cut(s) 99, 465
StyI CCWWGG 1 cut(s) 397
TaaI ACNGT 1 cut(s) 170
TaqI TCGA 3 cut(s) 157, 303, 457
TasI AATT 3 cut(s) 305, 345, 504
TatI WGTACW 3 cut(s) 127, 500, 522
TfiI GAWTC 1 cut(s) 300
Tru1I TTAA 1 cut(s) 311
Tru9I TTAA 1 cut(s) 311
TscAI CASTG 3 cut(s) 124, 175, 486
TseFI GTSAC 1 cut(s) 240
Tsp45I GTSAC 1 cut(s) 240
TspDTI ATGAA 2 cut(s) 105, 420
TspRI CASTG 3 cut(s) 124, 175, 486
VpaK11BI GGWCC 2 cut(s) 270, 382
XspI CTAG 2 cut(s) 99, 465
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.