Rroxscaffold_4G00293150

Transcription elongation factor B polypeptide

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000004
OG0000297
Physical Location & Seq
Forward (+)
13444705 .. 13449194
4490 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_4G00293150.1

Sequence Viewer

Length: 927 bp
ATGGTCCTTGTTTATGGAGAAGCTAAGCAGATGGGAAGACTCAAGGATGAGCTCATGAAGAACCAGAATCGTGGCGGTGGTGGTAGTAATACAAGAGTCCTCACTTTAAATGAAAATGGGCAGCTGGTGAATAGTGTTGAGATTGAAAGTGAAGGTCTCAAGGAACAAGCAGAAAAGGAAACCACAGACCTCACTCACTTCACTTCACTCACAAAACAACCATCACAAATGGAGAAGGGGAGGTTAATCCGTCTGAATGATCACTGGGTCTCCGTTGCTATAGACAATCTTGATTCTTTTGGGGATGTTGGGTACCTAGACTTCAGGTTTCTCGATCAACTCTTACCCCACTGCTCCAAAGACCAGTTAGTTCACATCGAGAAGTGCACAAAAGGTACAGACCTGACTCCGATCACCGATAAGCTTTGGAAGAAGTTCTTCGAGAGAGACTTCGGTGGCAAAGCCACTCATCAGGTGATCGAGGAGATGAGGATCAAGAAAGTGAGCTTCAAGTGGTCAGAGTTGTACCAGGAAAAGTCCAAGAGAGTGGAAAAGGCTGAGAAAGAAGTCGGTGAAAGGTTGAAAAAGCTGTATGAGAAAGAAGCCGCTCGGAAACAAAGCCGGCAAGTTAGGGTGTTAGACAAGGTTCCACCTTCTTCGTCAAGCAACAAAAGAACCGGCTCCAACAAAGATAGCAAACTGATGAGCAAATTGAGGAAACAGCATCTGAATTGTCTGGAAATGAGAAATATTCAAGCTATGAAGATGAAGAGAGCTGCTGCCAACTATTCTGTTTCGACTAGCACTTGGACAGTGAAGAAAGACATGATCCCCAGATTGCTGCCCCTTTTTACATGTGATGCACCAGTACTTAAGAACTCAAGAGATAGGGAAGAGCCTCATCTTCTCCTTCAAACCTTGACATAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
Elongin_A

Protein Analysis

308

Amino Acids

35.46

Weight (kDa)

9.5

Isoelectric Point (pI)

40.57

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Elongin_A PF06881 101 - 209 8.8e-23 RNA polymerase II transcription factor SIII (Elongin) subunit A
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: OG0000297)

Species Orthologous Gene IDs
arabidopsis_thaliana AT2G42780 AT2G42780
fragaria_vesca FvH4_6g37640 FvH4_6g37640 FvH4_7g18970 FvH4_7g19430 FvH4_7g20490
malus_domestica MD04G1219900.v1.1 MD09G1156600.v1.1 MD11G1064800.v1.1 MD17G1143100.v1.1
prunus_persica Prupe.3G169700_v2.0.a1 Prupe.3G169700_v2.0.a1 Prupe.3G169700_v2.0.a1 Prupe.3G169700_v2.0.a1
pyrus_communis pycom09g07530 pycom11g05390 pycom12g21760 pycom17g13620
rosa_chinensis RchiOBHm_Chr1g0363261 RchiOBHm_Chr1g0363291 RchiOBHm_Chr1g0363311 RchiOBHm_Chr1g0363471 RchiOBHm_Chr1g0363891 RchiOBHm_Chr1g0377321 RchiOBHm_Chr2g0097481 RchiOBHm_Chr2g0101011 RchiOBHm_Chr2g0137701 RchiOBHm_Chr2g0150641 RchiOBHm_Chr2g0150701 RchiOBHm_Chr3g0476421 RchiOBHm_Chr5g0057921 RchiOBHm_Chr5g0057931 RchiOBHm_Chr5g0057951 RchiOBHm_Chr5g0057981 RchiOBHm_Chr5g0058001 RchiOBHm_Chr5g0058031 RchiOBHm_Chr5g0058051 RchiOBHm_Chr5g0058081 RchiOBHm_Chr5g0058101
rosa_laevigata RLG00000017036 RLG00000019670 RLG00000020502 RLG00000023768 RLG00000027563 RLG00000027575 RLG00000027577 RLG00000027578 RLG00000034860 RLG00000035193
rosa_multiflora Rmu_co8175074.1_g000001 Rmu_sc0000367.1_g000008 Rmu_sc0001862.1_g000004 Rmu_sc0001944.1_g000004 Rmu_sc0002483.1_g000004 Rmu_sc0004027.1_g000010 Rmu_sc0004458.1_g000001 Rmu_sc0004556.1_g000009 Rmu_sc0007226.1_g000008 Rmu_sc0011095.1_g000003 Rmu_sc0027954.1_g000002 Rmu_sc0028722.1_g000001
rosa_roxburghii Rroxscaffold_1G00022510 Rroxscaffold_1G00028200 Rroxscaffold_2G00097050 Rroxscaffold_2G00106910 Rroxscaffold_2G00106930 Rroxscaffold_2G00141650 Rroxscaffold_4G00293150 Rroxscaffold_4G00293320 Rroxscaffold_6G00405280
rosa_rugosa Rorug01G0305900 Rorug01G0306000 Rorug01G0306200 Rorug01G0307100 Rorug01G0307100 Rorug01G0307200 Rorug01G0310800 Rorug01G0402700 Rorug02G0095200 Rorug02G0344100.1 Rorug02G0421900 Rorug02G0422000 Rorug02G0422100 Rorug02G0422200 Rorug03G0154300 Rorug05G0310800 Rorug05G0310900 Rorug05G0337400
rosa_samantha Rh1AG314800 Rh1AG315000 Rh1AG316200 Rh1AG318700 Rh1AG420300 Rh1DG309100 Rh1DG309300 Rh1DG310600 Rh1DG313200 Rh1DG410200 Rh2AG142500 Rh2AG392100 Rh2AG481600 Rh2BG147600 Rh2BG399400 Rh2BG399600 Rh2BG493800 Rh2DG502800 Rh3BG237100 Rh3CG231600 Rh5BG390600 Rh5DG405200
rosa_wichuraiana Rw1G027900 Rw1G027910 Rw1G028000 Rw1G036850 Rw2G011180 Rw2G032110 Rw2G032120 Rw2G039370 Rw2G039510 Rw3G018680 Rw5G035730

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc65I GGTACC 1 cut(s) 312
AccB1I GGYRCC 1 cut(s) 312
AccBSI CCGCTC 1 cut(s) 608
AciI CCGC 2 cut(s) 75, 606
AclWI GGATC 2 cut(s) 500, 823
AcuI CTGAAG 1 cut(s) 307
AfaI GTAC 4 cut(s) 314, 397, 527, 870
AflII CTTAAG 1 cut(s) 872
AflIII ACRYGT 1 cut(s) 854
AgsI TTSAA 5 cut(s) 146, 511, 583, 755, 914
AjnI CCWGG 1 cut(s) 528
AluBI AGCT 8 cut(s) 23, 52, 124, 424, 507, 589, 758, 776
AluI AGCT 8 cut(s) 23, 52, 124, 424, 507, 589, 758, 776
Alw21I GWGCWC 2 cut(s) 54, 389
Alw26I GTCTC 3 cut(s) 161, 274, 441
Alw44I GTGCAC 1 cut(s) 385
AlwI GGATC 2 cut(s) 500, 823
AlwNI CAGNNNCTG 1 cut(s) 727
ApaLI GTGCAC 1 cut(s) 385
ApeKI GCWGC 4 cut(s) 121, 776, 779, 841
Asp700I GAANNNNTTC 2 cut(s) 434, 437
Asp718I GGTACC 1 cut(s) 312
AspS9I GGNCC 1 cut(s) 4
AsuHPI GGTGA 4 cut(s) 139, 406, 487, 584
AvaII GGWCC 1 cut(s) 4
BaeGI GKGCMC 1 cut(s) 389
BanI GGYRCC 1 cut(s) 312
BanII GRGCYC 1 cut(s) 54
BarI GAAGNNNNNNTAC 2 cut(s) 305, 337
BbsI GAAGAC 1 cut(s) 43
Bbv12I GWGCWC 2 cut(s) 54, 389
BbvI GCAGC 4 cut(s) 133, 763, 766, 828
BccI CCATC 2 cut(s) 25, 229
BciT130I CCWGG 1 cut(s) 530
BclI TGATCA 1 cut(s) 259
BcoDI GTCTC 3 cut(s) 161, 274, 441
BfaI CTAG 2 cut(s) 317, 801
BfmI CTRYAG 1 cut(s) 279
BfrI CTTAAG 1 cut(s) 872
BisI GCNGC 5 cut(s) 122, 606, 777, 780, 842
BlpI GCTNAGC 1 cut(s) 24
BlsI GCNGC 5 cut(s) 123, 607, 778, 781, 843
BmcAI AGTACT 1 cut(s) 870
Bme1390I CCNGG 1 cut(s) 530
Bme18I GGWCC 1 cut(s) 4
BmgT120I GGNCC 1 cut(s) 4
BmiI GGNNCC 3 cut(s) 314, 648, 682
BmrFI CCNGG 1 cut(s) 530
BmrI ACTGGG 1 cut(s) 274
BmsI GCATC 2 cut(s) 733, 850
BmuI ACTGGG 1 cut(s) 274
BpiI GAAGAC 1 cut(s) 43
Bpu1102I GCTNAGC 1 cut(s) 24
BpuEI CTTGAG 3 cut(s) 26, 143, 865
BsaBI GATNNNNATC 1 cut(s) 491
BsaI GGTCTC 2 cut(s) 161, 274
BsaXI ACNNNNNCTCC 2 cut(s) 254, 284
Bse118I RCCGGY 2 cut(s) 621, 677
Bse1I ACTGG 3 cut(s) 269, 364, 866
Bse8I GATNNNNATC 1 cut(s) 491
BseBI CCWGG 1 cut(s) 530
BseGI GGATG 2 cut(s) 52, 310
BseJI GATNNNNATC 1 cut(s) 491
BseMII CTCAG 1 cut(s) 549
BseNI ACTGG 3 cut(s) 269, 364, 866
BseRI GAGGAG 1 cut(s) 497
BseSI GKGCMC 1 cut(s) 389
BseXI GCAGC 4 cut(s) 133, 763, 766, 828
BshNI GGYRCC 1 cut(s) 312
BsiHKAI GWGCWC 2 cut(s) 54, 389
BsiSI CCGG 2 cut(s) 622, 678
BsmAI GTCTC 3 cut(s) 161, 274, 441
Bso31I GGTCTC 2 cut(s) 161, 274
Bsp1286I GDGCHC 2 cut(s) 54, 389
Bsp143I GATC 6 cut(s) 259, 334, 411, 477, 492, 828
Bsp1720I GCTNAGC 1 cut(s) 24
BspACI CCGC 2 cut(s) 75, 606
BspCNI CTCAG 1 cut(s) 550
BspHI TCATGA 1 cut(s) 54
BspLI GGNNCC 3 cut(s) 314, 648, 682
BspPI GGATC 2 cut(s) 500, 823
BspQI GCTCTTC 1 cut(s) 888
BspT107I GGYRCC 1 cut(s) 312
BspTI CTTAAG 1 cut(s) 872
BspTNI GGTCTC 2 cut(s) 161, 274
BsrBI CCGCTC 1 cut(s) 608
BsrFI RCCGGY 2 cut(s) 621, 677
BsrI ACTGG 3 cut(s) 269, 364, 866
BssAI RCCGGY 2 cut(s) 621, 677
BssMI GATC 6 cut(s) 259, 334, 411, 477, 492, 828
Bst2UI CCWGG 1 cut(s) 530
Bst4CI ACNGT 1 cut(s) 814
Bst6I CTCTTC 2 cut(s) 764, 888
BstAFI CTTAAG 1 cut(s) 872
BstC8I GCNNGC 1 cut(s) 623
BstDEI CTNAG 2 cut(s) 24, 558
BstF5I GGATG 2 cut(s) 52, 310
BstKTI GATC 6 cut(s) 262, 337, 414, 480, 495, 831
BstMAI GTCTC 3 cut(s) 161, 274, 441
BstMBI GATC 6 cut(s) 259, 334, 411, 477, 492, 828
BstNI CCWGG 1 cut(s) 530
BstNSI RCATGY 1 cut(s) 858
BstSCI CCNGG 1 cut(s) 528
BstSFI CTRYAG 1 cut(s) 279
BstSLI GKGCMC 1 cut(s) 389
BstV1I GCAGC 4 cut(s) 133, 763, 766, 828
BstV2I GAAGAC 1 cut(s) 43
BstXI CCANNNNNNTGG 2 cut(s) 71, 547
BtsCI GGATG 2 cut(s) 52, 310
BtsI GCAGTG 1 cut(s) 349
BtsIMutI CAGTG 3 cut(s) 262, 349, 819
Cac8I GCNNGC 1 cut(s) 623
CaiI CAGNNNCTG 1 cut(s) 727
CciI TCATGA 1 cut(s) 54
Cfr10I RCCGGY 2 cut(s) 621, 677
Cfr13I GGNCC 1 cut(s) 4
Csp6I GTAC 4 cut(s) 313, 396, 526, 869
CviAII CATG 3 cut(s) 55, 826, 855
CviQI GTAC 4 cut(s) 313, 396, 526, 869
DdeI CTNAG 2 cut(s) 24, 558
DpnI GATC 6 cut(s) 261, 336, 413, 479, 494, 830
DpnII GATC 6 cut(s) 259, 334, 411, 477, 492, 828
DraI TTTAAA 1 cut(s) 108
Eam1104I CTCTTC 2 cut(s) 764, 888
EarI CTCTTC 2 cut(s) 764, 888
Ecl136II GAGCTC 1 cut(s) 52
Eco24I GRGCYC 1 cut(s) 54
Eco31I GGTCTC 2 cut(s) 161, 274
Eco47I GGWCC 1 cut(s) 4
Eco53kI GAGCTC 1 cut(s) 52
Eco57I CTGAAG 1 cut(s) 307
EcoICRI GAGCTC 1 cut(s) 52
EcoRII CCWGG 1 cut(s) 528
EcoT38I GRGCYC 1 cut(s) 54
FaeI CATG 3 cut(s) 58, 829, 858
FaiI YATR 8 cut(s) 15, 56, 281, 594, 761, 827, 856, 925
FalI AAGNNNNNCTT 2 cut(s) 422, 454
FatI CATG 3 cut(s) 54, 825, 854
FbaI TGATCA 1 cut(s) 259
Fnu4HI GCNGC 5 cut(s) 122, 606, 777, 780, 842
FokI GGATG 2 cut(s) 59, 317
FriOI GRGCYC 1 cut(s) 54
Fsp4HI GCNGC 5 cut(s) 122, 606, 777, 780, 842
FspBI CTAG 2 cut(s) 317, 801
GluI GCNGC 5 cut(s) 122, 606, 777, 780, 842
HapII CCGG 2 cut(s) 622, 678
Hin1II CATG 3 cut(s) 58, 829, 858
HindIII AAGCTT 1 cut(s) 422
HinfI GANTC 5 cut(s) 39, 67, 96, 293, 406
HpaII CCGG 2 cut(s) 622, 678
HphI GGTGA 4 cut(s) 139, 406, 487, 584
Hpy166II GTNNAC 2 cut(s) 373, 387
Hpy188I TCNGA 5 cut(s) 255, 411, 520, 612, 729
Hpy188III TCNNGA 8 cut(s) 55, 290, 332, 379, 442, 496, 737, 882
Hpy8I GTNNAC 2 cut(s) 373, 387
HpyAV CCTTC 4 cut(s) 146, 229, 663, 920
HpyCH4III ACNGT 1 cut(s) 814
HpyCH4V TGCA 2 cut(s) 387, 863
HpyF3I CTNAG 2 cut(s) 24, 558
Hsp92II CATG 3 cut(s) 58, 829, 858
KpnI GGTACC 1 cut(s) 316
KroI GCCGGC 1 cut(s) 621
KroNI GCCGGC 1 cut(s) 623
Ksp22I TGATCA 1 cut(s) 259
Kzo9I GATC 6 cut(s) 259, 334, 411, 477, 492, 828
LguI GCTCTTC 1 cut(s) 888
LmnI GCTCC 2 cut(s) 359, 686
Lsp1109I GCAGC 4 cut(s) 133, 763, 766, 828
LweI GCATC 2 cut(s) 733, 850
MaeI CTAG 2 cut(s) 317, 801
MalI GATC 6 cut(s) 261, 336, 413, 479, 494, 830
MbiI CCGCTC 1 cut(s) 608
MboI GATC 6 cut(s) 259, 334, 411, 477, 492, 828
MhlI GDGCHC 2 cut(s) 54, 389
MluCI AATT 2 cut(s) 710, 730
MlyI GAGTC 3 cut(s) 33, 105, 400
MmeI TCCRAC 1 cut(s) 708
MnlI CCTC 7 cut(s) 110, 200, 234, 475, 483, 708, 909
MroNI GCCGGC 1 cut(s) 621
MroXI GAANNNNTTC 2 cut(s) 434, 437
MseI TTAA 3 cut(s) 107, 245, 873
MspA1I CMGCKG 1 cut(s) 124
MspCI CTTAAG 1 cut(s) 872
MspI CCGG 2 cut(s) 622, 678
MspR9I CCNGG 1 cut(s) 530
MvaI CCWGG 1 cut(s) 530
NaeI GCCGGC 1 cut(s) 623
NdeII GATC 6 cut(s) 259, 334, 411, 477, 492, 828
NgoMIV GCCGGC 1 cut(s) 621
NlaIII CATG 3 cut(s) 58, 829, 858
NlaIV GGNNCC 3 cut(s) 314, 648, 682
NspI RCATGY 1 cut(s) 858
PagI TCATGA 1 cut(s) 54
PciI ACATGT 1 cut(s) 854
PciSI GCTCTTC 1 cut(s) 888
PdiI GCCGGC 1 cut(s) 623
PdmI GAANNNNTTC 2 cut(s) 434, 437
PfeI GAWTC 2 cut(s) 67, 293
PkrI GCNGC 5 cut(s) 123, 607, 778, 781, 843
PleI GAGTC 3 cut(s) 33, 104, 400
PpsI GAGTC 3 cut(s) 33, 104, 400
PscI ACATGT 1 cut(s) 854
Psp124BI GAGCTC 1 cut(s) 54
Psp6I CCWGG 1 cut(s) 528
PspGI CCWGG 1 cut(s) 528
PspN4I GGNNCC 3 cut(s) 314, 648, 682
PspPI GGNCC 1 cut(s) 4
PstNI CAGNNNCTG 1 cut(s) 727
PvuII CAGCTG 1 cut(s) 124
RsaI GTAC 4 cut(s) 314, 397, 527, 870
RsaNI GTAC 4 cut(s) 313, 396, 526, 869
SacI GAGCTC 1 cut(s) 54
SapI GCTCTTC 1 cut(s) 888
SaqAI TTAA 3 cut(s) 107, 245, 873
SatI GCNGC 5 cut(s) 122, 606, 777, 780, 842
Sau3AI GATC 6 cut(s) 259, 334, 411, 477, 492, 828
Sau96I GGNCC 1 cut(s) 4
ScaI AGTACT 1 cut(s) 870
SchI GAGTC 3 cut(s) 33, 105, 400
ScrFI CCNGG 1 cut(s) 530
SduI GDGCHC 2 cut(s) 54, 389
SfaNI GCATC 2 cut(s) 733, 850
SfcI CTRYAG 1 cut(s) 279
SinI GGWCC 1 cut(s) 4
SmlI CTYRAG 4 cut(s) 41, 158, 872, 880
SmoI CTYRAG 4 cut(s) 41, 158, 872, 880
Sse9I AATT 2 cut(s) 710, 730
SsiI CCGC 2 cut(s) 75, 606
SspI AATATT 1 cut(s) 751
SspMI CTAG 2 cut(s) 317, 801
SstI GAGCTC 1 cut(s) 54
StyD4I CCNGG 1 cut(s) 528
TaaI ACNGT 1 cut(s) 814
TaqI TCGA 5 cut(s) 333, 378, 441, 480, 797
TasI AATT 2 cut(s) 710, 730
TatI WGTACW 1 cut(s) 868
TauI GCSGC 1 cut(s) 608
TfiI GAWTC 2 cut(s) 67, 293
Tru1I TTAA 3 cut(s) 107, 245, 873
Tru9I TTAA 3 cut(s) 107, 245, 873
TscAI CASTG 3 cut(s) 269, 356, 819
TseI GCWGC 4 cut(s) 121, 776, 779, 841
TspDTI ATGAA 4 cut(s) 71, 126, 776, 782
TspGWI ACGGA 2 cut(s) 239, 262
TspRI CASTG 3 cut(s) 269, 356, 819
Vha464I CTTAAG 1 cut(s) 872
VneI GTGCAC 1 cut(s) 385
VpaK11BI GGWCC 1 cut(s) 4
XceI RCATGY 1 cut(s) 858
XmnI GAANNNNTTC 2 cut(s) 434, 437
XspI CTAG 2 cut(s) 317, 801
ZrmI AGTACT 1 cut(s) 870
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.