AT2G42780

Transcription elongation factor B polypeptide

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
2
OG0000297
Physical Location & Seq
Forward (+)
17800312 .. 17802816
2505 bp
Loading structure...
UTR
Exon/CDS
Intron
AT2G42780.1

Sequence Viewer

Length: 882 bp
ATGTTATTTGAGAGGCTTACCAAGAAACCACCTTCGCTTGTTGATCTTTGCGTAAGGAAAGCGATTGATAATGTAAAGTACATTGGATATGTTGGTGGGGTTGATTTTCAGCTCCTTGAGCAGATTCTGCAACACTGTACACTAGAACAGCTGAAGCACATAGAGGATGCTACTGACGACACAGATCTTAGTCCAATCACCGATAAGTTTTGGAAGGGATTCTATAAGAAGCACTATGGAGAAGAGGACATGAAGGATCTTATAGAGGACCTGGAGTGGAATAAAGTAAATGATTTCAAATGGAGGAACTTATATGAGTTGAAGGTTATAGCTGTGCAACAAAAGGAGAAGGAACTTGGTGGTCGACTGAAAGAACGTTACAAGGACGAAAATGAAAGGAAACAAAGTCGACAAACTAAGGTCTGCTCGAAAGCTCCTCCAAGCAAAAGACCATTTTGGGGTAATAGTGCATCAGGTTACAATCTTGGGCATGTGAAGAGCAACATCATGAAGAAGGCAAAAATAGATCTGTTGAAGAGTCAAGAAGTGAAAAATCTTACTGCGATTAAAAGGAACACCATTCAGAAGAGTTTCAGTATTTCTACTCCAAAGAAAACTGGCTTATCTGCGAATTCGCCTTCAACTTCAAGAAGCATTCCTTATGGTGGACGAAATCTTACTGAAACTAAAAAGAACACGATTCAGAAGAGTTTCAGTATATCTGCTCCAAAGAGGACTGGCTTATCCGCTAATGCGCCTTCAACTTCAAGAAGCGTTCCTTCTGGTGGACAAAAGCTACCTCCAAGGAGGATCAACGGCCTTCCTGGGACTGCTCCTTCAACTTCAAAAAATGCAGCCACCAGACAAAAACATGTAATGTAA
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

293

Amino Acids

33.08

Weight (kDa)

9.89

Isoelectric Point (pI)

48.83

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Elongin_A PF06881 28 - 139 4.5e-22 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)
AccI GTMKAC 2 cut(s) 364, 409
AciI CCGC 1 cut(s) 747
AclI AACGTT 1 cut(s) 376
AclWI GGATC 2 cut(s) 264, 818
AcsI RAATTY 1 cut(s) 631
AcuI CTGAAG 1 cut(s) 173
AfaI GTAC 2 cut(s) 80, 139
AfiI CCNNNNNNNGG 3 cut(s) 458, 665, 785
AflIII ACRYGT 1 cut(s) 871
AgsI TTSAA 9 cut(s) 298, 322, 535, 642, 648, 762, 768, 840, 846
AjnI CCWGG 2 cut(s) 270, 823
AluBI AGCT 5 cut(s) 112, 151, 332, 434, 796
AluI AGCT 5 cut(s) 112, 151, 332, 434, 796
AlwI GGATC 2 cut(s) 264, 818
AlwNI CAGNNNCTG 1 cut(s) 127
AoxI GGCC 1 cut(s) 817
ApeKI GCWGC 1 cut(s) 854
ApoI RAATTY 1 cut(s) 631
Asp700I GAANNNNTTC 3 cut(s) 218, 590, 710
AspLEI GCGC 1 cut(s) 757
AspS9I GGNCC 1 cut(s) 268
AsuHPI GGTGA 1 cut(s) 190
AvaII GGWCC 1 cut(s) 268
BbvI GCAGC 1 cut(s) 866
BceAI ACGGC 1 cut(s) 832
BciT130I CCWGG 2 cut(s) 272, 825
BfaI CTAG 1 cut(s) 143
BglII AGATCT 2 cut(s) 184, 526
BisI GCNGC 1 cut(s) 855
BlsI GCNGC 1 cut(s) 856
Bme1390I CCNGG 2 cut(s) 272, 825
Bme18I GGWCC 1 cut(s) 268
BmgT120I GGNCC 1 cut(s) 268
BmrFI CCNGG 2 cut(s) 272, 825
BmsI GCATC 2 cut(s) 157, 479
BpmI CTGGAG 1 cut(s) 293
BpuEI CTTGAG 1 cut(s) 137
BsaJI CCNNGG 2 cut(s) 803, 824
Bsc4I CCNNNNNNNGG 3 cut(s) 458, 665, 785
Bse1I ACTGG 2 cut(s) 622, 742
BseBI CCWGG 2 cut(s) 272, 825
BseDI CCNNGG 2 cut(s) 803, 824
BseGI GGATG 1 cut(s) 172
BseLI CCNNNNNNNGG 3 cut(s) 458, 665, 785
BseNI ACTGG 2 cut(s) 622, 742
BseRI GAGGAG 1 cut(s) 426
BseXI GCAGC 1 cut(s) 866
BshFI GGCC 1 cut(s) 819
BslFI GGGAC 1 cut(s) 841
BslI CCNNNNNNNGG 3 cut(s) 458, 665, 785
BsmFI GGGAC 1 cut(s) 841
BsmI GAATGC 1 cut(s) 654
BsnI GGCC 1 cut(s) 819
Bsp1407I TGTACA 1 cut(s) 137
Bsp143I GATC 5 cut(s) 43, 184, 256, 526, 810
BspACI CCGC 1 cut(s) 747
BspANI GGCC 1 cut(s) 819
BspHI TCATGA 1 cut(s) 507
BspPI GGATC 2 cut(s) 264, 818
BspQI GCTCTTC 1 cut(s) 491
BsrGI TGTACA 1 cut(s) 137
BsrI ACTGG 2 cut(s) 622, 742
BssECI CCNNGG 2 cut(s) 803, 824
BssMI GATC 5 cut(s) 43, 184, 256, 526, 810
BssT1I CCWWGG 1 cut(s) 803
Bst2UI CCWGG 2 cut(s) 272, 825
Bst4CI ACNGT 1 cut(s) 137
Bst6I CTCTTC 5 cut(s) 237, 491, 530, 581, 701
BstAPI GCANNNNNTGC 1 cut(s) 127
BstAUI TGTACA 1 cut(s) 137
BstDEI CTNAG 2 cut(s) 188, 417
BstF5I GGATG 1 cut(s) 172
BstHHI GCGC 1 cut(s) 757
BstKTI GATC 5 cut(s) 46, 187, 259, 529, 813
BstMBI GATC 5 cut(s) 43, 184, 256, 526, 810
BstMWI GCNNNNNNNGC 2 cut(s) 118, 127
BstNI CCWGG 2 cut(s) 272, 825
BstNSI RCATGY 2 cut(s) 494, 875
BstSCI CCNGG 2 cut(s) 270, 823
BstV1I GCAGC 1 cut(s) 866
BstX2I RGATCY 3 cut(s) 184, 256, 526
BstYI RGATCY 3 cut(s) 184, 256, 526
BsuRI GGCC 1 cut(s) 819
BtsCI GGATG 1 cut(s) 172
BtsIMutI CAGTG 1 cut(s) 133
CaiI CAGNNNCTG 1 cut(s) 127
CciI TCATGA 1 cut(s) 507
CfoI GCGC 1 cut(s) 757
Cfr13I GGNCC 1 cut(s) 268
Csp6I GTAC 2 cut(s) 79, 138
CviAII CATG 4 cut(s) 250, 491, 508, 872
CviQI GTAC 2 cut(s) 79, 138
DdeI CTNAG 2 cut(s) 188, 417
DpnI GATC 5 cut(s) 45, 186, 258, 528, 812
DpnII GATC 5 cut(s) 43, 184, 256, 526, 810
Eam1104I CTCTTC 5 cut(s) 237, 491, 530, 581, 701
EarI CTCTTC 5 cut(s) 237, 491, 530, 581, 701
Eco130I CCWWGG 1 cut(s) 803
Eco47I GGWCC 1 cut(s) 268
Eco57I CTGAAG 1 cut(s) 173
EcoO109I RGGNCCY 1 cut(s) 268
EcoRI GAATTC 1 cut(s) 631
EcoRII CCWGG 2 cut(s) 270, 823
EcoT14I CCWWGG 1 cut(s) 803
ErhI CCWWGG 1 cut(s) 803
FaeI CATG 4 cut(s) 253, 494, 511, 875
FalI AAGNNNNNCTT 4 cut(s) 643, 675, 763, 795
FaqI GGGAC 1 cut(s) 841
FatI CATG 4 cut(s) 249, 490, 507, 871
FblI GTMKAC 2 cut(s) 364, 409
Fnu4HI GCNGC 1 cut(s) 855
FokI GGATG 1 cut(s) 179
Fsp4HI GCNGC 1 cut(s) 855
FspBI CTAG 1 cut(s) 143
GlaI GCGC 1 cut(s) 756
GluI GCNGC 1 cut(s) 855
GsuI CTGGAG 1 cut(s) 293
HaeIII GGCC 1 cut(s) 819
HhaI GCGC 1 cut(s) 757
Hin1II CATG 4 cut(s) 253, 494, 511, 875
Hin6I GCGC 1 cut(s) 755
HinP1I GCGC 1 cut(s) 755
HincII GTYRAC 2 cut(s) 365, 410
HindII GTYRAC 2 cut(s) 365, 410
HinfI GANTC 4 cut(s) 124, 219, 538, 700
HphI GGTGA 1 cut(s) 190
Hpy166II GTNNAC 5 cut(s) 140, 365, 410, 668, 788
Hpy188I TCNGA 2 cut(s) 585, 705
Hpy188III TCNNGA 4 cut(s) 508, 542, 648, 768
Hpy8I GTNNAC 5 cut(s) 140, 365, 410, 668, 788
HpyCH4III ACNGT 1 cut(s) 137
HpyCH4IV ACGT 1 cut(s) 376
HpyCH4V TGCA 4 cut(s) 130, 337, 470, 854
HpyF10VI GCNNNNNNNGC 2 cut(s) 118, 127
HpyF3I CTNAG 2 cut(s) 188, 417
HpySE526I ACGT 1 cut(s) 376
Hsp92II CATG 4 cut(s) 253, 494, 511, 875
HspAI GCGC 1 cut(s) 755
Kzo9I GATC 5 cut(s) 43, 184, 256, 526, 810
LguI GCTCTTC 1 cut(s) 491
LmnI GCTCC 4 cut(s) 117, 439, 730, 838
LpnPI CCDG 9 cut(s) 257, 284, 459, 603, 723, 768, 810, 837, 874
Lsp1109I GCAGC 1 cut(s) 866
LweI GCATC 2 cut(s) 157, 479
MaeI CTAG 1 cut(s) 143
MaeII ACGT 1 cut(s) 376
MaeIII GTNAC 2 cut(s) 377, 476
MalI GATC 5 cut(s) 45, 186, 258, 528, 812
MboI GATC 5 cut(s) 43, 184, 256, 526, 810
MboII GAAGA 6 cut(s) 254, 508, 523, 547, 598, 718
MflI RGATCY 3 cut(s) 184, 256, 526
MluCI AATT 1 cut(s) 631
MlyI GAGTC 1 cut(s) 547
MnlI CCTC 9 cut(s) 6, 157, 238, 259, 297, 447, 726, 801, 810
MroXI GAANNNNTTC 3 cut(s) 218, 590, 710
MseI TTAA 1 cut(s) 567
MspA1I CMGCKG 1 cut(s) 151
MspR9I CCNGG 2 cut(s) 272, 825
Mva1269I GAATGC 1 cut(s) 654
MvaI CCWGG 2 cut(s) 272, 825
MwoI GCNNNNNNNGC 2 cut(s) 118, 127
NdeII GATC 5 cut(s) 43, 184, 256, 526, 810
NlaIII CATG 4 cut(s) 253, 494, 511, 875
NspI RCATGY 2 cut(s) 494, 875
PagI TCATGA 1 cut(s) 507
PciI ACATGT 1 cut(s) 871
PciSI GCTCTTC 1 cut(s) 491
PctI GAATGC 1 cut(s) 654
PdmI GAANNNNTTC 3 cut(s) 218, 590, 710
PfeI GAWTC 3 cut(s) 124, 219, 700
PkrI GCNGC 1 cut(s) 856
PleI GAGTC 1 cut(s) 546
PpsI GAGTC 1 cut(s) 546
PpuMI RGGWCCY 1 cut(s) 268
PscI ACATGT 1 cut(s) 871
Psp1406I AACGTT 1 cut(s) 376
Psp5II RGGWCCY 1 cut(s) 268
Psp6I CCWGG 2 cut(s) 270, 823
PspGI CCWGG 2 cut(s) 270, 823
PspPI GGNCC 1 cut(s) 268
PspPPI RGGWCCY 1 cut(s) 268
PstNI CAGNNNCTG 1 cut(s) 127
PsuI RGATCY 3 cut(s) 184, 256, 526
PvuII CAGCTG 1 cut(s) 151
RsaI GTAC 2 cut(s) 80, 139
RsaNI GTAC 2 cut(s) 79, 138
SalI GTCGAC 2 cut(s) 363, 408
SapI GCTCTTC 1 cut(s) 491
SaqAI TTAA 1 cut(s) 567
SatI GCNGC 1 cut(s) 855
Sau3AI GATC 5 cut(s) 43, 184, 256, 526, 810
Sau96I GGNCC 1 cut(s) 268
SchI GAGTC 1 cut(s) 547
ScrFI CCNGG 2 cut(s) 272, 825
SfaNI GCATC 2 cut(s) 157, 479
SinI GGWCC 1 cut(s) 268
SmlI CTYRAG 1 cut(s) 116
SmoI CTYRAG 1 cut(s) 116
Sse9I AATT 1 cut(s) 631
SsiI CCGC 1 cut(s) 747
SspMI CTAG 1 cut(s) 143
StyD4I CCNGG 2 cut(s) 270, 823
StyI CCWWGG 1 cut(s) 803
TaaI ACNGT 1 cut(s) 137
TaiI ACGT 1 cut(s) 379
TaqI TCGA 3 cut(s) 364, 409, 428
TasI AATT 1 cut(s) 631
TatI WGTACW 2 cut(s) 78, 137
TfiI GAWTC 3 cut(s) 124, 219, 700
Tru1I TTAA 1 cut(s) 567
Tru9I TTAA 1 cut(s) 567
TscAI CASTG 1 cut(s) 140
TseI GCWGC 1 cut(s) 854
TspDTI ATGAA 3 cut(s) 266, 408, 524
TspRI CASTG 1 cut(s) 140
VpaK11BI GGWCC 1 cut(s) 268
XapI RAATTY 1 cut(s) 631
XceI RCATGY 2 cut(s) 494, 875
XmiI GTMKAC 2 cut(s) 364, 409
XmnI GAANNNNTTC 3 cut(s) 218, 590, 710
XspI CTAG 1 cut(s) 143
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.