AT5G38050

RNA polymerase II transcription elongation factor

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
5
OG0021905
Physical Location & Seq
Forward (+)
15187487 .. 15189290
1804 bp
Loading structure...
UTR
Exon/CDS
Intron
AT5G38050.1

Sequence Viewer

Length: 846 bp
ATGGACAATCACAATGAAGAACCAAAAATCGCACCAGAACCTAATCGTTGGTACAACATTACGTTAGGACCAACACTACTCAACAACAATCACTCATACTCTCCCAAATTCTGCACTTTACGATATGAGTTTAAACCTGCTTCAATTGACAGTACTAAACCAGGATTGTTACATAAGAGTAAAGACAATAAGGTTACGTTGGAGTTTCAAAACAATCAACTTAATAAACCAAAAGTTAGATTTGATGGTGTTAGTGAGGATTACAATGACAGAGATAAAGATGCAATCCTCTTCTTTGATGGCGAAAATTTCCGATTGGAGAAGCTTCACCGCTCTGTTAAGCGTTTAAAATGCTTACGTGTGCCTGATGAATCTGCTTCAGCTAGTAGAGTAGTAACAAAGATTGTTCCTCCAGTTGAAAAACCGGTTAAGATGGCACATATTGACATTAACAACCCTGTAGACTTTGAGGAGGATGTGAACATTGAAGATGACAATGAAGAAGAAACTTTATCGAGAAAGGAGTTTCAAACGGGTGGCCTTGACATTGACATTAACCTTCCGCATCCTGCTGAAATGGAAGATGATGAGATAGCAGTTGTAGACATTAATGATGACGAATCTTACAAAGGTCTTAACGCGGCAGAAGCACTCAGAGCGCAAGTAAATGCAGAAGCGAGAGAGGAGTCTCGAAAGAGTTCGAGTTCAGGTAGCGGGAGAGAAAGTGAGAGTAGTGAAAGTGGAGTTGAGAGTAGTGGTAGCGGTAGTAGTAGTACCAGTGAAAGCAGAAAAAGCGGTAGTGAAGGTGGAACCGCTAGCGAGAGCGGAAGCCGAGATAGTCTCTAG
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
EAF

Protein Analysis

281

Amino Acids

31.19

Weight (kDa)

4.8

Isoelectric Point (pI)

61.81

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
EAF PF09816 18 - 120 7.3e-23 RNA polymerase II transcription elongation factor
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Orthologous Genes (Group: OG0021905)

Species Orthologous Gene IDs
arabidopsis_thaliana AT5G38050
malus_domestica MD09G1260000.v1.1
prunus_persica Prupe.3G151600_v2.0.a1
pyrus_communis pycom09g17460

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 145
AccBSI CCGCTC 2 cut(s) 333, 825
AccI GTMKAC 2 cut(s) 462, 603
AccII CGCG 1 cut(s) 641
AciI CCGC 8 cut(s) 331, 563, 641, 714, 762, 795, 813, 825
AcsI RAATTY 2 cut(s) 107, 307
AcuI CTGAAG 1 cut(s) 363
AfaI GTAC 3 cut(s) 53, 154, 775
AflIII ACRYGT 1 cut(s) 358
AgeI ACCGGT 1 cut(s) 424
AgsI TTSAA 5 cut(s) 144, 209, 419, 488, 530
AjnI CCWGG 1 cut(s) 160
AluBI AGCT 2 cut(s) 325, 383
AluI AGCT 2 cut(s) 325, 383
Alw26I GTCTC 1 cut(s) 693
AoxI GGCC 1 cut(s) 538
ApoI RAATTY 2 cut(s) 107, 307
AseI ATTAAT 1 cut(s) 609
AsiGI ACCGGT 1 cut(s) 424
Asp700I GAANNNNTTC 1 cut(s) 697
AspLEI GCGC 1 cut(s) 661
AspS9I GGNCC 1 cut(s) 68
AsuHPI GGTGA 1 cut(s) 320
AsuNHI GCTAGC 1 cut(s) 815
AvaII GGWCC 1 cut(s) 68
BccI CCATC 3 cut(s) 239, 293, 427
BciT130I CCWGG 1 cut(s) 162
BcoDI GTCTC 1 cut(s) 693
BfaI CTAG 3 cut(s) 384, 816, 844
BfmI CTRYAG 1 cut(s) 459
BfuAI ACCTGC 1 cut(s) 145
BisI GCNGC 1 cut(s) 642
BlsI GCNGC 1 cut(s) 643
BmcAI AGTACT 1 cut(s) 154
Bme1390I CCNGG 1 cut(s) 162
Bme18I GGWCC 1 cut(s) 68
BmgT120I GGNCC 1 cut(s) 68
BmiI GGNNCC 1 cut(s) 811
BmrFI CCNGG 1 cut(s) 162
BmsI GCATC 2 cut(s) 271, 574
BmtI GCTAGC 1 cut(s) 819
BplI GAGNNNNNCTC 1 cut(s) 825
BpmI CTGGAG 1 cut(s) 396
BsaAI YACGTR 1 cut(s) 359
BsaWI WCCGGW 1 cut(s) 424
BsaXI ACNNNNNCTCC 2 cut(s) 709, 739
Bse118I RCCGGY 1 cut(s) 424
Bse1I ACTGG 2 cut(s) 413, 777
BseBI CCWGG 1 cut(s) 162
BseGI GGATG 2 cut(s) 481, 565
BseMII CTCAG 1 cut(s) 667
BseNI ACTGG 2 cut(s) 413, 777
BseRI GAGGAG 2 cut(s) 485, 698
BsgI GTGCAG 1 cut(s) 97
Bsh1236I CGCG 1 cut(s) 641
BshFI GGCC 1 cut(s) 540
BshTI ACCGGT 1 cut(s) 424
BsiSI CCGG 1 cut(s) 425
BsmAI GTCTC 1 cut(s) 693
BsnI GGCC 1 cut(s) 540
BspACI CCGC 8 cut(s) 331, 563, 641, 714, 762, 795, 813, 825
BspANI GGCC 1 cut(s) 540
BspCNI CTCAG 1 cut(s) 666
BspFNI CGCG 1 cut(s) 641
BspLI GGNNCC 1 cut(s) 811
BspMI ACCTGC 1 cut(s) 145
BspOI GCTAGC 1 cut(s) 819
BsrBI CCGCTC 2 cut(s) 333, 825
BsrFI RCCGGY 1 cut(s) 424
BsrI ACTGG 2 cut(s) 413, 777
BssAI RCCGGY 1 cut(s) 424
Bst2UI CCWGG 1 cut(s) 162
Bst4CI ACNGT 1 cut(s) 152
Bst6I CTCTTC 1 cut(s) 296
BstBAI YACGTR 1 cut(s) 359
BstC8I GCNNGC 1 cut(s) 817
BstDEI CTNAG 1 cut(s) 653
BstF5I GGATG 2 cut(s) 481, 565
BstFNI CGCG 1 cut(s) 641
BstHHI GCGC 1 cut(s) 661
BstMAI GTCTC 1 cut(s) 693
BstMWI GCNNNNNNNGC 3 cut(s) 647, 656, 792
BstNI CCWGG 1 cut(s) 162
BstSCI CCNGG 1 cut(s) 160
BstSFI CTRYAG 1 cut(s) 459
BstUI CGCG 1 cut(s) 641
BsuRI GGCC 1 cut(s) 540
BtsCI GGATG 2 cut(s) 481, 565
BtsIMutI CAGTG 1 cut(s) 784
BveI ACCTGC 1 cut(s) 145
Cac8I GCNNGC 1 cut(s) 817
CfoI GCGC 1 cut(s) 661
Cfr10I RCCGGY 1 cut(s) 424
Cfr13I GGNCC 1 cut(s) 68
Csp6I GTAC 3 cut(s) 52, 153, 774
CspAI ACCGGT 1 cut(s) 424
CviJI RGCY 4 cut(s) 325, 383, 540, 831
CviKI_1 RGCY 4 cut(s) 325, 383, 540, 831
CviQI GTAC 3 cut(s) 52, 153, 774
DdeI CTNAG 1 cut(s) 653
DraI TTTAAA 2 cut(s) 133, 348
Eam1104I CTCTTC 1 cut(s) 296
EarI CTCTTC 1 cut(s) 296
Eco47I GGWCC 1 cut(s) 68
Eco57I CTGAAG 1 cut(s) 363
EcoRII CCWGG 1 cut(s) 160
FaiI YATR 4 cut(s) 97, 126, 174, 441
FauI CCCGC 1 cut(s) 707
FblI GTMKAC 2 cut(s) 462, 603
Fnu4HI GCNGC 1 cut(s) 642
FokI GGATG 2 cut(s) 488, 552
Fsp4HI GCNGC 1 cut(s) 642
FspBI CTAG 3 cut(s) 384, 816, 844
GlaI GCGC 1 cut(s) 660
GluI GCNGC 1 cut(s) 642
GsuI CTGGAG 1 cut(s) 396
HaeIII GGCC 1 cut(s) 540
HapII CCGG 1 cut(s) 425
HhaI GCGC 1 cut(s) 661
Hin6I GCGC 1 cut(s) 659
HinP1I GCGC 1 cut(s) 659
HindIII AAGCTT 1 cut(s) 323
HinfI GANTC 3 cut(s) 371, 620, 686
HpaII CCGG 1 cut(s) 425
HphI GGTGA 1 cut(s) 320
Hpy166II GTNNAC 3 cut(s) 463, 481, 604
Hpy188I TCNGA 2 cut(s) 314, 656
Hpy188III TCNNGA 2 cut(s) 516, 690
Hpy8I GTNNAC 3 cut(s) 463, 481, 604
HpyAV CCTTC 2 cut(s) 569, 797
HpyCH4III ACNGT 1 cut(s) 152
HpyCH4IV ACGT 3 cut(s) 62, 197, 358
HpyCH4V TGCA 3 cut(s) 114, 284, 671
HpyF10VI GCNNNNNNNGC 3 cut(s) 647, 656, 792
HpyF3I CTNAG 1 cut(s) 653
HpySE526I ACGT 3 cut(s) 62, 197, 358
HspAI GCGC 1 cut(s) 659
LweI GCATC 2 cut(s) 271, 574
MaeI CTAG 3 cut(s) 384, 816, 844
MaeII ACGT 3 cut(s) 62, 197, 358
MaeIII GTNAC 3 cut(s) 168, 193, 394
MbiI CCGCTC 2 cut(s) 333, 825
MboII GAAGA 6 cut(s) 29, 283, 500, 512, 515, 593
MfeI CAATTG 1 cut(s) 144
MluCI AATT 3 cut(s) 107, 144, 307
MlyI GAGTC 1 cut(s) 695
MmeI TCCRAC 1 cut(s) 180
MnlI CCTC 6 cut(s) 250, 299, 420, 463, 466, 676
MroXI GAANNNNTTC 1 cut(s) 697
MseI TTAA 9 cut(s) 132, 222, 339, 347, 429, 450, 555, 609, 636
MspI CCGG 1 cut(s) 425
MspR9I CCNGG 1 cut(s) 162
MssI GTTTAAAC 1 cut(s) 133
MunI CAATTG 1 cut(s) 144
MvaI CCWGG 1 cut(s) 162
MvnI CGCG 1 cut(s) 641
MwoI GCNNNNNNNGC 3 cut(s) 647, 656, 792
NheI GCTAGC 1 cut(s) 815
NlaIV GGNNCC 1 cut(s) 811
PdmI GAANNNNTTC 1 cut(s) 697
PfeI GAWTC 2 cut(s) 371, 620
PinAI ACCGGT 1 cut(s) 424
PkrI GCNGC 1 cut(s) 643
PleI GAGTC 1 cut(s) 694
PmeI GTTTAAAC 1 cut(s) 133
PpsI GAGTC 1 cut(s) 694
Ppu21I YACGTR 1 cut(s) 359
PshBI ATTAAT 1 cut(s) 609
Psp6I CCWGG 1 cut(s) 160
PspGI CCWGG 1 cut(s) 160
PspN4I GGNNCC 1 cut(s) 811
PspPI GGNCC 1 cut(s) 68
RsaI GTAC 3 cut(s) 53, 154, 775
RsaNI GTAC 3 cut(s) 52, 153, 774
SaqAI TTAA 9 cut(s) 132, 222, 339, 347, 429, 450, 555, 609, 636
SatI GCNGC 1 cut(s) 642
Sau96I GGNCC 1 cut(s) 68
ScaI AGTACT 1 cut(s) 154
SchI GAGTC 1 cut(s) 695
ScrFI CCNGG 1 cut(s) 162
SfaNI GCATC 2 cut(s) 271, 574
SfcI CTRYAG 1 cut(s) 459
SinI GGWCC 1 cut(s) 68
Sse9I AATT 3 cut(s) 107, 144, 307
SsiI CCGC 8 cut(s) 331, 563, 641, 714, 762, 795, 813, 825
SspMI CTAG 3 cut(s) 384, 816, 844
StyD4I CCNGG 1 cut(s) 160
TaaI ACNGT 1 cut(s) 152
TaiI ACGT 3 cut(s) 65, 200, 361
TaqI TCGA 3 cut(s) 515, 691, 701
TasI AATT 3 cut(s) 107, 144, 307
TatI WGTACW 1 cut(s) 152
TauI GCSGC 1 cut(s) 644
TfiI GAWTC 2 cut(s) 371, 620
Tru1I TTAA 9 cut(s) 132, 222, 339, 347, 429, 450, 555, 609, 636
Tru9I TTAA 9 cut(s) 132, 222, 339, 347, 429, 450, 555, 609, 636
TscAI CASTG 1 cut(s) 784
TspDTI ATGAA 3 cut(s) 30, 384, 513
TspRI CASTG 1 cut(s) 784
VpaK11BI GGWCC 1 cut(s) 68
VspI ATTAAT 1 cut(s) 609
XapI RAATTY 2 cut(s) 107, 307
XmiI GTMKAC 2 cut(s) 462, 603
XmnI GAANNNNTTC 1 cut(s) 697
XspI CTAG 3 cut(s) 384, 816, 844
ZrmI AGTACT 1 cut(s) 154
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.