AT5G08565

May regulate transcription elongation by RNA polymerase II. May enhance transcriptional pausing at sites proximal to the promoter, which may in turn facilitate the assembly of an elongation competent RNA polymerase II complex

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
5
OG0013184
Physical Location & Seq
Forward (+)
2775897 .. 2777474
1578 bp
Loading structure...
UTR
Exon/CDS
Intron
AT5G08565.1

Sequence Viewer

Length: 351 bp
ATGGGAGAAGCGCCTGCCCAGATTCCGACGAGTTTCGGCCACGAGCTTAGGGCTTGTCTTCGATGCCGCCTCGTCAAGACCTACGATCAGTTTAGGGATTCTGGATGCGAGAACTGTCCTTTCTTCAAAATAGAAGACGATCATGAACGCATCGTCGATGTTACAACTCCCAACTTCAATGGTATAATCTCTATGATGGATCCACGCAGAAGTTGGGCAGCAAGATGGTTAAGAATTGGGAAGTTTGCTCCTGGTTGCTACACTCTTGCTGTCTCAGAGGCACTCCCAGAGGAAATGCAGTTCATATGCCAACAAGCACGGGTGCAGTACGTTCCACCCAAACGTATTTGA
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
Spt4

Protein Analysis

116

Amino Acids

13.37

Weight (kDa)

7.6

Isoelectric Point (pI)

51.53

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Spt4 PF06093 16 - 92 2.8e-31 Spt4/RpoE2 zinc finger
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: OG0013184)

Species Orthologous Gene IDs
arabidopsis_thaliana AT5G08565 AT5G08565 AT5G63670
fragaria_vesca FvH4_4g10630
malus_domestica MD04G1047800.v1.1 MD07G1114100.v1.1 MD09G1278200.v1.1 MD17G1271200.v1.1
prunus_persica Prupe.3G015100_v2.0.a1
pyrus_communis pycom04g04180
rosa_chinensis RchiOBHm_Chr4g0406241
rosa_laevigata RLG00000008786
rosa_multiflora Rmu_ssc0000456.1_g000008
rosa_roxburghii Rroxscaffold_5G00350980
rosa_rugosa Rorug04G0067100
rosa_samantha Rh4BG134100
rosa_wichuraiana Rw4G011070 Rw4G011210

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 1 cut(s) 67
AclWI GGATC 2 cut(s) 194, 207
AcoI YGGCCR 1 cut(s) 37
AfaI GTAC 1 cut(s) 329
AgsI TTSAA 2 cut(s) 127, 178
AjnI CCWGG 1 cut(s) 250
AloI GAACNNNNNNTCC 2 cut(s) 284, 316
AluBI AGCT 1 cut(s) 46
AluI AGCT 1 cut(s) 46
Alw26I GTCTC 1 cut(s) 277
AlwI GGATC 2 cut(s) 194, 207
AoxI GGCC 1 cut(s) 37
ApeKI GCWGC 1 cut(s) 218
AspLEI GCGC 1 cut(s) 13
BamHI GGATCC 1 cut(s) 199
BauI CACGAG 1 cut(s) 41
BbsI GAAGAC 2 cut(s) 50, 141
BbvI GCAGC 1 cut(s) 230
BccI CCATC 2 cut(s) 190, 219
BciT130I CCWGG 1 cut(s) 252
BcoDI GTCTC 1 cut(s) 277
BfoI RGCGCY 1 cut(s) 14
BisI GCNGC 2 cut(s) 67, 219
BlsI GCNGC 2 cut(s) 68, 220
Bme1390I CCNGG 1 cut(s) 252
BmiI GGNNCC 1 cut(s) 201
BmrFI CCNGG 1 cut(s) 252
BmsI GCATC 3 cut(s) 53, 95, 159
BpiI GAAGAC 2 cut(s) 50, 141
Bpu10I CCTNAGC 1 cut(s) 47
BseBI CCWGG 1 cut(s) 252
BseGI GGATG 1 cut(s) 110
BseMII CTCAG 1 cut(s) 288
BseXI GCAGC 1 cut(s) 230
BsgI GTGCAG 1 cut(s) 344
BshFI GGCC 1 cut(s) 39
BsmAI GTCTC 1 cut(s) 277
BsnI GGCC 1 cut(s) 39
Bsp143I GATC 3 cut(s) 85, 139, 199
BspACI CCGC 1 cut(s) 67
BspANI GGCC 1 cut(s) 39
BspCNI CTCAG 1 cut(s) 287
BspHI TCATGA 1 cut(s) 142
BspLI GGNNCC 1 cut(s) 201
BspPI GGATC 2 cut(s) 194, 207
BssMI GATC 3 cut(s) 85, 139, 199
BssSI CACGAG 1 cut(s) 41
Bst2BI CACGAG 1 cut(s) 41
Bst2UI CCWGG 1 cut(s) 252
Bst4CI ACNGT 1 cut(s) 116
BstC8I GCNNGC 1 cut(s) 15
BstDEI CTNAG 2 cut(s) 47, 274
BstF5I GGATG 1 cut(s) 110
BstH2I RGCGCY 1 cut(s) 14
BstHHI GCGC 1 cut(s) 13
BstKTI GATC 3 cut(s) 88, 142, 202
BstMAI GTCTC 1 cut(s) 277
BstMBI GATC 3 cut(s) 85, 139, 199
BstNI CCWGG 1 cut(s) 252
BstSCI CCNGG 1 cut(s) 250
BstV1I GCAGC 1 cut(s) 230
BstV2I GAAGAC 2 cut(s) 50, 141
BstX2I RGATCY 1 cut(s) 199
BstYI RGATCY 1 cut(s) 199
BsuRI GGCC 1 cut(s) 39
BtsCI GGATG 1 cut(s) 110
Cac8I GCNNGC 1 cut(s) 15
CciI TCATGA 1 cut(s) 142
CfoI GCGC 1 cut(s) 13
Csp6I GTAC 1 cut(s) 328
CviAII CATG 1 cut(s) 143
CviJI RGCY 3 cut(s) 39, 46, 53
CviKI_1 RGCY 3 cut(s) 39, 46, 53
CviQI GTAC 1 cut(s) 328
DdeI CTNAG 2 cut(s) 47, 274
DpnI GATC 3 cut(s) 87, 141, 201
DpnII GATC 3 cut(s) 85, 139, 199
EaeI YGGCCR 1 cut(s) 37
EcoRII CCWGG 1 cut(s) 250
FaeI CATG 1 cut(s) 146
FaiI YATR 5 cut(s) 144, 185, 194, 305, 307
FatI CATG 1 cut(s) 142
FauNDI CATATG 1 cut(s) 305
Fnu4HI GCNGC 2 cut(s) 67, 219
FokI GGATG 1 cut(s) 117
Fsp4HI GCNGC 2 cut(s) 67, 219
GlaI GCGC 1 cut(s) 12
GluI GCNGC 2 cut(s) 67, 219
HaeII RGCGCY 1 cut(s) 14
HaeIII GGCC 1 cut(s) 39
HhaI GCGC 1 cut(s) 13
Hin1II CATG 1 cut(s) 146
Hin6I GCGC 1 cut(s) 11
HinP1I GCGC 1 cut(s) 11
HinfI GANTC 2 cut(s) 22, 98
Hpy188I TCNGA 2 cut(s) 27, 277
Hpy188III TCNNGA 3 cut(s) 76, 102, 143
Hpy99I CGWCG 2 cut(s) 31, 158
HpyCH4III ACNGT 1 cut(s) 116
HpyCH4IV ACGT 2 cut(s) 330, 343
HpyCH4V TGCA 2 cut(s) 298, 325
HpyF3I CTNAG 2 cut(s) 47, 274
HpySE526I ACGT 2 cut(s) 330, 343
Hsp92II CATG 1 cut(s) 146
HspAI GCGC 1 cut(s) 11
Kzo9I GATC 3 cut(s) 85, 139, 199
LmnI GCTCC 1 cut(s) 253
LpnPI CCDG 6 cut(s) 27, 32, 87, 237, 264, 300
Lsp1109I GCAGC 1 cut(s) 230
LweI GCATC 3 cut(s) 53, 95, 159
MaeII ACGT 2 cut(s) 330, 343
MaeIII GTNAC 1 cut(s) 160
MalI GATC 3 cut(s) 87, 141, 201
MboI GATC 3 cut(s) 85, 139, 199
MboII GAAGA 3 cut(s) 50, 115, 146
MflI RGATCY 1 cut(s) 199
MluCI AATT 1 cut(s) 234
MmeI TCCRAC 1 cut(s) 50
MnlI CCTC 3 cut(s) 80, 271, 283
MseI TTAA 1 cut(s) 230
MspR9I CCNGG 1 cut(s) 252
MvaI CCWGG 1 cut(s) 252
NdeI CATATG 1 cut(s) 305
NdeII GATC 3 cut(s) 85, 139, 199
NlaIII CATG 1 cut(s) 146
NlaIV GGNNCC 1 cut(s) 201
PagI TCATGA 1 cut(s) 142
PfeI GAWTC 2 cut(s) 22, 98
PkrI GCNGC 2 cut(s) 68, 220
Psp6I CCWGG 1 cut(s) 250
PspGI CCWGG 1 cut(s) 250
PspN4I GGNNCC 1 cut(s) 201
PsuI RGATCY 1 cut(s) 199
RsaI GTAC 1 cut(s) 329
RsaNI GTAC 1 cut(s) 328
SaqAI TTAA 1 cut(s) 230
SatI GCNGC 2 cut(s) 67, 219
Sau3AI GATC 3 cut(s) 85, 139, 199
ScrFI CCNGG 1 cut(s) 252
SetI ASST 4 cut(s) 48, 83, 333, 346
SfaNI GCATC 3 cut(s) 53, 95, 159
Sse9I AATT 1 cut(s) 234
SsiI CCGC 1 cut(s) 67
StyD4I CCNGG 1 cut(s) 250
TaaI ACNGT 1 cut(s) 116
TaiI ACGT 2 cut(s) 333, 346
TaqI TCGA 2 cut(s) 61, 156
TasI AATT 1 cut(s) 234
TauI GCSGC 1 cut(s) 69
TfiI GAWTC 2 cut(s) 22, 98
Tru1I TTAA 1 cut(s) 230
Tru9I TTAA 1 cut(s) 230
TseI GCWGC 1 cut(s) 218
TspDTI ATGAA 2 cut(s) 159, 292
XcmI CCANNNNNNNNNTGG 1 cut(s) 210
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.