Basic Information

Type: gene

Biological Identity

Species

arabidopsis_thaliana

Chromosome

Orthogroup ID

OG0001390

Physical Location & Seq

Genomic Coordinates Reverse (-)

10980401 .. 10982757

Gene Structure 2357 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

AT3G28956.7

Sequence Viewer

CDS Protein Promoter (2k)

Length: 414 bp

ATGAAGGCAAATGCAGGAGCACTTACCAATTTCGAGTTGCTTGACTTCTTAAACTCAAGAGGTGCTTCAAAAGATACTACAAGAGTTATTGCTCCAATTGCTAGATCAGAATACAAGGTCTATGATTATTTGGTGGAGACTGCTGCTTCCACTCAAACACGAGAGAGCGTTAACAAATCCGCAGACAAGTGTAAAGATTTCAAACTCGCTAAAGCTGAGATTCTCAATATCATCAATCTCTGGCCTTCTTCTATAGTCGAACTGTTACCGATCATAGAGAACCTTGATGATCGAGAAATCGACACAGATGGGATATTAGAGCTTGTGAAGGATTTGCTACCTCCTCTGCCTACAGCTGAAAGTCCTAAAGATAATGATGAAGAAGAAGAAACAGAGAATGGTGAACAGTCGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0003674 GO:0003824 GO:0003899 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0005737 GO:0005886 GO:0006139 GO:0006351 GO:0006352 GO:0006383 GO:0006384 GO:0006725 GO:0006807 GO:0007568 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009360 GO:0009987 GO:0010467 GO:0016020 GO:0016070 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019438 GO:0030424 GO:0030425 GO:0030880 GO:0031974 GO:0031981 GO:0032502 GO:0032774 GO:0032991 GO:0034062 GO:0034641 GO:0034645 GO:0034654 GO:0036477 GO:0042575 GO:0042995 GO:0043005 GO:0043025 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044297 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044463 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0071944 GO:0090304 GO:0097447 GO:0097458 GO:0097659 GO:0097747 GO:0120025 GO:0120038 GO:0140098 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

RNA_pol_Rpb4

Protein Analysis

137

Amino Acids

15.24

Weight (kDa)

4.35

Isoelectric Point (pI)

46.51

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb4	PF03874	10 - 91	2.3e-08	RNA polymerase Rpb4

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Align Labels (Cladogram)

Image

Tree File

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Orthologous Genes (Group: OG0001390)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT5G62950 AT5G62950 AT5G62950 AT5G62950 AT5G62950 AT5G62950 AT5G62950
fragaria_vesca	FvH4_4g01070 FvH4_4g01070 FvH4_5g27570
malus_domestica	MD13G1198900.v1.1
prunus_persica	Prupe.1G020700_v2.0.a1 Prupe.1G020700_v2.0.a1 Prupe.1G020700_v2.0.a1 Prupe.1G020700_v2.0.a1
pyrus_communis	pycom13g17270
rosa_chinensis	RchiOBHm_Chr4g0387641 RchiOBHm_Chr6g0280701
rosa_laevigata	RLG00000010104 RLG00000013035
rosa_multiflora	Rmu_sc0000976.1_g000021 Rmu_sc0003953.1_g000006
rosa_roxburghii	Rroxscaffold_7G00187720
rosa_rugosa	Rorug03G0311800 Rorug03G0311900 Rorug03G0312000 Rorug03G0312100 Rorug06G0133900 Rorug06G0133900 Rorug06G0133900 Rorug06G0134000
rosa_samantha	Rh4AG017400 Rh4BG012200 Rh4CG018600 Rh4DG013200 Rh6AG246600 Rh6BG248900 Rh6CG250000 Rh6DG241500
rosa_wichuraiana	Rw4G001120 Rw6G021350

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AciI	CCGC	1 cut(s)	180
AgsI	TTSAA	2 cut(s)	69, 202
AluBI	AGCT	3 cut(s)	215, 322, 356
AluI	AGCT	3 cut(s)	215, 322, 356
Alw21I	GWGCWC	1 cut(s)	22
Alw26I	GTCTC	1 cut(s)	131
AoxI	GGCC	1 cut(s)	242
ApeKI	GCWGC	1 cut(s)	143
AsuHPI	GGTGA	1 cut(s)	413
BauI	CACGAG	1 cut(s)	159
Bbv12I	GWGCWC	1 cut(s)	22
BbvI	GCAGC	1 cut(s)	130
BccI	CCATC	1 cut(s)	302
BcoDI	GTCTC	1 cut(s)	131
BfaI	CTAG	1 cut(s)	102
BfmI	CTRYAG	2 cut(s)	252, 351
BisI	GCNGC	1 cut(s)	144
BlsI	GCNGC	1 cut(s)	145
BpuEI	CTTGAG	1 cut(s)	40
BseMII	CTCAG	1 cut(s)	207
BseRI	GAGGAG	1 cut(s)	333
BseXI	GCAGC	1 cut(s)	130
BshFI	GGCC	1 cut(s)	244
BsiHKAI	GWGCWC	1 cut(s)	22
BsmAI	GTCTC	1 cut(s)	131
BsnI	GGCC	1 cut(s)	244
Bsp1286I	GDGCHC	1 cut(s)	22
Bsp143I	GATC	3 cut(s)	104, 270, 289
BspACI	CCGC	1 cut(s)	180
BspANI	GGCC	1 cut(s)	244
BspCNI	CTCAG	1 cut(s)	208
BssMI	GATC	3 cut(s)	104, 270, 289
BssSI	CACGAG	1 cut(s)	159
Bst2BI	CACGAG	1 cut(s)	159
Bst4CI	ACNGT	2 cut(s)	264, 408
BstDEI	CTNAG	1 cut(s)	216
BstKTI	GATC	3 cut(s)	107, 273, 292
BstMAI	GTCTC	1 cut(s)	131
BstMBI	GATC	3 cut(s)	104, 270, 289
BstMWI	GCNNNNNNNGC	1 cut(s)	98
BstSFI	CTRYAG	2 cut(s)	252, 351
BstV1I	GCAGC	1 cut(s)	130
BsuRI	GGCC	1 cut(s)	244
CviJI	RGCY	4 cut(s)	215, 244, 322, 356
CviKI_1	RGCY	4 cut(s)	215, 244, 322, 356
DdeI	CTNAG	1 cut(s)	216
DpnI	GATC	3 cut(s)	106, 272, 291
DpnII	GATC	3 cut(s)	104, 270, 289
FaiI	YATR	3 cut(s)	123, 254, 275
FalI	AAGNNNNNCTT	2 cut(s)	49, 81
Fnu4HI	GCNGC	1 cut(s)	144
Fsp4HI	GCNGC	1 cut(s)	144
FspBI	CTAG	1 cut(s)	102
GluI	GCNGC	1 cut(s)	144
HaeIII	GGCC	1 cut(s)	244
HincII	GTYRAC	1 cut(s)	172
HindII	GTYRAC	1 cut(s)	172
HinfI	GANTC	1 cut(s)	220
HpaI	GTTAAC	1 cut(s)	172
HphI	GGTGA	1 cut(s)	413
Hpy166II	GTNNAC	2 cut(s)	172, 404
Hpy188I	TCNGA	1 cut(s)	109
Hpy188III	TCNNGA	3 cut(s)	57, 293, 411
Hpy8I	GTNNAC	2 cut(s)	172, 404
HpyAV	CCTTC	2 cut(s)	255, 322
HpyCH4III	ACNGT	2 cut(s)	264, 408
HpyCH4V	TGCA	1 cut(s)	14
HpyF10VI	GCNNNNNNNGC	1 cut(s)	98
HpyF3I	CTNAG	1 cut(s)	216
KspAI	GTTAAC	1 cut(s)	172
Kzo9I	GATC	3 cut(s)	104, 270, 289
LmnI	GCTCC	2 cut(s)	17, 97
LpnPI	CCDG	1 cut(s)	226
Lsp1109I	GCAGC	1 cut(s)	130
MaeI	CTAG	1 cut(s)	102
MaeIII	GTNAC	1 cut(s)	264
MalI	GATC	3 cut(s)	106, 272, 291
MboI	GATC	3 cut(s)	104, 270, 289
MboII	GAAGA	4 cut(s)	240, 392, 395, 398
MfeI	CAATTG	1 cut(s)	96
MhlI	GDGCHC	1 cut(s)	22
MluCI	AATT	2 cut(s)	28, 96
MnlI	CCTC	3 cut(s)	53, 351, 354
MseI	TTAA	2 cut(s)	50, 171
MspA1I	CMGCKG	1 cut(s)	356
MunI	CAATTG	1 cut(s)	96
MwoI	GCNNNNNNNGC	1 cut(s)	98
NdeII	GATC	3 cut(s)	104, 270, 289
PfeI	GAWTC	1 cut(s)	220
PkrI	GCNGC	1 cut(s)	145
PvuII	CAGCTG	1 cut(s)	356
SaqAI	TTAA	2 cut(s)	50, 171
SatI	GCNGC	1 cut(s)	144
Sau3AI	GATC	3 cut(s)	104, 270, 289
SduI	GDGCHC	1 cut(s)	22
SetI	ASST	7 cut(s)	64, 120, 217, 285, 324, 343, 358
SfcI	CTRYAG	2 cut(s)	252, 351
SmlI	CTYRAG	1 cut(s)	55
SmoI	CTYRAG	1 cut(s)	55
Sse9I	AATT	2 cut(s)	28, 96
SsiI	CCGC	1 cut(s)	180
SspMI	CTAG	1 cut(s)	102
TaaI	ACNGT	2 cut(s)	264, 408
TaqI	TCGA	4 cut(s)	33, 258, 292, 300
TasI	AATT	2 cut(s)	28, 96
TfiI	GAWTC	1 cut(s)	220
Tru1I	TTAA	2 cut(s)	50, 171
Tru9I	TTAA	2 cut(s)	50, 171
TseI	GCWGC	1 cut(s)	143
TspDTI	ATGAA	2 cut(s)	17, 393
XspI	CTAG	1 cut(s)	102

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.