Basic Information

Type: gene

Biological Identity

Species

arabidopsis_thaliana

Chromosome

Orthogroup ID

OG0003142

Physical Location & Seq

Genomic Coordinates Forward (+)

20254938 .. 20256688

Gene Structure 1751 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

AT1G54250.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 441 bp

ATGGCGAGCAATATCATCTTGTTCGAGGATATCTTCGTGGTCGATCAGTTAGACCCTGATGGCAAAAAGTTCGATAAAGTTACTCGCGTTCAAGCTACGAGCCACAACTTGGAAATGTTTATGCATTTAGATGTTAATACAGAGGTTTATCCATTGGCTGTTGGTGATAAGTTCACACTTGCGTTGGCTCCTACGCTGAATCTCGATGGAACCCCTGATACCGGTTATTTTACTCCGGGAGCAAAGAAAACACTTGCCGATAAGTATGAATACATAATGCACGGGAAGCTTTACAAGATCTCTGAGCGTGACGGCAAAACTCCAAAAGCAGAGCTATATGTTTCGTTTGGCGGCCTCCTGATGTTGCTTAAGGGAGATCCAGCTCACATTTCTCACTTCGAACTCGACCAGAGGCTCTTCCTACTCATGAGGAAGCTGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000418 GO:0000419 GO:0000428 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005665 GO:0005666 GO:0005730 GO:0005736 GO:0016591 GO:0030880 GO:0031974 GO:0031981 GO:0032991 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044452 GO:0044464 GO:0055029 GO:0061695 GO:0070013 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko04623 ko05016 ko05169 map00230 map00240 map01100 map03020 map04623 map05016 map05169

Pfam Domains

Protein Families

RNA_pol_Rpb8

Protein Analysis

146

Amino Acids

16.51

Weight (kDa)

5.92

Isoelectric Point (pI)

18.44

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb8	PF03870	9 - 145	1.4e-52	RNA polymerase Rpb8

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)

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Orthologous Genes (Group: OG0003142)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G54250 AT3G59600
fragaria_vesca	FvH4_7g05580 FvH4_7g05580 FvH4_7g05580 FvH4_7g05580 FvH4_7g05580 FvH4_7g05580 FvH4_7g05580
malus_domestica	MD03G1174900.v1.1 MD04G1053300.v1.1 MD05G1057600.v1.1 MD11G1193000.v1.1
prunus_persica	Prupe.4G249600_v2.0.a1 Prupe.4G249600_v2.0.a1
pyrus_communis	pycom03g13240 pycom11g16850
rosa_chinensis	RchiOBHm_Chr1g0332731 RchiOBHm_Chr5g0052071 RchiOBHm_Chr6g0273601
rosa_laevigata	RLG00000034845
rosa_multiflora	Rmu_sc0001587.1_g000001 Rmu_sc0032204.1_g000001 Rmu_ssc0000098.1_g000004
rosa_roxburghii	Rroxscaffold_1G00027860 Rroxscaffold_4G00318050
rosa_rugosa	Rorug01G0104600 Rorug05G0275000 Rorug05G0275100
rosa_samantha	Rh1AG127600 Rh1BG097000 Rh1CG121400 Rh5BG358000 Rh5CG383500 Rh5DG373400 Rh6CG194200
rosa_wichuraiana	Rw5G032800

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	109
AccII	CGCG	1 cut(s)	87
AciI	CCGC	1 cut(s)	351
AclWI	GGATC	1 cut(s)	371
AfiI	CCNNNNNNNGG	2 cut(s)	109, 221
AflII	CTTAAG	1 cut(s)	368
AgeI	ACCGGT	1 cut(s)	221
AgsI	TTSAA	1 cut(s)	92
AluBI	AGCT	5 cut(s)	95, 289, 334, 383, 436
AluI	AGCT	5 cut(s)	95, 289, 334, 383, 436
AlwI	GGATC	1 cut(s)	371
AoxI	GGCC	1 cut(s)	352
AsiGI	ACCGGT	1 cut(s)	221
AsuC2I	CCSGG	1 cut(s)	237
AsuHPI	GGTGA	1 cut(s)	176
AsuII	TTCGAA	1 cut(s)	399
BccI	CCATC	2 cut(s)	53, 200
BceAI	ACGGC	1 cut(s)	328
BcgI	CGANNNNNNTGC	2 cut(s)	52, 86
BcnI	CCSGG	1 cut(s)	237
BfrI	CTTAAG	1 cut(s)	368
BglII	AGATCT	1 cut(s)	297
BisI	GCNGC	1 cut(s)	352
BlsI	GCNGC	1 cut(s)	353
Bme1390I	CCNGG	1 cut(s)	237
BmiI	GGNNCC	2 cut(s)	189, 211
BmrFI	CCNGG	1 cut(s)	237
Bpu14I	TTCGAA	1 cut(s)	399
BpuMI	CCSGG	1 cut(s)	237
BsaWI	WCCGGW	1 cut(s)	221
Bsc4I	CCNNNNNNNGG	2 cut(s)	109, 221
Bse118I	RCCGGY	1 cut(s)	221
BseLI	CCNNNNNNNGG	2 cut(s)	109, 221
BseMII	CTCAG	1 cut(s)	294
Bsh1236I	CGCG	1 cut(s)	87
BshFI	GGCC	1 cut(s)	354
BshTI	ACCGGT	1 cut(s)	221
BsiSI	CCGG	2 cut(s)	222, 236
BslI	CCNNNNNNNGG	2 cut(s)	109, 221
BsnI	GGCC	1 cut(s)	354
Bsp119I	TTCGAA	1 cut(s)	399
Bsp143I	GATC	3 cut(s)	43, 297, 376
BspACI	CCGC	1 cut(s)	351
BspANI	GGCC	1 cut(s)	354
BspCNI	CTCAG	1 cut(s)	295
BspFNI	CGCG	1 cut(s)	87
BspHI	TCATGA	1 cut(s)	426
BspLI	GGNNCC	2 cut(s)	189, 211
BspPI	GGATC	1 cut(s)	371
BspQI	GCTCTTC	1 cut(s)	422
BspT104I	TTCGAA	1 cut(s)	399
BspTI	CTTAAG	1 cut(s)	368
BsrFI	RCCGGY	1 cut(s)	221
BssAI	RCCGGY	1 cut(s)	221
BssMI	GATC	3 cut(s)	43, 297, 376
Bst6I	CTCTTC	1 cut(s)	422
BstAFI	CTTAAG	1 cut(s)	368
BstBI	TTCGAA	1 cut(s)	399
BstC8I	GCNNGC	1 cut(s)	7
BstDEI	CTNAG	1 cut(s)	303
BstFNI	CGCG	1 cut(s)	87
BstKTI	GATC	3 cut(s)	46, 300, 379
BstMBI	GATC	3 cut(s)	43, 297, 376
BstMWI	GCNNNNNNNGC	1 cut(s)	286
BstSCI	CCNGG	1 cut(s)	235
BstUI	CGCG	1 cut(s)	87
BstX2I	RGATCY	2 cut(s)	297, 376
BstYI	RGATCY	2 cut(s)	297, 376
BsuRI	GGCC	1 cut(s)	354
Cac8I	GCNNGC	1 cut(s)	7
CciI	TCATGA	1 cut(s)	426
Cfr10I	RCCGGY	1 cut(s)	221
CspAI	ACCGGT	1 cut(s)	221
CviAII	CATG	1 cut(s)	427
DdeI	CTNAG	1 cut(s)	303
DpnI	GATC	3 cut(s)	45, 299, 378
DpnII	GATC	3 cut(s)	43, 297, 376
Eam1104I	CTCTTC	1 cut(s)	422
EarI	CTCTTC	1 cut(s)	422
Eco32I	GATATC	1 cut(s)	31
EcoRV	GATATC	1 cut(s)	31
EcoT22I	ATGCAT	1 cut(s)	126
FaeI	CATG	1 cut(s)	430
FaiI	YATR	6 cut(s)	122, 267, 275, 337, 339, 428
FatI	CATG	1 cut(s)	426
Fnu4HI	GCNGC	1 cut(s)	352
Fsp4HI	GCNGC	1 cut(s)	352
GluI	GCNGC	1 cut(s)	352
HaeIII	GGCC	1 cut(s)	354
HapII	CCGG	2 cut(s)	222, 236
Hin1II	CATG	1 cut(s)	430
HindIII	AAGCTT	1 cut(s)	287
HinfI	GANTC	1 cut(s)	199
HpaII	CCGG	2 cut(s)	222, 236
HphI	GGTGA	1 cut(s)	176
Hpy166II	GTNNAC	1 cut(s)	174
Hpy188I	TCNGA	1 cut(s)	304
Hpy188III	TCNNGA	3 cut(s)	203, 358, 427
Hpy8I	GTNNAC	1 cut(s)	174
HpyCH4V	TGCA	2 cut(s)	124, 280
HpyF10VI	GCNNNNNNNGC	1 cut(s)	286
HpyF3I	CTNAG	1 cut(s)	303
Hsp92II	CATG	1 cut(s)	430
Kzo9I	GATC	3 cut(s)	43, 297, 376
LguI	GCTCTTC	1 cut(s)	422
LmnI	GCTCC	2 cut(s)	193, 239
LpnPI	CCDG	7 cut(s)	69, 228, 235, 249, 371, 393, 422
MaeIII	GTNAC	2 cut(s)	79, 308
MalI	GATC	3 cut(s)	45, 299, 378
MboI	GATC	3 cut(s)	43, 297, 376
MboII	GAAGA	2 cut(s)	25, 409
MflI	RGATCY	2 cut(s)	297, 376
MnlI	CCTC	5 cut(s)	19, 136, 365, 405, 423
Mph1103I	ATGCAT	1 cut(s)	126
MseI	TTAA	2 cut(s)	135, 369
MslI	CAYNNNNRTG	1 cut(s)	129
MspCI	CTTAAG	1 cut(s)	368
MspI	CCGG	2 cut(s)	222, 236
MspR9I	CCNGG	1 cut(s)	237
MvnI	CGCG	1 cut(s)	87
MwoI	GCNNNNNNNGC	1 cut(s)	286
NciI	CCSGG	1 cut(s)	237
NdeII	GATC	3 cut(s)	43, 297, 376
NlaIII	CATG	1 cut(s)	430
NlaIV	GGNNCC	2 cut(s)	189, 211
NmuCI	GTSAC	1 cut(s)	308
NsiI	ATGCAT	1 cut(s)	126
NspV	TTCGAA	1 cut(s)	399
PagI	TCATGA	1 cut(s)	426
PciSI	GCTCTTC	1 cut(s)	422
PfeI	GAWTC	1 cut(s)	199
PflMI	CCANNNNNTGG	1 cut(s)	109
PfoI	TCCNGGA	1 cut(s)	235
PinAI	ACCGGT	1 cut(s)	221
PkrI	GCNGC	1 cut(s)	353
PspN4I	GGNNCC	2 cut(s)	189, 211
PsrI	GAACNNNNNNTAC	2 cut(s)	202, 234
PsuI	RGATCY	2 cut(s)	297, 376
RseI	CAYNNNNRTG	1 cut(s)	129
SapI	GCTCTTC	1 cut(s)	422
SaqAI	TTAA	2 cut(s)	135, 369
SatI	GCNGC	1 cut(s)	352
Sau3AI	GATC	3 cut(s)	43, 297, 376
ScrFI	CCNGG	1 cut(s)	237
SetI	ASST	6 cut(s)	97, 147, 291, 336, 385, 438
SfuI	TTCGAA	1 cut(s)	399
SmiMI	CAYNNNNRTG	1 cut(s)	129
SmlI	CTYRAG	1 cut(s)	368
SmoI	CTYRAG	1 cut(s)	368
SsiI	CCGC	1 cut(s)	351
StyD4I	CCNGG	1 cut(s)	235
TaqI	TCGA	6 cut(s)	24, 42, 72, 204, 399, 405
TauI	GCSGC	1 cut(s)	354
TfiI	GAWTC	1 cut(s)	199
Tru1I	TTAA	2 cut(s)	135, 369
Tru9I	TTAA	2 cut(s)	135, 369
TseFI	GTSAC	1 cut(s)	308
Tsp45I	GTSAC	1 cut(s)	308
TspDTI	ATGAA	1 cut(s)	282
Van91I	CCANNNNNTGG	1 cut(s)	109
Vha464I	CTTAAG	1 cut(s)	368
Zsp2I	ATGCAT	1 cut(s)	126

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