Basic Information

Type: gene

Biological Identity

Species

arabidopsis_thaliana

Chromosome

Orthogroup ID

OG0003142

Physical Location & Seq

Genomic Coordinates Forward (+)

22016376 .. 22018361

Gene Structure 1986 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

AT3G59600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 441 bp

ATGGCGAGCAATATTATCATGTTCGAGGATATCTTCGTGGTCGATAAGCTAGACCCTGATGGCAAAAAGTTCGATAAAGTTACGCGTGTTGAAGCAAGGAGCCACAACTTGGAAATGTTTATGCATTTAGATGTTAACACTGAGGTTTATCCATTGGCTGTTGGTGATAAGTTCACGCTGGCTATGGCTCCCACGCTTAATCTCGATGGAACTCCTGATACCGGATACTTTACTCCGGGAGCAAAGAAAACACTTGCAGATAAGTATGAATACATCATGCACGGGAAGCTTTACAAGATCTCTGAGCGTGACGGCAAAACTCCAAAAGCAGAGTTATATGTTTCGTTCGGGGGGCTCCTGATGTTGCTTCAGGGAGATCCAGCTCATATTTCTCACTTCGAACTTGACCAGAGGCTCTTTCTACTCATGAGGAAGCTTTGA

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

16.6

Weight (kDa)

5.93

Isoelectric Point (pI)

23.21

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb8	PF03870	9 - 145	3.2e-52	RNA polymerase Rpb8

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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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)	85
AclWI	GGATC	1 cut(s)	371
AcuI	CTGAAG	1 cut(s)	353
AfiI	CCNNNNNNNGG	2 cut(s)	109, 221
AflIII	ACRYGT	1 cut(s)	83
AgsI	TTSAA	1 cut(s)	92
AluBI	AGCT	4 cut(s)	49, 289, 383, 436
AluI	AGCT	4 cut(s)	49, 289, 383, 436
AlwI	GGATC	1 cut(s)	371
AsuC2I	CCSGG	1 cut(s)	237
AsuHPI	GGTGA	1 cut(s)	176
AsuII	TTCGAA	1 cut(s)	399
BanII	GRGCYC	1 cut(s)	357
BccI	CCATC	2 cut(s)	53, 200
BceAI	ACGGC	1 cut(s)	328
BcgI	CGANNNNNNTGC	2 cut(s)	52, 86
BciVI	GTATCC	1 cut(s)	218
BcnI	CCSGG	1 cut(s)	237
BfaI	CTAG	1 cut(s)	50
BfuI	GTATCC	1 cut(s)	218
BglII	AGATCT	1 cut(s)	297
Bme1390I	CCNGG	1 cut(s)	237
BmiI	GGNNCC	3 cut(s)	101, 189, 356
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
BseLI	CCNNNNNNNGG	2 cut(s)	109, 221
BseMII	CTCAG	2 cut(s)	132, 294
Bsh1236I	CGCG	1 cut(s)	85
BsiSI	CCGG	2 cut(s)	222, 236
BslI	CCNNNNNNNGG	2 cut(s)	109, 221
Bsp119I	TTCGAA	1 cut(s)	399
Bsp1286I	GDGCHC	1 cut(s)	357
Bsp143I	GATC	2 cut(s)	297, 376
BspCNI	CTCAG	2 cut(s)	133, 295
BspFNI	CGCG	1 cut(s)	85
BspHI	TCATGA	1 cut(s)	426
BspLI	GGNNCC	3 cut(s)	101, 189, 356
BspPI	GGATC	1 cut(s)	371
BspT104I	TTCGAA	1 cut(s)	399
BssMI	GATC	2 cut(s)	297, 376
BstBI	TTCGAA	1 cut(s)	399
BstC8I	GCNNGC	2 cut(s)	7, 180
BstDEI	CTNAG	2 cut(s)	141, 303
BstFNI	CGCG	1 cut(s)	85
BstKTI	GATC	2 cut(s)	300, 379
BstMBI	GATC	2 cut(s)	297, 376
BstMWI	GCNNNNNNNGC	1 cut(s)	286
BstSCI	CCNGG	1 cut(s)	235
BstUI	CGCG	1 cut(s)	85
BstX2I	RGATCY	2 cut(s)	297, 376
BstYI	RGATCY	2 cut(s)	297, 376
BsuI	GTATCC	1 cut(s)	218
BtsIMutI	CAGTG	1 cut(s)	138
Cac8I	GCNNGC	2 cut(s)	7, 180
CciI	TCATGA	1 cut(s)	426
CviAII	CATG	3 cut(s)	19, 277, 427
DdeI	CTNAG	2 cut(s)	141, 303
DpnI	GATC	2 cut(s)	299, 378
DpnII	GATC	2 cut(s)	297, 376
Eco24I	GRGCYC	1 cut(s)	357
Eco32I	GATATC	1 cut(s)	31
Eco57I	CTGAAG	1 cut(s)	353
EcoRV	GATATC	1 cut(s)	31
EcoT22I	ATGCAT	1 cut(s)	126
EcoT38I	GRGCYC	1 cut(s)	357
FaeI	CATG	3 cut(s)	22, 280, 430
FaiI	YATR	9 cut(s)	20, 122, 185, 267, 278, 337, 339, 387, 428
FatI	CATG	3 cut(s)	18, 276, 426
FriOI	GRGCYC	1 cut(s)	357
FspBI	CTAG	1 cut(s)	50
HapII	CCGG	2 cut(s)	222, 236
Hin1II	CATG	3 cut(s)	22, 280, 430
HincII	GTYRAC	1 cut(s)	136
HindII	GTYRAC	1 cut(s)	136
HindIII	AAGCTT	2 cut(s)	287, 434
HpaI	GTTAAC	1 cut(s)	136
HpaII	CCGG	2 cut(s)	222, 236
HphI	GGTGA	1 cut(s)	176
Hpy166II	GTNNAC	2 cut(s)	136, 174
Hpy188I	TCNGA	1 cut(s)	304
Hpy188III	TCNNGA	4 cut(s)	203, 215, 358, 427
Hpy8I	GTNNAC	2 cut(s)	136, 174
HpyCH4V	TGCA	3 cut(s)	124, 257, 280
HpyF10VI	GCNNNNNNNGC	1 cut(s)	286
HpyF3I	CTNAG	2 cut(s)	141, 303
Hsp92II	CATG	3 cut(s)	22, 280, 430
KspAI	GTTAAC	1 cut(s)	136
Kzo9I	GATC	2 cut(s)	297, 376
LmnI	GCTCC	4 cut(s)	99, 193, 239, 360
LpnPI	CCDG	9 cut(s)	69, 164, 228, 235, 249, 356, 371, 393, 422
MaeI	CTAG	1 cut(s)	50
MaeIII	GTNAC	2 cut(s)	79, 308
MalI	GATC	2 cut(s)	299, 378
MboI	GATC	2 cut(s)	297, 376
MboII	GAAGA	1 cut(s)	25
MflI	RGATCY	2 cut(s)	297, 376
MhlI	GDGCHC	1 cut(s)	357
MluI	ACGCGT	1 cut(s)	83
MnlI	CCTC	4 cut(s)	19, 136, 405, 423
Mph1103I	ATGCAT	1 cut(s)	126
MseI	TTAA	2 cut(s)	135, 198
MslI	CAYNNNNRTG	1 cut(s)	129
MspI	CCGG	2 cut(s)	222, 236
MspR9I	CCNGG	1 cut(s)	237
MvnI	CGCG	1 cut(s)	85
MwoI	GCNNNNNNNGC	1 cut(s)	286
NciI	CCSGG	1 cut(s)	237
NdeII	GATC	2 cut(s)	297, 376
NlaIII	CATG	3 cut(s)	22, 280, 430
NlaIV	GGNNCC	3 cut(s)	101, 189, 356
NmuCI	GTSAC	1 cut(s)	308
NsiI	ATGCAT	1 cut(s)	126
NspV	TTCGAA	1 cut(s)	399
PagI	TCATGA	1 cut(s)	426
PflMI	CCANNNNNTGG	1 cut(s)	109
PfoI	TCCNGGA	1 cut(s)	235
PspN4I	GGNNCC	3 cut(s)	101, 189, 356
PsrI	GAACNNNNNNTAC	2 cut(s)	202, 234
PsuI	RGATCY	2 cut(s)	297, 376
RseI	CAYNNNNRTG	1 cut(s)	129
SaqAI	TTAA	2 cut(s)	135, 198
Sau3AI	GATC	2 cut(s)	297, 376
ScrFI	CCNGG	1 cut(s)	237
SduI	GDGCHC	1 cut(s)	357
SetI	ASST	5 cut(s)	51, 147, 291, 385, 438
SfuI	TTCGAA	1 cut(s)	399
SmiMI	CAYNNNNRTG	1 cut(s)	129
SspI	AATATT	1 cut(s)	13
SspMI	CTAG	1 cut(s)	50
StyD4I	CCNGG	1 cut(s)	235
TaqI	TCGA	5 cut(s)	24, 42, 72, 204, 399
Tru1I	TTAA	2 cut(s)	135, 198
Tru9I	TTAA	2 cut(s)	135, 198
TscAI	CASTG	1 cut(s)	145
TseFI	GTSAC	1 cut(s)	308
Tsp45I	GTSAC	1 cut(s)	308
TspDTI	ATGAA	1 cut(s)	282
TspRI	CASTG	1 cut(s)	145
Van91I	CCANNNNNTGG	1 cut(s)	109
XspI	CTAG	1 cut(s)	50
Zsp2I	ATGCAT	1 cut(s)	126

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