Basic Information

Type: gene

Biological Identity

Species

arabidopsis_thaliana

Chromosome

Orthogroup ID

OG0009947

Physical Location & Seq

Genomic Coordinates Forward (+)

21125725 .. 21128075

Gene Structure 2351 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

AT3G57080.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 669 bp

ATGGAAGTGAAAGGGAAAGAGACAGCTTCGGTTCTGTGTCTGAGCAAATACGTGGATCTATCGAGTGAAGAGAGTCATAGATACTATCTTGCGCGGCGAAATGGCTTGCAGATGCTCCGAGACAGAGGCTACGAAGTCTCCGACGAAGATATCAATCTCTCCCTTCACGATTTTCGAACTGTTTACGGTGAACGTCCCGATGTTGATCGTCTTCGCATCTCCGCTCTGCATCGCTCCGATTCTACCAAAAAGGTAAAAATTGTCTTTTTTGGTACTAGTATGGTTAAAGTCAACGCAATCCGCAGTGTAGTAGCGGATATACTTAGCCAAGAAACCATAACTGGGCTGATATTGGTTCTGCAAAACCATGTAACCAATCAAGCCTTGAAAGCCATTGAACTTTTTTCTTTCAAGGTCGAGATATTCCAGATAACGGATCTGCTAGTCAACATAACCAAACATTCACTGAAGCCACAACATCAGGTGTTGAATGATGAAGAGAAGACAACACTTCTCAAGAAGTTCAGCATTGAGGAAAAACAGCTTCCTCGGATTTCAAAGAAAGATGCTATCGTCCGGTACTACGGATTAGAGAAAGGGCAAGTTGTGAAGGTGAATTACAGAGGCGAACTCACGGAATCGCATGTTGCCTTCCGATGTGTGTGGTGA

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_Rpb5_C RNA_pol_Rpb5_N

Protein Analysis

222

Amino Acids

25.59

Weight (kDa)

9.08

Isoelectric Point (pI)

29.61

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	23 - 105	6e-22	RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_C	PF01191	149 - 221	3.9e-29	RNA polymerase Rpb5, C-terminal domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0009947)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G57080
fragaria_vesca	FvH4_6g25210
malus_domestica	MD00G1170800.v1.1 MD14G1084600.v1.1
prunus_persica	Prupe.7G043600_v2.0.a1 Prupe.7G043600_v2.0.a1 Prupe.7G043600_v2.0.a1
pyrus_communis	pycom12g07770 pycom14g07430
rosa_chinensis	RchiOBHm_Chr2g0125071
rosa_laevigata	RLG00000018847
rosa_multiflora	Rmu_sc0003505.1_g000022
rosa_roxburghii	Rroxscaffold_2G00118260 Rroxscaffold_2G00118720
rosa_rugosa	Rorug02G0255400 Rorug02G0255500.1
rosa_samantha	Rh2AG313900 Rh2BG322200 Rh2CG304500 Rh2DG340600
rosa_wichuraiana	Rw2G025400

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccBSI	CCGCTC	1 cut(s)	224
AccII	CGCG	1 cut(s)	94
AciI	CCGC	4 cut(s)	94, 222, 301, 314
AclWI	GGATC	2 cut(s)	63, 444
AcuI	CTGAAG	1 cut(s)	488
AfaI	GTAC	2 cut(s)	274, 581
AfiI	CCNNNNNNNGG	2 cut(s)	342, 433
AgsI	TTSAA	5 cut(s)	388, 398, 412, 490, 558
AhlI	ACTAGT	1 cut(s)	275
AluBI	AGCT	2 cut(s)	26, 544
AluI	AGCT	2 cut(s)	26, 544
Alw26I	GTCTC	3 cut(s)	14, 114, 142
AlwI	GGATC	2 cut(s)	63, 444
AspLEI	GCGC	1 cut(s)	94
AsuHPI	GGTGA	2 cut(s)	200, 625
AsuII	TTCGAA	1 cut(s)	175
BarI	GAAGNNNNNNTAC	2 cut(s)	602, 634
BbsI	GAAGAC	2 cut(s)	203, 509
BcoDI	GTCTC	3 cut(s)	14, 114, 142
BcuI	ACTAGT	1 cut(s)	275
BfaI	CTAG	2 cut(s)	276, 443
BisI	GCNGC	1 cut(s)	95
BlsI	GCNGC	1 cut(s)	96
BmrI	ACTGGG	1 cut(s)	351
BmsI	GCATC	4 cut(s)	102, 225, 238, 556
BmuI	ACTGGG	1 cut(s)	351
BpiI	GAAGAC	2 cut(s)	203, 509
BplI	GAGNNNNNCTC	2 cut(s)	615, 647
Bpu14I	TTCGAA	1 cut(s)	175
BpuEI	CTTGAG	1 cut(s)	500
BsaAI	YACGTR	1 cut(s)	52
BsaBI	GATNNNNATC	2 cut(s)	153, 204
BsaJI	CCNNGG	1 cut(s)	548
BsaWI	WCCGGW	1 cut(s)	576
BsaXI	ACNNNNNCTCC	2 cut(s)	122, 152
Bsc4I	CCNNNNNNNGG	2 cut(s)	342, 433
Bse1I	ACTGG	1 cut(s)	346
Bse8I	GATNNNNATC	2 cut(s)	153, 204
BseDI	CCNNGG	1 cut(s)	548
BseJI	GATNNNNATC	2 cut(s)	153, 204
BseLI	CCNNNNNNNGG	2 cut(s)	342, 433
BseMII	CTCAG	1 cut(s)	32
BseNI	ACTGG	1 cut(s)	346
Bsh1236I	CGCG	1 cut(s)	94
BsiSI	CCGG	1 cut(s)	577
BslFI	GGGAC	1 cut(s)	180
BslI	CCNNNNNNNGG	2 cut(s)	342, 433
BsmAI	GTCTC	3 cut(s)	14, 114, 142
BsmFI	GGGAC	1 cut(s)	180
Bsp119I	TTCGAA	1 cut(s)	175
Bsp143I	GATC	3 cut(s)	55, 205, 436
BspACI	CCGC	4 cut(s)	94, 222, 301, 314
BspCNI	CTCAG	1 cut(s)	33
BspFNI	CGCG	1 cut(s)	94
BspPI	GGATC	2 cut(s)	63, 444
BspT104I	TTCGAA	1 cut(s)	175
BsrBI	CCGCTC	1 cut(s)	224
BsrI	ACTGG	1 cut(s)	346
BssECI	CCNNGG	1 cut(s)	548
BssMI	GATC	3 cut(s)	55, 205, 436
Bst4CI	ACNGT	2 cut(s)	181, 188
Bst6I	CTCTTC	2 cut(s)	63, 492
BstBAI	YACGTR	1 cut(s)	52
BstBI	TTCGAA	1 cut(s)	175
BstC8I	GCNNGC	1 cut(s)	107
BstDEI	CTNAG	2 cut(s)	41, 323
BstFNI	CGCG	1 cut(s)	94
BstHHI	GCGC	1 cut(s)	94
BstKTI	GATC	3 cut(s)	58, 208, 439
BstMAI	GTCTC	3 cut(s)	14, 114, 142
BstMBI	GATC	3 cut(s)	55, 205, 436
BstMWI	GCNNNNNNNGC	1 cut(s)	389
BstNSI	RCATGY	1 cut(s)	647
BstUI	CGCG	1 cut(s)	94
BstV2I	GAAGAC	2 cut(s)	203, 509
BstX2I	RGATCY	2 cut(s)	55, 436
BstYI	RGATCY	2 cut(s)	55, 436
BtgZI	GCGATG	1 cut(s)	215
BtsI	GCAGTG	1 cut(s)	310
BtsIMutI	CAGTG	2 cut(s)	310, 464
Cac8I	GCNNGC	1 cut(s)	107
CfoI	GCGC	1 cut(s)	94
Csp6I	GTAC	2 cut(s)	273, 580
CviAII	CATG	2 cut(s)	368, 644
CviJI	RGCY	9 cut(s)	26, 105, 129, 327, 346, 383, 392, 472, 544
CviKI_1	RGCY	9 cut(s)	26, 105, 129, 327, 346, 383, 392, 472, 544
CviQI	GTAC	2 cut(s)	273, 580
DdeI	CTNAG	2 cut(s)	41, 323
DpnI	GATC	3 cut(s)	57, 207, 438
DpnII	GATC	3 cut(s)	55, 205, 436
Eam1104I	CTCTTC	2 cut(s)	63, 492
EarI	CTCTTC	2 cut(s)	63, 492
Eco32I	GATATC	1 cut(s)	151
Eco57I	CTGAAG	1 cut(s)	488
EcoRV	GATATC	1 cut(s)	151
FaeI	CATG	2 cut(s)	371, 647
FaiI	YATR	7 cut(s)	78, 281, 320, 338, 369, 452, 645
FaqI	GGGAC	1 cut(s)	180
FatI	CATG	2 cut(s)	367, 643
Fnu4HI	GCNGC	1 cut(s)	95
Fsp4HI	GCNGC	1 cut(s)	95
FspBI	CTAG	2 cut(s)	276, 443
GlaI	GCGC	1 cut(s)	93
GluI	GCNGC	1 cut(s)	95
HapII	CCGG	1 cut(s)	577
HhaI	GCGC	1 cut(s)	94
Hin1II	CATG	2 cut(s)	371, 647
Hin6I	GCGC	1 cut(s)	92
HinP1I	GCGC	1 cut(s)	92
HincII	GTYRAC	2 cut(s)	292, 448
HindII	GTYRAC	2 cut(s)	292, 448
HinfI	GANTC	3 cut(s)	73, 239, 638
HpaII	CCGG	1 cut(s)	577
HphI	GGTGA	2 cut(s)	200, 625
Hpy166II	GTNNAC	4 cut(s)	184, 191, 292, 448
Hpy188I	TCNGA	6 cut(s)	42, 119, 142, 238, 552, 656
Hpy188III	TCNNGA	5 cut(s)	167, 197, 418, 427, 517
Hpy8I	GTNNAC	4 cut(s)	184, 191, 292, 448
Hpy99I	CGWCG	1 cut(s)	146
HpyAV	CCTTC	3 cut(s)	173, 604, 661
HpyCH4III	ACNGT	2 cut(s)	181, 188
HpyCH4IV	ACGT	2 cut(s)	51, 193
HpyCH4V	TGCA	3 cut(s)	109, 229, 361
HpyF10VI	GCNNNNNNNGC	1 cut(s)	389
HpyF3I	CTNAG	2 cut(s)	41, 323
HpySE526I	ACGT	2 cut(s)	51, 193
Hsp92II	CATG	2 cut(s)	371, 647
HspAI	GCGC	1 cut(s)	92
Kzo9I	GATC	3 cut(s)	55, 205, 436
LmnI	GCTCC	2 cut(s)	120, 239
LpnPI	CCDG	4 cut(s)	327, 440, 467, 590
LweI	GCATC	4 cut(s)	102, 225, 238, 556
MaeI	CTAG	2 cut(s)	276, 443
MaeII	ACGT	2 cut(s)	51, 193
MaeIII	GTNAC	1 cut(s)	370
MalI	GATC	3 cut(s)	57, 207, 438
MbiI	CCGCTC	1 cut(s)	224
MboI	GATC	3 cut(s)	55, 205, 436
MboII	GAAGA	5 cut(s)	80, 158, 203, 509, 514
MflI	RGATCY	2 cut(s)	55, 436
MluCI	AATT	2 cut(s)	258, 616
MlyI	GAGTC	1 cut(s)	82
MmeI	TCCRAC	1 cut(s)	165
MnlI	CCTC	4 cut(s)	119, 526, 558, 617
MseI	TTAA	1 cut(s)	285
MspI	CCGG	1 cut(s)	577
MvnI	CGCG	1 cut(s)	94
MwoI	GCNNNNNNNGC	1 cut(s)	389
NdeII	GATC	3 cut(s)	55, 205, 436
NlaIII	CATG	2 cut(s)	371, 647
NspI	RCATGY	1 cut(s)	647
NspV	TTCGAA	1 cut(s)	175
PcsI	WCGNNNNNNNCGW	1 cut(s)	138
PfeI	GAWTC	2 cut(s)	239, 638
PkrI	GCNGC	1 cut(s)	96
PleI	GAGTC	1 cut(s)	81
PpsI	GAGTC	1 cut(s)	81
Ppu21I	YACGTR	1 cut(s)	52
PsuI	RGATCY	2 cut(s)	55, 436
RsaI	GTAC	2 cut(s)	274, 581
RsaNI	GTAC	2 cut(s)	273, 580
SaqAI	TTAA	1 cut(s)	285
SatI	GCNGC	1 cut(s)	95
Sau3AI	GATC	3 cut(s)	55, 205, 436
SchI	GAGTC	1 cut(s)	82
SetI	ASST	8 cut(s)	28, 54, 196, 255, 417, 486, 546, 615
SfaNI	GCATC	4 cut(s)	102, 225, 238, 556
SfuI	TTCGAA	1 cut(s)	175
SmlI	CTYRAG	1 cut(s)	515
SmoI	CTYRAG	1 cut(s)	515
SpeI	ACTAGT	1 cut(s)	275
Sse9I	AATT	2 cut(s)	258, 616
SsiI	CCGC	4 cut(s)	94, 222, 301, 314
SspMI	CTAG	2 cut(s)	276, 443
TaaI	ACNGT	2 cut(s)	181, 188
TaiI	ACGT	2 cut(s)	54, 196
TaqI	TCGA	3 cut(s)	62, 175, 417
TasI	AATT	2 cut(s)	258, 616
TauI	GCSGC	1 cut(s)	97
TfiI	GAWTC	2 cut(s)	239, 638
Tru1I	TTAA	1 cut(s)	285
Tru9I	TTAA	1 cut(s)	285
TscAI	CASTG	2 cut(s)	310, 471
TspDTI	ATGAA	1 cut(s)	510
TspGWI	ACGGA	3 cut(s)	449, 600, 650
TspRI	CASTG	2 cut(s)	310, 471
XceI	RCATGY	1 cut(s)	647
XspI	CTAG	2 cut(s)	276, 443

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