Basic Information

Type: gene

Biological Identity

Species

arabidopsis_thaliana

Chromosome

Orthogroup ID

OG0003607

Physical Location & Seq

Genomic Coordinates Forward (+)

20173605 .. 20175462

Gene Structure 1858 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

AT3G54490.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 702 bp

ATGGAGGAGACAATGGCCGAAGAAGGGTGCTGTGAAAATGTTGAGTCGACGTTTGACGACGGTACCAACTGTATTTCGAAGACTGAGGACACCGGAGGAATCGAAAGCAAGAGGTTTTACTTGGCTCGCACGACAGCTTTTGAGATGCTTCGCGATAGAGGCTACGAAGTTAATGAAGCTGAGCTCTCTCTCACTCTTTCTGAGTTTCGTTCTGTTTTTGGTGAGAAGCCTGAGCTTGAACGCCTCCGTATCTGCGTTCCTCTTCGCTCAGATCCCAAGAAAAAGATCCTTGTTGTGTTCATGGGAACTGAACCAATCACCGTGAAGTCAGTTCGTGCTCTTCATATTCAGATTTCCAACAATGTAGGCTTGCATGCTATGATTCTGGTTTTACAGAGCAAAATGAACCACTTTGCCCAGAAGGCATTGACTACCTTCCCTTTTACAGTTGAAACTTTCCCGATTGAAGATTTGTTGGTCAACATCACAAAGCACATTCAGCAGCCAAAGATTGAGATTTTAAACAAAGAGGAGAAAGAACAACTGCTGAGGAAGCATGCACTTGAGGACAAACAGCTTCCTTATTTGCAGGAGAAGGACAGCTTTGTGAGGTACTATGGGTTAAAGAAAAAACAGGTGGTGAAGATTACATACAGTAAAGAGCCTGTTGGGGATTTTGTGACATACCGATGCATCATCTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000419 GO:0000428 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0030880 GO:0032991 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0055029 GO:0061695 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

233

Amino Acids

26.89

Weight (kDa)

6.26

Isoelectric Point (pI)

58.71

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	35 - 115	3.9e-22	RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_C	PF01191	160 - 232	4.7e-26	RNA polymerase Rpb5, C-terminal domain

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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Publication-ready

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Orthologous Genes (Group: OG0003607)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G54490
fragaria_vesca	FvH4_7g02710 FvH4_7g02710 FvH4_7g02710
malus_domestica	MD07G1036700.v1.1
prunus_persica	Prupe.2G032100_v2.0.a1
rosa_chinensis	RchiOBHm_Chr1g0321871 RchiOBHm_Chr1g0321951 RchiOBHm_Chr3g0472601
rosa_laevigata	RLG00000030400 RLG00000030402
rosa_multiflora	Rmu_sc0000427.1_g000005 Rmu_sc0002872.1_g000006 Rmu_sc0003510.1_g000023 Rmu_sc0015497.1_g000006
rosa_roxburghii	Rroxscaffold_4G00327410 Rroxscaffold_4G00327450
rosa_rugosa	Rorug01G0034400
rosa_samantha	Rh1AG047300 Rh1BG045400 Rh1CG051100 Rh1CG051500 Rh1DG055400 Rh1DG055800 Rh2CG536300 Rh3AG178800 Rh3BG204700 Rh3CG202100 Rh3CG224200 Rh5AG112100 Rh6AG330000
rosa_wichuraiana	Rw1G004250 Rw1G004290 Rw1G004310 Rw5G021040

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc65I	GGTACC	1 cut(s)	62
AccB1I	GGYRCC	1 cut(s)	62
AccI	GTMKAC	1 cut(s)	47
AccII	CGCG	1 cut(s)	153
AclWI	GGATC	2 cut(s)	266, 280
AcoI	YGGCCR	1 cut(s)	15
AfaI	GTAC	2 cut(s)	64, 614
AfiI	CCNNNNNNNGG	1 cut(s)	24
AgsI	TTSAA	3 cut(s)	239, 452, 467
AluBI	AGCT	6 cut(s)	137, 179, 184, 235, 577, 603
AluI	AGCT	6 cut(s)	137, 179, 184, 235, 577, 603
Alw21I	GWGCWC	2 cut(s)	186, 340
Alw26I	GTCTC	1 cut(s)	2
AlwI	GGATC	2 cut(s)	266, 280
AoxI	GGCC	1 cut(s)	15
ApeKI	GCWGC	1 cut(s)	502
Asp718I	GGTACC	1 cut(s)	62
AsuHPI	GGTGA	3 cut(s)	233, 310, 652
AsuII	TTCGAA	1 cut(s)	77
BaeI	ACNNNNGTAYC	2 cut(s)	46, 79
BanI	GGYRCC	1 cut(s)	62
BanII	GRGCYC	1 cut(s)	186
BarI	GAAGNNNNNNTAC	2 cut(s)	635, 667
BbsI	GAAGAC	1 cut(s)	86
Bbv12I	GWGCWC	2 cut(s)	186, 340
BbvCI	CCTCAGC	1 cut(s)	548
BbvI	GCAGC	1 cut(s)	514
BcoDI	GTCTC	1 cut(s)	2
BglI	GCCNNNNNGGC	1 cut(s)	422
BisI	GCNGC	1 cut(s)	503
BlpI	GCTNAGC	1 cut(s)	180
BlsI	GCNGC	1 cut(s)	504
BmiI	GGNNCC	1 cut(s)	64
BmsI	GCATC	2 cut(s)	135, 680
BpiI	GAAGAC	1 cut(s)	86
Bpu10I	CCTNAGC	2 cut(s)	231, 548
Bpu1102I	GCTNAGC	1 cut(s)	180
Bpu14I	TTCGAA	1 cut(s)	77
BpuEI	CTTGAG	1 cut(s)	584
BsaWI	WCCGGW	1 cut(s)	92
Bsc4I	CCNNNNNNNGG	1 cut(s)	24
BseLI	CCNNNNNNNGG	1 cut(s)	24
BseMII	CTCAG	6 cut(s)	75, 171, 192, 222, 282, 539
BseRI	GAGGAG	2 cut(s)	20, 545
BseXI	GCAGC	1 cut(s)	514
Bsh1236I	CGCG	1 cut(s)	153
BshFI	GGCC	1 cut(s)	17
BshNI	GGYRCC	1 cut(s)	62
BsiHKAI	GWGCWC	2 cut(s)	186, 340
BsiSI	CCGG	1 cut(s)	93
BslI	CCNNNNNNNGG	1 cut(s)	24
BsmAI	GTCTC	1 cut(s)	2
BsnI	GGCC	1 cut(s)	17
Bsp119I	TTCGAA	1 cut(s)	77
Bsp1286I	GDGCHC	2 cut(s)	186, 340
Bsp143I	GATC	2 cut(s)	271, 285
Bsp1720I	GCTNAGC	1 cut(s)	180
Bsp68I	TCGCGA	1 cut(s)	153
BspANI	GGCC	1 cut(s)	17
BspCNI	CTCAG	6 cut(s)	76, 172, 193, 223, 281, 540
BspFNI	CGCG	1 cut(s)	153
BspLI	GGNNCC	1 cut(s)	64
BspPI	GGATC	2 cut(s)	266, 280
BspQI	GCTCTTC	1 cut(s)	345
BspT104I	TTCGAA	1 cut(s)	77
BspT107I	GGYRCC	1 cut(s)	62
BssMI	GATC	2 cut(s)	271, 285
Bst4CI	ACNGT	5 cut(s)	62, 71, 322, 448, 656
Bst6I	CTCTTC	2 cut(s)	267, 345
BstBI	TTCGAA	1 cut(s)	77
BstC8I	GCNNGC	4 cut(s)	127, 371, 375, 558
BstDEI	CTNAG	6 cut(s)	84, 180, 201, 231, 268, 548
BstFNI	CGCG	1 cut(s)	153
BstKTI	GATC	2 cut(s)	274, 288
BstMAI	GTCTC	1 cut(s)	2
BstMBI	GATC	2 cut(s)	271, 285
BstMWI	GCNNNNNNNGC	4 cut(s)	159, 422, 499, 553
BstNSI	RCATGY	2 cut(s)	377, 560
BstUI	CGCG	1 cut(s)	153
BstV1I	GCAGC	1 cut(s)	514
BstV2I	GAAGAC	1 cut(s)	86
BstX2I	RGATCY	2 cut(s)	271, 285
BstYI	RGATCY	2 cut(s)	271, 285
BsuRI	GGCC	1 cut(s)	17
BtuMI	TCGCGA	1 cut(s)	153
Cac8I	GCNNGC	4 cut(s)	127, 371, 375, 558
Csp6I	GTAC	2 cut(s)	63, 613
CviAII	CATG	3 cut(s)	301, 374, 557
CviQI	GTAC	2 cut(s)	63, 613
DdeI	CTNAG	6 cut(s)	84, 180, 201, 231, 268, 548
DpnI	GATC	2 cut(s)	273, 287
DpnII	GATC	2 cut(s)	271, 285
DraI	TTTAAA	1 cut(s)	522
EaeI	YGGCCR	1 cut(s)	15
Eam1104I	CTCTTC	2 cut(s)	267, 345
EarI	CTCTTC	2 cut(s)	267, 345
Ecl136II	GAGCTC	1 cut(s)	184
Eco24I	GRGCYC	1 cut(s)	186
Eco53kI	GAGCTC	1 cut(s)	184
EcoICRI	GAGCTC	1 cut(s)	184
EcoT22I	ATGCAT	1 cut(s)	695
EcoT38I	GRGCYC	1 cut(s)	186
FaeI	CATG	3 cut(s)	304, 377, 560
FaiI	YATR	8 cut(s)	302, 345, 375, 380, 558, 618, 652, 685
FalI	AAGNNNNNCTT	2 cut(s)	587, 619
FatI	CATG	3 cut(s)	300, 373, 556
FblI	GTMKAC	1 cut(s)	47
Fnu4HI	GCNGC	1 cut(s)	503
FriOI	GRGCYC	1 cut(s)	186
Fsp4HI	GCNGC	1 cut(s)	503
GluI	GCNGC	1 cut(s)	503
HaeIII	GGCC	1 cut(s)	17
HapII	CCGG	1 cut(s)	93
Hin1II	CATG	3 cut(s)	304, 377, 560
HincII	GTYRAC	2 cut(s)	48, 481
HindII	GTYRAC	2 cut(s)	48, 481
HinfI	GANTC	3 cut(s)	44, 99, 382
HpaII	CCGG	1 cut(s)	93
HphI	GGTGA	3 cut(s)	233, 310, 652
Hpy166II	GTNNAC	2 cut(s)	48, 481
Hpy188I	TCNGA	4 cut(s)	202, 271, 351, 701
Hpy188III	TCNNGA	2 cut(s)	152, 460
Hpy8I	GTNNAC	2 cut(s)	48, 481
Hpy99I	CGWCG	2 cut(s)	52, 62
HpyAV	CCTTC	4 cut(s)	17, 415, 445, 589
HpyCH4III	ACNGT	5 cut(s)	62, 71, 322, 448, 656
HpyCH4IV	ACGT	1 cut(s)	50
HpyCH4V	TGCA	4 cut(s)	373, 560, 589, 693
HpyF10VI	GCNNNNNNNGC	4 cut(s)	159, 422, 499, 553
HpyF3I	CTNAG	6 cut(s)	84, 180, 201, 231, 268, 548
HpySE526I	ACGT	1 cut(s)	50
Hsp92II	CATG	3 cut(s)	304, 377, 560
KpnI	GGTACC	1 cut(s)	66
Kzo9I	GATC	2 cut(s)	271, 285
LguI	GCTCTTC	1 cut(s)	345
LpnPI	CCDG	7 cut(s)	106, 243, 371, 431, 575, 620, 678
Lsp1109I	GCAGC	1 cut(s)	514
LweI	GCATC	2 cut(s)	135, 680
MaeII	ACGT	1 cut(s)	50
MaeIII	GTNAC	1 cut(s)	679
MalI	GATC	2 cut(s)	273, 287
MboI	GATC	2 cut(s)	271, 285
MboII	GAAGA	6 cut(s)	32, 91, 254, 332, 479, 655
MflI	RGATCY	2 cut(s)	271, 285
MhlI	GDGCHC	2 cut(s)	186, 340
MlyI	GAGTC	1 cut(s)	53
MmeI	TCCRAC	1 cut(s)	381
Mph1103I	ATGCAT	1 cut(s)	695
MseI	TTAA	3 cut(s)	171, 521, 623
MslI	CAYNNNNRTG	1 cut(s)	688
MspI	CCGG	1 cut(s)	93
MvnI	CGCG	1 cut(s)	153
MwoI	GCNNNNNNNGC	4 cut(s)	159, 422, 499, 553
NdeII	GATC	2 cut(s)	271, 285
NlaIII	CATG	3 cut(s)	304, 377, 560
NlaIV	GGNNCC	1 cut(s)	64
NmuCI	GTSAC	1 cut(s)	679
NruI	TCGCGA	1 cut(s)	153
NsiI	ATGCAT	1 cut(s)	695
NspI	RCATGY	2 cut(s)	377, 560
NspV	TTCGAA	1 cut(s)	77
PaeI	GCATGC	2 cut(s)	377, 560
PciSI	GCTCTTC	1 cut(s)	345
PfeI	GAWTC	2 cut(s)	99, 382
PkrI	GCNGC	1 cut(s)	504
PleI	GAGTC	1 cut(s)	52
PpsI	GAGTC	1 cut(s)	52
Psp124BI	GAGCTC	1 cut(s)	186
PspN4I	GGNNCC	1 cut(s)	64
PsuI	RGATCY	2 cut(s)	271, 285
RruI	TCGCGA	1 cut(s)	153
RsaI	GTAC	2 cut(s)	64, 614
RsaNI	GTAC	2 cut(s)	63, 613
RseI	CAYNNNNRTG	1 cut(s)	688
SacI	GAGCTC	1 cut(s)	186
SalI	GTCGAC	1 cut(s)	46
SapI	GCTCTTC	1 cut(s)	345
SaqAI	TTAA	3 cut(s)	171, 521, 623
SatI	GCNGC	1 cut(s)	503
Sau3AI	GATC	2 cut(s)	271, 285
SchI	GAGTC	1 cut(s)	53
SduI	GDGCHC	2 cut(s)	186, 340
SfaNI	GCATC	2 cut(s)	135, 680
SfuI	TTCGAA	1 cut(s)	77
SmiMI	CAYNNNNRTG	1 cut(s)	688
SmlI	CTYRAG	1 cut(s)	563
SmoI	CTYRAG	1 cut(s)	563
SphI	GCATGC	2 cut(s)	377, 560
SstI	GAGCTC	1 cut(s)	186
TaaI	ACNGT	5 cut(s)	62, 71, 322, 448, 656
TaiI	ACGT	1 cut(s)	53
TaqI	TCGA	3 cut(s)	47, 77, 102
TfiI	GAWTC	2 cut(s)	99, 382
Tru1I	TTAA	3 cut(s)	171, 521, 623
Tru9I	TTAA	3 cut(s)	171, 521, 623
TseFI	GTSAC	1 cut(s)	679
TseI	GCWGC	1 cut(s)	502
Tsp45I	GTSAC	1 cut(s)	679
TspDTI	ATGAA	4 cut(s)	189, 289, 332, 419
TspGWI	ACGGA	1 cut(s)	236
XceI	RCATGY	2 cut(s)	377, 560
XmiI	GTMKAC	1 cut(s)	47
Zsp2I	ATGCAT	1 cut(s)	695

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