Basic Information

Type: gene

Biological Identity

Species

arabidopsis_thaliana

Chromosome

Orthogroup ID

OG0009411

Physical Location & Seq

Genomic Coordinates Reverse (-)

19317737 .. 19319123

Gene Structure 1387 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

AT3G52090.2

Sequence Viewer

CDS Protein Promoter (2k)

Length: 351 bp

ATGAATGCTCCCGAACGATATGAGCGATTCGTCGTCCCTGAAGGCACCAAGAAGGTTTCTTATGATAGGGATACGAAGATCATCAATGCTGCTTCCTTCACGGTTGAGAGAGAAGACCATACGATTGGAAACATTGTCCGCATGCAACTTCATCGCGACGAGAATGTCTTGTTTGCTGGATACCAACTTCCTCATCCTCTTAAGTACAAAATCATAGTGAGGATTCACACAACAAGCCAGTCTTCCCCAATGCAAGCATACAACCAGGCCATCAATGACTTGGACAAGGAGCTCGACTACTTGAAGAACCAGTTTGAGGCAGAGGTGGCCAAGTTTTCGAATCAGTTTTAA

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:0016591 GO:0030880 GO:0031974 GO:0031981 GO:0032991 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044464 GO:0055029 GO:0061695 GO:0070013 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

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

Pfam Domains

Protein Families

RNA_pol_L_2

Protein Analysis

116

Amino Acids

13.56

Weight (kDa)

6.41

Isoelectric Point (pI)

19.3

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_L_2	PF13656	31 - 74	8.3e-17	RNA polymerase Rpb3/Rpb11 dimerisation 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: OG0009411)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G52090 AT3G52090
fragaria_vesca	FvH4_2g07830
malus_domestica	MD05G1071600.v1.1 MD10G1083600.v1.1
prunus_persica	Prupe.8G106600_v2.0.a1 Prupe.8G106600_v2.0.a1
pyrus_communis	pycom05g06170 pycom10g06570
rosa_chinensis	RchiOBHm_Chr6g0262241
rosa_multiflora	Rmu_sc0002510.1_g000027 Rmu_sc0010083.1_g000004
rosa_roxburghii	Rroxscaffold_7G00207930
rosa_rugosa	Rorug05G0595600 Rorug05G0595700 Rorug05G0595700
rosa_samantha	Rh2AG296400 Rh2DG320300 Rh6AG115800 Rh6BG110100 Rh6DG098100
rosa_wichuraiana	Rw6G010080

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AasI	GACNNNNNNGTC	1 cut(s)	164
AccB1I	GGYRCC	1 cut(s)	44
AccII	CGCG	1 cut(s)	156
AciI	CCGC	1 cut(s)	139
AcoI	YGGCCR	1 cut(s)	327
AcuI	CTGAAG	1 cut(s)	60
AfaI	GTAC	1 cut(s)	206
AfiI	CCNNNNNNNGG	1 cut(s)	316
AflII	CTTAAG	1 cut(s)	200
AgsI	TTSAA	1 cut(s)	304
AjnI	CCWGG	1 cut(s)	264
AluBI	AGCT	1 cut(s)	292
AluI	AGCT	1 cut(s)	292
Alw21I	GWGCWC	1 cut(s)	294
AoxI	GGCC	2 cut(s)	267, 327
ApeKI	GCWGC	1 cut(s)	89
AsuII	TTCGAA	1 cut(s)	338
BalI	TGGCCA	1 cut(s)	329
BanI	GGYRCC	1 cut(s)	44
BanII	GRGCYC	1 cut(s)	294
BbsI	GAAGAC	2 cut(s)	120, 234
Bbv12I	GWGCWC	1 cut(s)	294
BbvI	GCAGC	1 cut(s)	76
BccI	CCATC	1 cut(s)	278
BcgI	CGANNNNNNTGC	2 cut(s)	134, 168
BciT130I	CCWGG	1 cut(s)	266
BciVI	GTATCC	2 cut(s)	64, 173
BfrI	CTTAAG	1 cut(s)	200
BfuI	GTATCC	2 cut(s)	64, 173
BisI	GCNGC	1 cut(s)	90
BlsI	GCNGC	1 cut(s)	91
Bme1390I	CCNGG	1 cut(s)	266
BmiI	GGNNCC	1 cut(s)	46
BmrFI	CCNGG	1 cut(s)	266
BpiI	GAAGAC	2 cut(s)	120, 234
Bpu14I	TTCGAA	1 cut(s)	338
Bsc4I	CCNNNNNNNGG	1 cut(s)	316
Bse1I	ACTGG	2 cut(s)	238, 310
BseBI	CCWGG	1 cut(s)	266
BseGI	GGATG	1 cut(s)	193
BseLI	CCNNNNNNNGG	1 cut(s)	316
BseNI	ACTGG	2 cut(s)	238, 310
BseXI	GCAGC	1 cut(s)	76
Bsh1236I	CGCG	1 cut(s)	156
BshFI	GGCC	2 cut(s)	269, 329
BshNI	GGYRCC	1 cut(s)	44
BsiHKAI	GWGCWC	1 cut(s)	294
BslFI	GGGAC	1 cut(s)	20
BslI	CCNNNNNNNGG	1 cut(s)	316
BsmFI	GGGAC	1 cut(s)	20
BsmI	GAATGC	1 cut(s)	10
BsnI	GGCC	2 cut(s)	269, 329
Bsp119I	TTCGAA	1 cut(s)	338
Bsp1286I	GDGCHC	1 cut(s)	294
Bsp143I	GATC	1 cut(s)	78
Bsp68I	TCGCGA	1 cut(s)	156
BspACI	CCGC	1 cut(s)	139
BspANI	GGCC	2 cut(s)	269, 329
BspFNI	CGCG	1 cut(s)	156
BspLI	GGNNCC	1 cut(s)	46
BspT104I	TTCGAA	1 cut(s)	338
BspT107I	GGYRCC	1 cut(s)	44
BspTI	CTTAAG	1 cut(s)	200
BsrI	ACTGG	2 cut(s)	238, 310
BssMI	GATC	1 cut(s)	78
Bst2UI	CCWGG	1 cut(s)	266
Bst4CI	ACNGT	1 cut(s)	103
BstAFI	CTTAAG	1 cut(s)	200
BstBI	TTCGAA	1 cut(s)	338
BstC8I	GCNNGC	2 cut(s)	143, 255
BstF5I	GGATG	1 cut(s)	193
BstFNI	CGCG	1 cut(s)	156
BstKTI	GATC	1 cut(s)	81
BstMBI	GATC	1 cut(s)	78
BstMWI	GCNNNNNNNGC	1 cut(s)	326
BstNI	CCWGG	1 cut(s)	266
BstNSI	RCATGY	1 cut(s)	145
BstSCI	CCNGG	1 cut(s)	264
BstUI	CGCG	1 cut(s)	156
BstV1I	GCAGC	1 cut(s)	76
BstV2I	GAAGAC	2 cut(s)	120, 234
BstXI	CCANNNNNNTGG	1 cut(s)	125
BsuI	GTATCC	2 cut(s)	64, 173
BsuRI	GGCC	2 cut(s)	269, 329
BtgZI	GCGATG	1 cut(s)	137
BtsCI	GGATG	1 cut(s)	193
BtuMI	TCGCGA	1 cut(s)	156
Cac8I	GCNNGC	2 cut(s)	143, 255
Csp6I	GTAC	1 cut(s)	205
CviAII	CATG	1 cut(s)	142
CviJI	RGCY	4 cut(s)	237, 269, 292, 329
CviKI_1	RGCY	4 cut(s)	237, 269, 292, 329
CviQI	GTAC	1 cut(s)	205
DpnI	GATC	1 cut(s)	80
DpnII	GATC	1 cut(s)	78
DrdI	GACNNNNNNGTC	1 cut(s)	164
DseDI	GACNNNNNNGTC	1 cut(s)	164
EaeI	YGGCCR	1 cut(s)	327
Ecl136II	GAGCTC	1 cut(s)	292
Eco24I	GRGCYC	1 cut(s)	294
Eco53kI	GAGCTC	1 cut(s)	292
Eco57I	CTGAAG	1 cut(s)	60
EcoICRI	GAGCTC	1 cut(s)	292
EcoRII	CCWGG	1 cut(s)	264
EcoT38I	GRGCYC	1 cut(s)	294
FaeI	CATG	1 cut(s)	145
FaiI	YATR	6 cut(s)	21, 63, 120, 143, 215, 259
FalI	AAGNNNNNCTT	2 cut(s)	226, 258
FaqI	GGGAC	1 cut(s)	20
FatI	CATG	1 cut(s)	141
Fnu4HI	GCNGC	1 cut(s)	90
FokI	GGATG	1 cut(s)	180
FriOI	GRGCYC	1 cut(s)	294
Fsp4HI	GCNGC	1 cut(s)	90
GluI	GCNGC	1 cut(s)	90
HaeIII	GGCC	2 cut(s)	269, 329
Hin1II	CATG	1 cut(s)	145
HinfI	GANTC	3 cut(s)	27, 223, 340
Hpy188III	TCNNGA	2 cut(s)	11, 155
Hpy99I	CGWCG	2 cut(s)	35, 161
HpyAV	CCTTC	3 cut(s)	35, 46, 106
HpyCH4III	ACNGT	1 cut(s)	103
HpyCH4V	TGCA	2 cut(s)	145, 253
HpyF10VI	GCNNNNNNNGC	1 cut(s)	326
Hsp92II	CATG	1 cut(s)	145
Kzo9I	GATC	1 cut(s)	78
LmnI	GCTCC	2 cut(s)	13, 289
LpnPI	CCDG	6 cut(s)	51, 162, 251, 251, 278, 323
Lsp1109I	GCAGC	1 cut(s)	76
MalI	GATC	1 cut(s)	80
MboI	GATC	1 cut(s)	78
MboII	GAAGA	4 cut(s)	88, 125, 234, 316
MhlI	GDGCHC	1 cut(s)	294
MlsI	TGGCCA	1 cut(s)	329
MluNI	TGGCCA	1 cut(s)	329
MnlI	CCTC	5 cut(s)	201, 207, 213, 310, 316
Mox20I	TGGCCA	1 cut(s)	329
MscI	TGGCCA	1 cut(s)	329
MseI	TTAA	2 cut(s)	201, 349
Msp20I	TGGCCA	1 cut(s)	329
MspCI	CTTAAG	1 cut(s)	200
MspR9I	CCNGG	1 cut(s)	266
Mva1269I	GAATGC	1 cut(s)	10
MvaI	CCWGG	1 cut(s)	266
MvnI	CGCG	1 cut(s)	156
MwoI	GCNNNNNNNGC	1 cut(s)	326
NdeII	GATC	1 cut(s)	78
NlaIII	CATG	1 cut(s)	145
NlaIV	GGNNCC	1 cut(s)	46
NruI	TCGCGA	1 cut(s)	156
NspI	RCATGY	1 cut(s)	145
NspV	TTCGAA	1 cut(s)	338
PaeI	GCATGC	1 cut(s)	145
PcsI	WCGNNNNNNNCGW	1 cut(s)	22
PctI	GAATGC	1 cut(s)	10
PfeI	GAWTC	3 cut(s)	27, 223, 340
PkrI	GCNGC	1 cut(s)	91
Psp124BI	GAGCTC	1 cut(s)	294
Psp6I	CCWGG	1 cut(s)	264
PspGI	CCWGG	1 cut(s)	264
PspN4I	GGNNCC	1 cut(s)	46
RruI	TCGCGA	1 cut(s)	156
RsaI	GTAC	1 cut(s)	206
RsaNI	GTAC	1 cut(s)	205
SacI	GAGCTC	1 cut(s)	294
SaqAI	TTAA	2 cut(s)	201, 349
SatI	GCNGC	1 cut(s)	90
Sau3AI	GATC	1 cut(s)	78
ScrFI	CCNGG	1 cut(s)	266
SduI	GDGCHC	1 cut(s)	294
SetI	ASST	3 cut(s)	57, 294, 327
SfuI	TTCGAA	1 cut(s)	338
SmlI	CTYRAG	1 cut(s)	200
SmoI	CTYRAG	1 cut(s)	200
SphI	GCATGC	1 cut(s)	145
SsiI	CCGC	1 cut(s)	139
SstI	GAGCTC	1 cut(s)	294
StyD4I	CCNGG	1 cut(s)	264
TaaI	ACNGT	1 cut(s)	103
TaqI	TCGA	2 cut(s)	294, 338
TatI	WGTACW	1 cut(s)	204
TfiI	GAWTC	3 cut(s)	27, 223, 340
Tru1I	TTAA	2 cut(s)	201, 349
Tru9I	TTAA	2 cut(s)	201, 349
TseI	GCWGC	1 cut(s)	89
TspDTI	ATGAA	2 cut(s)	17, 140
Vha464I	CTTAAG	1 cut(s)	200
XceI	RCATGY	1 cut(s)	145
XcmI	CCANNNNNNNNNTGG	1 cut(s)	277

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