Basic Information

Type: gene

Biological Identity

Species

arabidopsis_thaliana

Chromosome

Orthogroup ID

OG0001390

Physical Location & Seq

Genomic Coordinates Reverse (-)

25262162 .. 25264053

Gene Structure 1892 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

AT5G62950.3

Sequence Viewer

CDS Protein Promoter (2k)

Length: 420 bp

ATGAAAATAGTCAAGGCAAATGCAGGAGCACTGACCAATTTCGAAGTGCTTGACTTTCTTAACTCGAGAGGTGCATCAAAAGATACTACAAGAGTTATAGCTCCAATTGCTAGATCAGAATACAAGGTCTATGATTATTTGGTGGAGACTGCTGCTTCCACTCAAACACGAGAGAGCATTAACAAATTCGCAGACAAGTGTAAAGATTTCAAACTCGCTAAAGCTGAGATTCTCAATATCATCAATCTCCGGCCTTCTTCTATAGTCGAACTGTTACCGATCATAGAGAACCTGGATGATCGAGAAATCGACACTGATGGGATATTAGAGCTTGTGAAGGATTTGTTACCTCCTCTGCCTACAACTGCAAGTCCTAAAGATGATGATGAAGAAGAAACAGAGAATGGTGAACAGTCGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0003674 GO:0003824 GO:0003899 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0005737 GO:0005886 GO:0006139 GO:0006351 GO:0006352 GO:0006383 GO:0006384 GO:0006725 GO:0006807 GO:0007568 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009360 GO:0009987 GO:0010467 GO:0016020 GO:0016070 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019438 GO:0030424 GO:0030425 GO:0030880 GO:0031974 GO:0031981 GO:0032502 GO:0032774 GO:0032991 GO:0034062 GO:0034641 GO:0034645 GO:0034654 GO:0036477 GO:0042575 GO:0042995 GO:0043005 GO:0043025 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044297 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044463 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0071944 GO:0090304 GO:0097447 GO:0097458 GO:0097659 GO:0097747 GO:0120025 GO:0120038 GO:0140098 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

RNA_pol_Rpb4

Protein Analysis

139

Amino Acids

15.46

Weight (kDa)

4.51

Isoelectric Point (pI)

41.9

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb4	PF03874	10 - 114	4.5e-14	RNA polymerase Rpb4

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)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0001390)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT5G62950 AT5G62950 AT5G62950 AT5G62950 AT5G62950 AT5G62950 AT5G62950
fragaria_vesca	FvH4_4g01070 FvH4_4g01070 FvH4_5g27570
malus_domestica	MD13G1198900.v1.1
prunus_persica	Prupe.1G020700_v2.0.a1 Prupe.1G020700_v2.0.a1 Prupe.1G020700_v2.0.a1 Prupe.1G020700_v2.0.a1
pyrus_communis	pycom13g17270
rosa_chinensis	RchiOBHm_Chr4g0387641 RchiOBHm_Chr6g0280701
rosa_laevigata	RLG00000010104 RLG00000013035
rosa_multiflora	Rmu_sc0000976.1_g000021 Rmu_sc0003953.1_g000006
rosa_roxburghii	Rroxscaffold_7G00187720
rosa_rugosa	Rorug03G0311800 Rorug03G0311900 Rorug03G0312000 Rorug03G0312100 Rorug06G0133900 Rorug06G0133900 Rorug06G0133900 Rorug06G0134000
rosa_samantha	Rh4AG017400 Rh4BG012200 Rh4CG018600 Rh4DG013200 Rh6AG246600 Rh6BG248900 Rh6CG250000 Rh6DG241500
rosa_wichuraiana	Rw4G001120 Rw6G021350

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AcsI	RAATTY	1 cut(s)	185
AgsI	TTSAA	1 cut(s)	211
AjnI	CCWGG	1 cut(s)	291
AluBI	AGCT	3 cut(s)	101, 224, 331
AluI	AGCT	3 cut(s)	101, 224, 331
Alw21I	GWGCWC	1 cut(s)	31
Alw26I	GTCTC	1 cut(s)	140
Ama87I	CYCGRG	1 cut(s)	64
AoxI	GGCC	1 cut(s)	251
ApeKI	GCWGC	1 cut(s)	152
ApoI	RAATTY	1 cut(s)	185
AsuHPI	GGTGA	1 cut(s)	419
AsuII	TTCGAA	1 cut(s)	42
AvaI	CYCGRG	1 cut(s)	64
BauI	CACGAG	1 cut(s)	168
Bbv12I	GWGCWC	1 cut(s)	31
BbvI	GCAGC	1 cut(s)	139
BccI	CCATC	1 cut(s)	311
BciT130I	CCWGG	1 cut(s)	293
BcoDI	GTCTC	1 cut(s)	140
BfaI	CTAG	1 cut(s)	111
BfmI	CTRYAG	1 cut(s)	261
BisI	GCNGC	1 cut(s)	153
BlsI	GCNGC	1 cut(s)	154
Bme1390I	CCNGG	1 cut(s)	293
BmeT110I	CYCGRG	1 cut(s)	64
BmrFI	CCNGG	1 cut(s)	293
BmsI	GCATC	1 cut(s)	83
Bpu14I	TTCGAA	1 cut(s)	42
BseBI	CCWGG	1 cut(s)	293
BseGI	GGATG	1 cut(s)	301
BseMII	CTCAG	1 cut(s)	216
BseRI	GAGGAG	1 cut(s)	342
BseXI	GCAGC	1 cut(s)	139
BshFI	GGCC	1 cut(s)	253
BsiHKAI	GWGCWC	1 cut(s)	31
BsiHKCI	CYCGRG	1 cut(s)	64
BsiSI	CCGG	1 cut(s)	250
BsmAI	GTCTC	1 cut(s)	140
BsnI	GGCC	1 cut(s)	253
BsoBI	CYCGRG	1 cut(s)	64
Bsp119I	TTCGAA	1 cut(s)	42
Bsp1286I	GDGCHC	1 cut(s)	31
Bsp143I	GATC	3 cut(s)	113, 279, 298
BspANI	GGCC	1 cut(s)	253
BspCNI	CTCAG	1 cut(s)	217
BspT104I	TTCGAA	1 cut(s)	42
BssMI	GATC	3 cut(s)	113, 279, 298
BssSI	CACGAG	1 cut(s)	168
Bst2BI	CACGAG	1 cut(s)	168
Bst2UI	CCWGG	1 cut(s)	293
Bst4CI	ACNGT	2 cut(s)	273, 414
BstBI	TTCGAA	1 cut(s)	42
BstDEI	CTNAG	1 cut(s)	225
BstF5I	GGATG	1 cut(s)	301
BstKTI	GATC	3 cut(s)	116, 282, 301
BstMAI	GTCTC	1 cut(s)	140
BstMBI	GATC	3 cut(s)	113, 279, 298
BstMWI	GCNNNNNNNGC	1 cut(s)	107
BstNI	CCWGG	1 cut(s)	293
BstSCI	CCNGG	1 cut(s)	291
BstSFI	CTRYAG	1 cut(s)	261
BstV1I	GCAGC	1 cut(s)	139
BsuRI	GGCC	1 cut(s)	253
BtsCI	GGATG	1 cut(s)	301
BtsIMutI	CAGTG	2 cut(s)	29, 312
CviJI	RGCY	4 cut(s)	101, 224, 253, 331
CviKI_1	RGCY	4 cut(s)	101, 224, 253, 331
DdeI	CTNAG	1 cut(s)	225
DpnI	GATC	3 cut(s)	115, 281, 300
DpnII	GATC	3 cut(s)	113, 279, 298
Eco88I	CYCGRG	1 cut(s)	64
EcoRII	CCWGG	1 cut(s)	291
FaiI	YATR	4 cut(s)	98, 132, 263, 284
Fnu4HI	GCNGC	1 cut(s)	153
FokI	GGATG	1 cut(s)	308
Fsp4HI	GCNGC	1 cut(s)	153
FspBI	CTAG	1 cut(s)	111
GluI	GCNGC	1 cut(s)	153
HaeIII	GGCC	1 cut(s)	253
HapII	CCGG	1 cut(s)	250
HinfI	GANTC	1 cut(s)	229
HpaII	CCGG	1 cut(s)	250
HphI	GGTGA	1 cut(s)	419
Hpy166II	GTNNAC	1 cut(s)	410
Hpy188I	TCNGA	1 cut(s)	118
Hpy188III	TCNNGA	3 cut(s)	66, 302, 417
Hpy8I	GTNNAC	1 cut(s)	410
HpyAV	CCTTC	2 cut(s)	264, 331
HpyCH4III	ACNGT	2 cut(s)	273, 414
HpyCH4V	TGCA	3 cut(s)	23, 74, 368
HpyF10VI	GCNNNNNNNGC	1 cut(s)	107
HpyF3I	CTNAG	1 cut(s)	225
Kzo9I	GATC	3 cut(s)	113, 279, 298
LmnI	GCTCC	2 cut(s)	26, 106
LpnPI	CCDG	4 cut(s)	9, 263, 278, 305
Lsp1109I	GCAGC	1 cut(s)	139
LweI	GCATC	1 cut(s)	83
MaeI	CTAG	1 cut(s)	111
MaeIII	GTNAC	2 cut(s)	273, 345
MalI	GATC	3 cut(s)	115, 281, 300
MboI	GATC	3 cut(s)	113, 279, 298
MboII	GAAGA	3 cut(s)	249, 401, 404
MfeI	CAATTG	1 cut(s)	105
MhlI	GDGCHC	1 cut(s)	31
MluCI	AATT	3 cut(s)	37, 105, 185
MnlI	CCTC	3 cut(s)	62, 360, 363
MseI	TTAA	2 cut(s)	60, 180
MspI	CCGG	1 cut(s)	250
MspR9I	CCNGG	1 cut(s)	293
MunI	CAATTG	1 cut(s)	105
MvaI	CCWGG	1 cut(s)	293
MwoI	GCNNNNNNNGC	1 cut(s)	107
NdeII	GATC	3 cut(s)	113, 279, 298
NspV	TTCGAA	1 cut(s)	42
PaeR7I	CTCGAG	1 cut(s)	64
PfeI	GAWTC	1 cut(s)	229
PkrI	GCNGC	1 cut(s)	154
Psp6I	CCWGG	1 cut(s)	291
PspGI	CCWGG	1 cut(s)	291
SaqAI	TTAA	2 cut(s)	60, 180
SatI	GCNGC	1 cut(s)	153
Sau3AI	GATC	3 cut(s)	113, 279, 298
ScrFI	CCNGG	1 cut(s)	293
SduI	GDGCHC	1 cut(s)	31
SetI	ASST	7 cut(s)	73, 103, 129, 226, 294, 333, 352
SfaNI	GCATC	1 cut(s)	83
SfcI	CTRYAG	1 cut(s)	261
Sfr274I	CTCGAG	1 cut(s)	64
SfuI	TTCGAA	1 cut(s)	42
SlaI	CTCGAG	1 cut(s)	64
SmlI	CTYRAG	1 cut(s)	64
SmoI	CTYRAG	1 cut(s)	64
Sse9I	AATT	3 cut(s)	37, 105, 185
SspMI	CTAG	1 cut(s)	111
StyD4I	CCNGG	1 cut(s)	291
TaaI	ACNGT	2 cut(s)	273, 414
TaqI	TCGA	5 cut(s)	42, 65, 267, 301, 309
TasI	AATT	3 cut(s)	37, 105, 185
TfiI	GAWTC	1 cut(s)	229
Tru1I	TTAA	2 cut(s)	60, 180
Tru9I	TTAA	2 cut(s)	60, 180
TscAI	CASTG	2 cut(s)	36, 319
TseI	GCWGC	1 cut(s)	152
TspDTI	ATGAA	2 cut(s)	17, 402
TspRI	CASTG	2 cut(s)	36, 319
XapI	RAATTY	1 cut(s)	185
XhoI	CTCGAG	1 cut(s)	64
XspI	CTAG	1 cut(s)	111

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