Basic Information

Type: gene

Biological Identity

Species

arabidopsis_thaliana

Chromosome

Orthogroup ID

OG0004175

Physical Location & Seq

Genomic Coordinates Forward (+)

23883356 .. 23885305

Gene Structure 1950 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

AT5G59180.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 531 bp

ATGTTTTTCCACATAGTATTGGAGCGGAACATGCAGTTGCATCCTCGTTTCTTTGGTCGTAACCTAAAAGAAAACCTCGTATCTAAGCTCATGAAAGATGTCGAAGGCACTTGCAGTGGCCGACATGGATTTGTAGTGGCGATAACTGGAATAGATACAATAGGAAAGGGTTTGATCAGAGATGGGACTGGTTTTGTCACCTTTCCAGTTAAATACCAATGCGTCGTTTTCAGACCTTTCAAAGGCGAGATTTTGGAAGCTGTTGTCACTTTGGTCAATAAGATGGGATTCTTCGCTGAAGCTGGCCCTGTTCAGATTTTTGTGTCTAAGCATTTGATTCCAGATGATATGGAGTTTCAAGCTGGAGACATGCCTAACTATACCACATCAGATGGATCAGTTAAGATCCAGAAGGAGTGTGAAGTGAGACTAAAGATTATTGGAACAAGAGTTGATGCCACTGCGATTTTTTGTGTGGGTACCATCAAAGACGATTTTTTGGGAGTCATAAACGACCCTGCAGCGGCATAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000291 GO:0000428 GO:0000932 GO:0000956 GO:0003674 GO:0003676 GO:0003677 GO:0003697 GO:0003723 GO:0003727 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005665 GO:0005737 GO:0006139 GO:0006351 GO:0006352 GO:0006366 GO:0006367 GO:0006401 GO:0006402 GO:0006417 GO:0006446 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009056 GO:0009057 GO:0009058 GO:0009059 GO:0009889 GO:0009891 GO:0009892 GO:0009893 GO:0009894 GO:0009896 GO:0009987 GO:0010467 GO:0010468 GO:0010556 GO:0010557 GO:0010604 GO:0010605 GO:0010608 GO:0010628 GO:0010629 GO:0016070 GO:0016071 GO:0016591 GO:0018130 GO:0019219 GO:0019222 GO:0019438 GO:0019439 GO:0030880 GO:0031323 GO:0031325 GO:0031326 GO:0031328 GO:0031329 GO:0031331 GO:0031369 GO:0031974 GO:0031981 GO:0032268 GO:0032270 GO:0032774 GO:0032991 GO:0034248 GO:0034250 GO:0034641 GO:0034645 GO:0034654 GO:0034655 GO:0035770 GO:0036464 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044248 GO:0044249 GO:0044260 GO:0044265 GO:0044270 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044451 GO:0044464 GO:0045727 GO:0045935 GO:0045948 GO:0046483 GO:0046700 GO:0048518 GO:0048519 GO:0048522 GO:0050789 GO:0050794 GO:0051171 GO:0051173 GO:0051246 GO:0051247 GO:0051252 GO:0051254 GO:0055029 GO:0060211 GO:0060213 GO:0060255 GO:0061013 GO:0061014 GO:0061695 GO:0065007 GO:0070013 GO:0071704 GO:0080090 GO:0090304 GO:0097159 GO:0097659 GO:1900151 GO:1900153 GO:1901360 GO:1901361 GO:1901362 GO:1901363 GO:1901575 GO:1901576 GO:1902494 GO:1903311 GO:1903313 GO:1990234 GO:1990904 GO:2000112

KEGG Pathways

Metabolic & Signaling

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

Pfam Domains

Protein Families

S1 SHS2_Rpb7-N

Protein Analysis

176

Amino Acids

19.46

Weight (kDa)

6.89

Isoelectric Point (pI)

15.22

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
SHS2_Rpb7-N	PF03876	8 - 64	6.2e-15	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
S1	PF00575	79 - 158	7.4e-15	S1 RNA binding 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)

Image

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Publication-ready

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Orthologous Genes (Group: OG0004175)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G59180
fragaria_vesca	FvH4_2g24550 FvH4_6g26920 FvH4_6g26920 FvH4_6g26920
malus_domestica	MD06G1239600.v1.1 MD14G1245600.v1.1
prunus_persica	Prupe.4G244700_v2.0.a1 Prupe.5G243500_v2.0.a1
pyrus_communis	pycom06g21510 pycom14g20650
rosa_chinensis	RchiOBHm_Chr2g0128671 RchiOBHm_Chr6g0292371
rosa_laevigata	RLG00000012035 RLG00000019016
rosa_multiflora	Rmu_sc0001354.1_g000012 Rmu_sc0003465.1_g000052 Rmu_sc0005514.1_g000001 Rmu_sc0023058.1_g000002
rosa_roxburghii	Rroxscaffold_2G00115380 Rroxscaffold_2G00115880 Rroxscaffold_7G00175130
rosa_rugosa	Rorug06G0226000
rosa_samantha	Rh2AG333500 Rh2BG341100 Rh2CG320100 Rh2DG357800 Rh6AG339300 Rh6BG346600 Rh6CG353400 Rh6DG339400
rosa_wichuraiana	Rw2G026920 Rw6G029530

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc65I	GGTACC	1 cut(s)	479
AccB1I	GGYRCC	1 cut(s)	479
AccBSI	CCGCTC	1 cut(s)	25
AciI	CCGC	2 cut(s)	25, 524
AclWI	GGATC	2 cut(s)	400, 403
AcoI	YGGCCR	1 cut(s)	118
AcuI	CTGAAG	1 cut(s)	318
AfaI	GTAC	1 cut(s)	481
AfiI	CCNNNNNNNGG	2 cut(s)	242, 523
AgsI	TTSAA	2 cut(s)	241, 359
AluBI	AGCT	4 cut(s)	88, 260, 302, 362
AluI	AGCT	4 cut(s)	88, 260, 302, 362
Alw26I	GTCTC	2 cut(s)	360, 421
AlwI	GGATC	2 cut(s)	400, 403
AoxI	GGCC	2 cut(s)	118, 304
ApeKI	GCWGC	1 cut(s)	521
Asp718I	GGTACC	1 cut(s)	479
AspS9I	GGNCC	1 cut(s)	305
AsuHPI	GGTGA	1 cut(s)	190
BanI	GGYRCC	1 cut(s)	479
BccI	CCATC	4 cut(s)	176, 277, 386, 491
BclI	TGATCA	1 cut(s)	174
BcoDI	GTCTC	2 cut(s)	360, 421
BfmI	CTRYAG	1 cut(s)	519
BisI	GCNGC	2 cut(s)	522, 525
BlsI	GCNGC	2 cut(s)	523, 526
BmgT120I	GGNCC	1 cut(s)	305
BmiI	GGNNCC	1 cut(s)	481
BmsI	GCATC	2 cut(s)	49, 445
BpmI	CTGGAG	1 cut(s)	384
Bsc4I	CCNNNNNNNGG	2 cut(s)	242, 523
Bse1I	ACTGG	3 cut(s)	151, 193, 206
BseGI	GGATG	1 cut(s)	40
BseLI	CCNNNNNNNGG	2 cut(s)	242, 523
BseNI	ACTGG	3 cut(s)	151, 193, 206
BshFI	GGCC	2 cut(s)	120, 306
BshNI	GGYRCC	1 cut(s)	479
BslFI	GGGAC	1 cut(s)	199
BslI	CCNNNNNNNGG	2 cut(s)	242, 523
BsmAI	GTCTC	2 cut(s)	360, 421
BsmFI	GGGAC	1 cut(s)	199
BsnI	GGCC	2 cut(s)	120, 306
Bsp143I	GATC	3 cut(s)	174, 395, 405
BspACI	CCGC	2 cut(s)	25, 524
BspANI	GGCC	2 cut(s)	120, 306
BspHI	TCATGA	1 cut(s)	90
BspLI	GGNNCC	1 cut(s)	481
BspMAI	CTGCAG	1 cut(s)	523
BspPI	GGATC	2 cut(s)	400, 403
BspT107I	GGYRCC	1 cut(s)	479
BsrBI	CCGCTC	1 cut(s)	25
BsrI	ACTGG	3 cut(s)	151, 193, 206
BssMI	GATC	3 cut(s)	174, 395, 405
BstC8I	GCNNGC	1 cut(s)	304
BstDEI	CTNAG	2 cut(s)	84, 327
BstENI	CCTNNNNNAGG	1 cut(s)	240
BstF5I	GGATG	1 cut(s)	40
BstKTI	GATC	3 cut(s)	177, 398, 408
BstMAI	GTCTC	2 cut(s)	360, 421
BstMBI	GATC	3 cut(s)	174, 395, 405
BstMWI	GCNNNNNNNGC	1 cut(s)	31
BstNSI	RCATGY	2 cut(s)	34, 373
BstSFI	CTRYAG	1 cut(s)	519
BstX2I	RGATCY	1 cut(s)	405
BstYI	RGATCY	1 cut(s)	405
BsuRI	GGCC	2 cut(s)	120, 306
BtsCI	GGATG	1 cut(s)	40
BtsI	GCAGTG	2 cut(s)	121, 459
BtsIMutI	CAGTG	2 cut(s)	121, 459
Cac8I	GCNNGC	1 cut(s)	304
CciI	TCATGA	1 cut(s)	90
Cfr13I	GGNCC	1 cut(s)	305
CseI	GACGC	1 cut(s)	211
Csp6I	GTAC	1 cut(s)	480
CviAII	CATG	4 cut(s)	31, 91, 125, 370
CviJI	RGCY	6 cut(s)	88, 120, 260, 302, 306, 362
CviKI_1	RGCY	6 cut(s)	88, 120, 260, 302, 306, 362
CviQI	GTAC	1 cut(s)	480
DdeI	CTNAG	2 cut(s)	84, 327
DpnI	GATC	3 cut(s)	176, 397, 407
DpnII	GATC	3 cut(s)	174, 395, 405
EaeI	YGGCCR	1 cut(s)	118
Eco57I	CTGAAG	1 cut(s)	318
EcoNI	CCTNNNNNAGG	1 cut(s)	240
FaeI	CATG	4 cut(s)	34, 94, 128, 373
FaiI	YATR	9 cut(s)	14, 32, 92, 126, 350, 371, 381, 509, 529
FaqI	GGGAC	1 cut(s)	199
FatI	CATG	4 cut(s)	30, 90, 124, 369
FbaI	TGATCA	1 cut(s)	174
Fnu4HI	GCNGC	2 cut(s)	522, 525
FokI	GGATG	1 cut(s)	27
Fsp4HI	GCNGC	2 cut(s)	522, 525
GluI	GCNGC	2 cut(s)	522, 525
GsuI	CTGGAG	1 cut(s)	384
HaeIII	GGCC	2 cut(s)	120, 306
HgaI	GACGC	1 cut(s)	211
Hin1II	CATG	4 cut(s)	34, 94, 128, 373
HinfI	GANTC	3 cut(s)	288, 337, 504
HphI	GGTGA	1 cut(s)	190
Hpy188I	TCNGA	4 cut(s)	179, 233, 315, 391
Hpy188III	TCNNGA	3 cut(s)	91, 341, 409
Hpy99I	CGWCG	1 cut(s)	227
HpyAV	CCTTC	2 cut(s)	98, 406
HpyCH4V	TGCA	4 cut(s)	34, 40, 114, 521
HpyF10VI	GCNNNNNNNGC	1 cut(s)	31
HpyF3I	CTNAG	2 cut(s)	84, 327
Hsp92II	CATG	4 cut(s)	34, 94, 128, 373
KpnI	GGTACC	1 cut(s)	483
Ksp22I	TGATCA	1 cut(s)	174
Kzo9I	GATC	3 cut(s)	174, 395, 405
LmnI	GCTCC	1 cut(s)	22
LpnPI	CCDG	8 cut(s)	132, 174, 219, 288, 321, 348, 354, 422
LweI	GCATC	2 cut(s)	49, 445
MaeIII	GTNAC	3 cut(s)	59, 196, 265
MalI	GATC	3 cut(s)	176, 397, 407
MbiI	CCGCTC	1 cut(s)	25
MboI	GATC	3 cut(s)	174, 395, 405
MboII	GAAGA	1 cut(s)	283
MflI	RGATCY	1 cut(s)	405
MlyI	GAGTC	1 cut(s)	513
MnlI	CCTC	2 cut(s)	54, 86
MseI	TTAA	2 cut(s)	210, 402
MspA1I	CMGCKG	1 cut(s)	524
MwoI	GCNNNNNNNGC	1 cut(s)	31
NdeII	GATC	3 cut(s)	174, 395, 405
NlaIII	CATG	4 cut(s)	34, 94, 128, 373
NlaIV	GGNNCC	1 cut(s)	481
NmuCI	GTSAC	2 cut(s)	196, 265
NspI	RCATGY	2 cut(s)	34, 373
PagI	TCATGA	1 cut(s)	90
PfeI	GAWTC	2 cut(s)	288, 337
PkrI	GCNGC	2 cut(s)	523, 526
PleI	GAGTC	1 cut(s)	512
PpsI	GAGTC	1 cut(s)	512
PspN4I	GGNNCC	1 cut(s)	481
PspPI	GGNCC	1 cut(s)	305
PstI	CTGCAG	1 cut(s)	523
PsuI	RGATCY	1 cut(s)	405
RsaI	GTAC	1 cut(s)	481
RsaNI	GTAC	1 cut(s)	480
SaqAI	TTAA	2 cut(s)	210, 402
SatI	GCNGC	2 cut(s)	522, 525
Sau3AI	GATC	3 cut(s)	174, 395, 405
Sau96I	GGNCC	1 cut(s)	305
SchI	GAGTC	1 cut(s)	513
SetI	ASST	8 cut(s)	66, 78, 90, 203, 238, 262, 304, 364
SfaNI	GCATC	2 cut(s)	49, 445
SfcI	CTRYAG	1 cut(s)	519
SsiI	CCGC	2 cut(s)	25, 524
TaqI	TCGA	1 cut(s)	102
TauI	GCSGC	1 cut(s)	527
TfiI	GAWTC	2 cut(s)	288, 337
Tru1I	TTAA	2 cut(s)	210, 402
Tru9I	TTAA	2 cut(s)	210, 402
TscAI	CASTG	2 cut(s)	121, 466
TseFI	GTSAC	2 cut(s)	196, 265
TseI	GCWGC	1 cut(s)	521
Tsp45I	GTSAC	2 cut(s)	196, 265
TspDTI	ATGAA	1 cut(s)	107
TspRI	CASTG	2 cut(s)	121, 466
XagI	CCTNNNNNAGG	1 cut(s)	240
XceI	RCATGY	2 cut(s)	34, 373

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