Basic Information

Type: gene

Biological Identity

Species

arabidopsis_thaliana

Chromosome

Orthogroup ID

OG0004276

Physical Location & Seq

Genomic Coordinates Forward (+)

15569418 .. 15571169

Gene Structure 1752 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

AT5G38890.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 576 bp

ATGACGACGGGGCTAGTAACGCCGGGAGATGTAATCGGGAAAGCGACAGAGTTTAAAGCTGGAAAAGGAGCTTACGTCAACGACGCCACCATCTACGCTTCCCTCACAGGAACTTGCCGGATTGTTTCTCCTCTTCCCGAATCAATTGATCAGAGAGCTATTGTGGAAGTTACAGGTCACAAGGCACATGGTCCTATTCCAGAGACTGGTTCTGTTGTCATAGCAAGAGTGACTAAAGTTATGACTAAGATGGCTGCTGTTGATATCTTGTGTGTTGGTTCAAAAGCCGTTCGTGAAAATTTTGCTGGTGTAATTAGGCAACAAGATGTTAGAGCAACAGAGATTGACAAAGTTGACATGCATCAGTCTTTCCATGCTGGTGACATTGTTAGAGCTATGGTTCTGTCTCTTGGTGATGCACGGGCTTACTACTTGTCAACTGCTAAGAATGAACTTGGTGTGGTCTCAGCTGAAAGTGCTGCGGGCGAAACAATGGTTCCGATAAGTTGGACAGAGATGCAGTGCCCCTTGTCGGGCCAAACCGAGCAGAGAAAAGTTGCCAAGGTGGGTAATTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

No ontology terms assigned.

KEGG Pathways

Metabolic & Signaling

ko03018 map03018

Pfam Domains

Protein Families

ECR1_N EXOSC1

Protein Analysis

191

Amino Acids

20.23

Weight (kDa)

6.9

Isoelectric Point (pI)

22.79

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
ECR1_N	PF14382	5 - 42	6.8e-13	Exosome complex exonuclease RRP4 N-terminal region
S1_RRP4	PF21266	67 - 134	4.8e-06	RRP4, S1 domain
EXOSC1	PF10447	95 - 137	5.9e-12	Exosome component EXOSC1/CSL4

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: OG0004276)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G38890
fragaria_vesca	FvH4_6g01503 FvH4_6g01503 FvH4_6g01503 FvH4_6g01503 FvH4_6g01510
malus_domestica	MD11G1123700.v1.1 MD11G1124300.v1.1 MD12G1250600.v1.1
prunus_persica	Prupe.6G093000_v2.0.a1 Prupe.6G093000_v2.0.a1 Prupe.6G352700_v2.0.a1 Prupe.6G352700_v2.0.a1
pyrus_communis	pycom11g10450 pycom12g23060
rosa_chinensis	RchiOBHm_Chr3g0449171 RchiOBHm_Chr3g0449181 RchiOBHm_Chr5g0061031
rosa_laevigata	RLG00000035421
rosa_multiflora	Rmu_co8387241.1_g000001 Rmu_sc0000640.1_g000004 Rmu_sc0004874.1_g000009 Rmu_sc0006661.1_g000007
rosa_roxburghii	Rroxscaffold_1G00019610 Rroxscaffold_6G00427230
rosa_rugosa	Rorug02G0618600 Rorug05G0336200
rosa_samantha	Rh1AG412000 Rh3AG016900
rosa_wichuraiana	Rw3G001270 Rw3G001280 Rw5G037580

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	206
AciI	CCGC	1 cut(s)	482
AcsI	RAATTY	1 cut(s)	298
AcyI	GRCGYC	1 cut(s)	84
AfiI	CCNNNNNNNGG	3 cut(s)	206, 532, 533
AgsI	TTSAA	1 cut(s)	282
AluBI	AGCT	5 cut(s)	59, 71, 158, 395, 470
AluI	AGCT	5 cut(s)	59, 71, 158, 395, 470
Alw26I	GTCTC	3 cut(s)	197, 411, 469
AlwNI	CAGNNNCTG	1 cut(s)	206
AoxI	GGCC	1 cut(s)	535
ApeKI	GCWGC	2 cut(s)	254, 479
ApoI	RAATTY	1 cut(s)	298
AspS9I	GGNCC	2 cut(s)	191, 535
AsuC2I	CCSGG	1 cut(s)	24
AsuHPI	GGTGA	2 cut(s)	392, 425
AvaII	GGWCC	1 cut(s)	191
BaeGI	GKGCMC	1 cut(s)	527
BbvI	GCAGC	2 cut(s)	241, 466
BccI	CCATC	2 cut(s)	98, 244
BceAI	ACGGC	1 cut(s)	272
BclI	TGATCA	1 cut(s)	148
BcnI	CCSGG	1 cut(s)	24
BcoDI	GTCTC	3 cut(s)	197, 411, 469
BfaI	CTAG	1 cut(s)	14
BisI	GCNGC	2 cut(s)	255, 480
BlsI	GCNGC	2 cut(s)	256, 481
Bme1390I	CCNGG	1 cut(s)	24
Bme18I	GGWCC	1 cut(s)	191
BmgT120I	GGNCC	2 cut(s)	191, 535
BmiI	GGNNCC	1 cut(s)	498
BmrFI	CCNGG	1 cut(s)	24
BmsI	GCATC	3 cut(s)	370, 406, 507
BpuMI	CCSGG	1 cut(s)	24
BsaHI	GRCGYC	1 cut(s)	84
BsaI	GGTCTC	1 cut(s)	469
BsaJI	CCNNGG	1 cut(s)	561
BsaXI	ACNNNNNCTCC	2 cut(s)	60, 90
Bsc4I	CCNNNNNNNGG	3 cut(s)	206, 532, 533
Bse1I	ACTGG	1 cut(s)	211
BseDI	CCNNGG	1 cut(s)	561
BseLI	CCNNNNNNNGG	3 cut(s)	206, 532, 533
BseMII	CTCAG	1 cut(s)	480
BseNI	ACTGG	1 cut(s)	211
BseRI	GAGGAG	1 cut(s)	120
BseSI	GKGCMC	1 cut(s)	527
BseXI	GCAGC	2 cut(s)	241, 466
BshFI	GGCC	1 cut(s)	537
BsiSI	CCGG	2 cut(s)	23, 118
BslI	CCNNNNNNNGG	3 cut(s)	206, 532, 533
BsmAI	GTCTC	3 cut(s)	197, 411, 469
BsnI	GGCC	1 cut(s)	537
Bso31I	GGTCTC	1 cut(s)	469
Bsp1286I	GDGCHC	1 cut(s)	527
Bsp143I	GATC	1 cut(s)	148
BspACI	CCGC	1 cut(s)	482
BspANI	GGCC	1 cut(s)	537
BspCNI	CTCAG	1 cut(s)	479
BspLI	GGNNCC	1 cut(s)	498
BspTNI	GGTCTC	1 cut(s)	469
BsrI	ACTGG	1 cut(s)	211
BssECI	CCNNGG	1 cut(s)	561
BssMI	GATC	1 cut(s)	148
BssNI	GRCGYC	1 cut(s)	84
BssT1I	CCWWGG	1 cut(s)	561
Bst6I	CTCTTC	1 cut(s)	138
BstACI	GRCGYC	1 cut(s)	84
BstC8I	GCNNGC	1 cut(s)	484
BstDEI	CTNAG	3 cut(s)	246, 444, 466
BstKTI	GATC	1 cut(s)	151
BstMAI	GTCTC	3 cut(s)	197, 411, 469
BstMBI	GATC	1 cut(s)	148
BstMWI	GCNNNNNNNGC	2 cut(s)	19, 476
BstNSI	RCATGY	1 cut(s)	361
BstSCI	CCNGG	1 cut(s)	22
BstSLI	GKGCMC	1 cut(s)	527
BstV1I	GCAGC	2 cut(s)	241, 466
BsuRI	GGCC	1 cut(s)	537
BtsI	GCAGTG	1 cut(s)	527
BtsIMutI	CAGTG	1 cut(s)	527
Cac8I	GCNNGC	1 cut(s)	484
CaiI	CAGNNNCTG	1 cut(s)	206
Cfr13I	GGNCC	2 cut(s)	191, 535
CseI	GACGC	1 cut(s)	92
CviAII	CATG	3 cut(s)	188, 358, 374
DdeI	CTNAG	3 cut(s)	246, 444, 466
DpnI	GATC	1 cut(s)	150
DpnII	GATC	1 cut(s)	148
DraI	TTTAAA	1 cut(s)	55
Eam1104I	CTCTTC	1 cut(s)	138
EarI	CTCTTC	1 cut(s)	138
Eco130I	CCWWGG	1 cut(s)	561
Eco31I	GGTCTC	1 cut(s)	469
Eco32I	GATATC	1 cut(s)	265
Eco47I	GGWCC	1 cut(s)	191
EcoRV	GATATC	1 cut(s)	265
EcoT14I	CCWWGG	1 cut(s)	561
EcoT22I	ATGCAT	1 cut(s)	363
ErhI	CCWWGG	1 cut(s)	561
FaeI	CATG	3 cut(s)	191, 361, 377
FaiI	YATR	6 cut(s)	189, 221, 242, 359, 375, 398
FatI	CATG	3 cut(s)	187, 357, 373
FauI	CCCGC	1 cut(s)	475
FbaI	TGATCA	1 cut(s)	148
Fnu4HI	GCNGC	2 cut(s)	255, 480
Fsp4HI	GCNGC	2 cut(s)	255, 480
FspBI	CTAG	1 cut(s)	14
GluI	GCNGC	2 cut(s)	255, 480
HaeIII	GGCC	1 cut(s)	537
HapII	CCGG	2 cut(s)	23, 118
HgaI	GACGC	1 cut(s)	92
Hin1I	GRCGYC	1 cut(s)	84
Hin1II	CATG	3 cut(s)	191, 361, 377
HincII	GTYRAC	3 cut(s)	79, 355, 438
HindII	GTYRAC	3 cut(s)	79, 355, 438
HinfI	GANTC	1 cut(s)	140
HpaII	CCGG	2 cut(s)	23, 118
HphI	GGTGA	2 cut(s)	392, 425
Hpy166II	GTNNAC	3 cut(s)	79, 355, 438
Hpy188I	TCNGA	2 cut(s)	153, 501
Hpy188III	TCNNGA	4 cut(s)	37, 137, 200, 293
Hpy8I	GTNNAC	3 cut(s)	79, 355, 438
Hpy99I	CGWCG	2 cut(s)	10, 86
HpyCH4IV	ACGT	1 cut(s)	75
HpyCH4V	TGCA	3 cut(s)	361, 419, 520
HpyF10VI	GCNNNNNNNGC	2 cut(s)	19, 476
HpyF3I	CTNAG	3 cut(s)	246, 444, 466
HpySE526I	ACGT	1 cut(s)	75
Hsp92I	GRCGYC	1 cut(s)	84
Hsp92II	CATG	3 cut(s)	191, 361, 377
Ksp22I	TGATCA	1 cut(s)	148
Kzo9I	GATC	1 cut(s)	148
LmnI	GCTCC	1 cut(s)	68
LpnPI	CCDG	9 cut(s)	36, 45, 93, 131, 159, 192, 213, 291, 363
Lsp1109I	GCAGC	2 cut(s)	241, 466
LweI	GCATC	3 cut(s)	370, 406, 507
MaeI	CTAG	1 cut(s)	14
MaeII	ACGT	1 cut(s)	75
MaeIII	GTNAC	5 cut(s)	16, 169, 176, 229, 380
MalI	GATC	1 cut(s)	150
MboI	GATC	1 cut(s)	148
MboII	GAAGA	1 cut(s)	125
MfeI	CAATTG	1 cut(s)	144
MhlI	GDGCHC	1 cut(s)	527
MluCI	AATT	4 cut(s)	144, 298, 312, 571
MmeI	TCCRAC	1 cut(s)	488
MnlI	CCTC	2 cut(s)	113, 141
Mph1103I	ATGCAT	1 cut(s)	363
MseI	TTAA	1 cut(s)	54
MslI	CAYNNNNRTG	1 cut(s)	378
MspA1I	CMGCKG	1 cut(s)	470
MspI	CCGG	2 cut(s)	23, 118
MspR9I	CCNGG	1 cut(s)	24
MunI	CAATTG	1 cut(s)	144
MwoI	GCNNNNNNNGC	2 cut(s)	19, 476
NciI	CCSGG	1 cut(s)	24
NdeII	GATC	1 cut(s)	148
NlaIII	CATG	3 cut(s)	191, 361, 377
NlaIV	GGNNCC	1 cut(s)	498
NmuCI	GTSAC	3 cut(s)	176, 229, 380
NsiI	ATGCAT	1 cut(s)	363
NspI	RCATGY	1 cut(s)	361
PfeI	GAWTC	1 cut(s)	140
PflMI	CCANNNNNTGG	1 cut(s)	206
PkrI	GCNGC	2 cut(s)	256, 481
PspN4I	GGNNCC	1 cut(s)	498
PspPI	GGNCC	2 cut(s)	191, 535
PstNI	CAGNNNCTG	1 cut(s)	206
PvuII	CAGCTG	1 cut(s)	470
RseI	CAYNNNNRTG	1 cut(s)	378
SaqAI	TTAA	1 cut(s)	54
SatI	GCNGC	2 cut(s)	255, 480
Sau3AI	GATC	1 cut(s)	148
Sau96I	GGNCC	2 cut(s)	191, 535
ScrFI	CCNGG	1 cut(s)	24
SduI	GDGCHC	1 cut(s)	527
SetI	ASST	8 cut(s)	61, 73, 78, 160, 178, 397, 472, 567
SfaNI	GCATC	3 cut(s)	370, 406, 507
SinI	GGWCC	1 cut(s)	191
SmiMI	CAYNNNNRTG	1 cut(s)	378
Sse9I	AATT	4 cut(s)	144, 298, 312, 571
SsiI	CCGC	1 cut(s)	482
SspMI	CTAG	1 cut(s)	14
StyD4I	CCNGG	1 cut(s)	22
StyI	CCWWGG	1 cut(s)	561
TaiI	ACGT	1 cut(s)	78
TasI	AATT	4 cut(s)	144, 298, 312, 571
TfiI	GAWTC	1 cut(s)	140
Tru1I	TTAA	1 cut(s)	54
Tru9I	TTAA	1 cut(s)	54
TscAI	CASTG	1 cut(s)	527
TseFI	GTSAC	3 cut(s)	176, 229, 380
TseI	GCWGC	2 cut(s)	254, 479
Tsp45I	GTSAC	3 cut(s)	176, 229, 380
TspDTI	ATGAA	1 cut(s)	465
TspRI	CASTG	1 cut(s)	527
Van91I	CCANNNNNTGG	1 cut(s)	206
VpaK11BI	GGWCC	1 cut(s)	191
XapI	RAATTY	1 cut(s)	298
XceI	RCATGY	1 cut(s)	361
XspI	CTAG	1 cut(s)	14
Zsp2I	ATGCAT	1 cut(s)	363

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