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[189303_at] Ubiquitin family

Description F56F3.4 /REP_DB=WormBase Gene ID /WP=CE01016 /TR=Q20899 /GB=CAA83606.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Ubiquitin family
Cluster 6grp_total > 77      4grp_total > 26      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 7
1 2 3 4 range
A 2.8
(-3)
A 		9.1
(3)
A 		4.1
(-1.8)
A 		6.8
(0.8)
A 		6
B 4.2
(3)
A 		4.1
(2.7)
A 		2.4
(-3)
A 		4.1
(2.7)
A 		2
C 2.7
(-3)
A 		3.5
(-2)
A 		6
(1)
A 		7.6
(3)
A 		5
avr 3.2
(-3) 		5.6
(1.8) 		4.2
(-1) 		6.2
(3) 		3

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 137
1 2 3 4 5 6 range
A 6.5
(-2.8)
A 		2
(-3)
A 		3.4
(-2.9)
A 		2.7
(-3)
A 		21.8
(-1.9)
A 		114.6
(3)
A 		113
B 5.7
(-2.9)
A 		4.7
(-3)
A 		8.2
(-2.8)
A 		3.7
(-3)
A 		13.5
(-2.6)
A 		138.8
(3)
A 		135
C 2.7
(-3)
A 		6.7
(-2.8)
A 		2.9
(-3)
A 		15
(-2.4)
A 		41.6
(-1.2)
A 		132.3
(3)
A 		130
avr 5
(-3) 		4.5
(-3) 		4.8
(-3) 		7.1
(-2.9) 		25.6
(-2) 		128.6
(3) 		124
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2
1 2 3 4 range
A 1
(-3)
A 		2
(3)
A 		1.1
(-2.4)
A 		1
(-3)
A 		1
B 1.4
(3)
A 		1
(0)
A 		0.6
(-3)
A 		0.9
(-0.8)
A 		1
C 0.9
(-3)
A 		1
(-2.5)
A 		2.1
(3)
A 		1.3
(-1)
A 		1
avr 1.1
(-3) 		1.3
(3) 		1.3
(3) 		1.1
(-3) 		0

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 51
1 2 3 4 5 6 range
A 1.2
(-2.9)
A 		0.7
(-3)
A 		0.7
(-3)
A 		0.7
(-3)
A 		6.6
(-1.7)
A 		27.9
(3)
A 		27
B 2
(-2.9)
A 		1.5
(-2.9)
A 		2
(-2.9)
A 		1
(-3)
A 		5.5
(-2.5)
A 		51.8
(3)
A 		51
C 1
(-3)
A 		2
(-2.8)
A 		0.7
(-3)
A 		3
(-2.7)
A 		13.5
(-1.2)
A 		44.3
(3)
A 		44
avr 1.4
(-3) 		1.4
(-3) 		1.1
(-3) 		1.6
(-2.9) 		8.5
(-1.9) 		41.3
(3) 		40
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189303_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7127
Sequence Type Exemplar sequence
Representative Public ID F56F3.4 NCBI
Target Description F56F3.4 /REP_DB=WormBase Gene ID /WP=CE01016 /TR=Q20899 /GB=CAA83606.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Ubiquitin family
Cluster Evidence This cluster is supported by a Sanger Annotation.
Annotation Method Description
Annotation Description This probe set was annotated using the Matching Probes based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_065507(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065507 NCBI Caenorhabditis elegans F56F3.4 (F56F3.4) mRNA, complete cds. 11/11 None
GENEFINDER00000037236 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:4469116:4471014:1 11/11 None
SNAP00000037230 ENSEMBL cdna:SNAP chromosome:CEL140:III:4469146:4470694:1 11/11 None
F56F3.4 ENSEMBL cdna:known chromosome:CEL140:III:4469116:4470711:1 gene:F56F3.4 11/11 None
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:4469115-4470694(+) 100.0 100.0
Public Domain and Genome References
Gene Title Ubiquitin family
Ensembl F56F3.4
Entrez Gene 186395 Entrez gene
SwissProt Q20899 EMBL-EBI
WormBase CE01016 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA83606 Hypothetical protein F56F3.4 [Caenorhabditis elegans] ref|NP_497908.1| F56F3.4 [Caenorhabditis elegans] 1.0E-173
blast CAA83606 Hypothetical protein F56F3.4 [Caenorhabditis elegans] ref|NP_497908.1| F56F3.4 [Caenorhabditis elegans] 1.0E-167
blast CAA83606 Hypothetical protein F56F3.4 [Caenorhabditis elegans] ref|NP_497908.1| F56F3.4 [Caenorhabditis elegans] 1.0E-165
blast CAE75027 Hypothetical protein CBG22933 [Caenorhabditis briggsae] 1.0E-127
blast CAE75027 Hypothetical protein CBG22933 [Caenorhabditis briggsae] 1.0E-120
Protein Domains
Database ID Description E-Value
Pfam IPR000626 EMBL-EBI Ubiquitin 1.5E-18
Pfam IPR000058 EMBL-EBI Zn-finger, AN1-like 1.1E-21
Pfam IPR000058 EMBL-EBI Zn-finger, AN1-like 1.1E-21
Pfam IPR000626 EMBL-EBI Ubiquitin 1.5E-18
Pfam IPR000058 EMBL-EBI Zn-finger, AN1-like 1.1E-21
Sequence
Target Sequence 
>C. ELEGANS:189303_AT
gcaagtctttggacaccggagaagcaaatggaaaatgagttcactagaaatcgaatgaaa
actttgcttcgccgtaagaaacacgcaccaatcttgtctggaacaccggttgattctgaa
atcggatctgcgcaaacattctcgccggttgcaactcctcccggagagttgtcttcgccg
tctacagtttcatctcatgtcagctctggaagtgaaccggaaagtgatgccgaggttgtt
accgaaaaagaactcaagctcttcttcgatccacctgaaacaattgaggaacacaaacaa
tgccgccgttcgatggttcttgctccgagcagcgaagaagaattgcttgagaacttgaaa
aaattcgaagcggagagaaagaccaagtgtaatacttgtttcaagaagctctccgcagct
caacagaccatgcattgcaagtgtcttagaatcttctgtgatcgtcatcgtca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCAAGTCTTTGGACACCGGAGAAGC 639 321 451 Antisense
GCTTCGCCGTAAGAAACACGCACCA 644 305 516 Antisense
CAATCTTGTCTGGAACACCGGTTGA 482 179 539 Antisense
TCGGATCTGCGCAAACATTCTCGCC 642 605 572 Antisense
GCAACTCCTCCCGGAGAGTTGTCTT 454 319 601 Antisense
TACAGTTTCATCTCATGTCAGCTCT 523 643 633 Antisense
TCTTCTTCGATCCACCTGAAACAAT 266 615 710 Antisense
GAACACAAACAATGCCGCCGTTCGA 587 351 739 Antisense
ACTTGTTTCAAGAAGCTCTCCGCAG 211 105 844 Antisense
GCAGCTCAACAGACCATGCATTGCA 37 315 865 Antisense
GAATCTTCTGTGATCGTCATCGTCA 175 329 899 Antisense
Sequence Source Affymetrix Proprietary Database