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[191998_at] Superoxide dismutase

Description F55H2.1 /REP_DB=WormBase Gene ID /WP=CE25009 /GEN=sod-4 /TR=O61260 /GB=CAB61015.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Superoxide dismutase
Cluster 6grp_highest_10_10 > 10      6grp_high1_10_10 > 0      4grp_highest_8_8 > 46      4grp_high_8_8 > 10      6grp_highest_nonorm > 31      6grp_total > 04      4grp_total > 22      6grp_cgc > 10      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 985
1 2 3 4 range
A 1154.1
(1.5)
P 		490
(-2.6)
P 		429.1
(-3)
P 		1394.7
(3)
P 		966
B 1011.5
(1.8)
P 		516.8
(-2.1)
P 		409.4
(-3)
P 		1164.5
(3)
P 		755
C 1278.8
(3)
P 		516.4
(-2.5)
P 		440.3
(-3)
P 		1121.1
(1.9)
P 		839
avr 1148.1
(2.4) 		507.7
(-2.4) 		426.3
(-3) 		1226.8
(3) 		801

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 700
1 2 3 4 5 6 range
A 1283.6
(3)
P 		894.2
(-0.6)
P 		937
(-0.2)
P 		1068.6
(1)
P 		852.7
(-1)
P 		637
(-3)
P 		647
B 1320.2
(3)
P 		983.3
(0.1)
P 		680.7
(-2.5)
P 		1048.1
(0.7)
P 		883.2
(-0.7)
P 		620.6
(-3)
P 		700
C 1099.8
(3)
P 		1028.7
(2)
P 		866
(-0.1)
P 		915.1
(0.5)
P 		761.9
(-1.5)
P 		653.2
(-3)
P 		447
avr 1234.5
(3) 		968.7
(0.3) 		827.9
(-1.1) 		1010.6
(0.8) 		832.6
(-1) 		636.9
(-3) 		598
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 328
1 2 3 4 range
A 420.2
(3)
P 		106.4
(-3)
P 		112.2
(-2.9)
P 		204.2
(-1.1)
P 		314
B 322.6
(3)
P 		127.6
(-2.1)
P 		94.9
(-3)
P 		248.2
(1)
P 		228
C 423.3
(3)
P 		148.5
(-3)
P 		153.5
(-2.9)
P 		189
(-2.1)
P 		275
avr 388.7
(3) 		127.5
(-2.8) 		120.2
(-3) 		213.8
(-0.9) 		269

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 304
1 2 3 4 5 6 range
A 236.6
(0)
P 		318
(3)
P 		204.1
(-1.2)
P 		271
(1.3)
P 		257.3
(0.8)
P 		155.1
(-3)
P 		163
B 459.4
(3)
P 		327.3
(0.3)
P 		165.3
(-3)
P 		277.6
(-0.7)
P 		358.8
(0.9)
P 		231.4
(-1.7)
P 		294
C 407.6
(3)
P 		313.9
(0.5)
P 		220.4
(-2)
P 		184
(-3)
P 		246.5
(-1.3)
P 		218.7
(-2.1)
P 		224
avr 367.9
(3) 		319.7
(1.3) 		196.6
(-3) 		244.2
(-1.3) 		287.5
(0.2) 		201.7
(-2.8) 		171
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191998_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7291
Sequence Type Exemplar sequence
Representative Public ID F55H2.1 NCBI
Target Description F55H2.1 /REP_DB=WormBase Gene ID /WP=CE25009 /GEN=sod-4 /TR=O61260 /GB=CAB61015.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Superoxide dismutase
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,GenBank identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_066690(11), AB190513(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066690 NCBI Caenorhabditis elegans SOD (superoxide dismutase) family member (sod-4) (sod-4) mRNA, complete cds. 11/11 None
AB190513 NCBI Caenorhabditis elegans SOD4-2 mRNA for superoxide dismutase, complete cds. 11/11 None
SNAP00000007115 ENSEMBL cdna:SNAP chromosome:CEL140:III:9498310:9500093:-1 11/11 None
GENEFINDER00000007124 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:9498310:9500093:-1 11/11 None
F55H2.1 ENSEMBL cdna:known chromosome:CEL140:III:9498055:9500093:-1 gene:F55H2.1 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:9498251-9500089(-) 100.0 100.0
Public Domain and Genome References
Gene Title Superoxide dismutase
Gene Symbol sod-4
Ensembl F55H2.1
Entrez Gene 176336 Entrez gene
SwissProt P34461 EMBL-EBI
WormBase CE25009 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6801 superoxide metabolism inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4785 copper, zinc superoxide dismutase activity inferred from electronic annotation QuickGO AmiGO
46872 metal ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast P34461 Extracellular superoxide dismutase [Cu-Zn] precursor (EC-SOD) 1.0E-121
blast CAB61015 Hypothetical protein F55H2.1 [Caenorhabditis elegans] ref|NP_499091.1| SOD (superoxide dismutase) family member (sod-4) [Caenorhabditis elegans] dbj|BAA28262.1| SOD-4 isoform [Caenorhabditis elegans] 6.0E-96
blast P34461 Extracellular superoxide dismutase [Cu-Zn] precursor (EC-SOD) 6.0E-96
blast BAD51397.1 superoxide dismutase [Caenorhabditis elegans] 3.0E-95
blast CAB61015 Hypothetical protein F55H2.1 [Caenorhabditis elegans] ref|NP_499091.1| SOD (superoxide dismutase) family member (sod-4) [Caenorhabditis elegans] dbj|BAA28262.1| SOD-4 isoform [Caenorhabditis elegans] 5.0E-95
blast BAD51397.1 superoxide dismutase [Caenorhabditis elegans] 8.0E-95
blast CAB61015 Hypothetical protein F55H2.1 [Caenorhabditis elegans] ref|NP_499091.1| SOD (superoxide dismutase) family member (sod-4) [Caenorhabditis elegans] dbj|BAA28262.1| SOD-4 isoform [Caenorhabditis elegans] 8.0E-95
Protein Domains
Database ID Description E-Value
Pfam IPR001424 EMBL-EBI Copper/Zinc superoxide dismutase 1.0E-89
Pfam IPR001424 EMBL-EBI Copper/Zinc superoxide dismutase 1.5E-91
Sequence
Target Sequence 
>C. ELEGANS:191998_AT
tcgtgttgttttaattctggctctctccgtttgcattgaagccgcttccgaagtgattcg
tgcacgtgcctacattttcaaagctgaagctggaaaaattccaactgaattgattggaac
tattgattttgatcaatctggaagttttctgaagcttaacggatcggtttccggattagc
agctggaaaacatggattccatattcatgaaaaaggagatactggaaatggttgtctaag
tgctggtggacattataatcctcataagctgagccatggtgcaccagatgactcgaacag
acatattggagatttgggaaatattgagtcaccggcttccggagacacattaatttcagt
ttccgactctcttgcctcattaagtggacaatattcaatcattggccgaagtgtggttat
tcatgaaaaaactgatgacttgggacgcggtacttcagaccaatcaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCGTGTTGTTTTAATTCTGGCTCTC 649 605 21 Antisense
GGCTCTCTCCGTTTGCATTGAAGCC 128 537 39 Antisense
GAAGCCGCTTCCGAAGTGATTCGTG 55 345 58 Antisense
TCGTGCACGTGCCTACATTTTCAAA 607 605 78 Antisense
GGATCGGTTTCCGGATTAGCAGCTG 82 513 181 Antisense
CATAAGCTGAGCCATGGTGCACCAG 642 213 283 Antisense
GGTGCACCAGATGACTCGAACAGAC 710 499 298 Antisense
TGAGTCACCGGCTTCCGGAGACACA 67 569 345 Antisense
TTAATTTCAGTTTCCGACTCTCTTG 472 683 370 Antisense
GACTCTCTTGCCTCATTAAGTGGAC 38 375 385 Antisense
GGACGCGGTACTTCAGACCAATCAA 238 523 463 Antisense
Sequence Source Affymetrix Proprietary Database