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[192617_at] superoxide dismutase

Description C08A9.1 /REP_DB=WormBase Gene ID /WP=CE08002 /GEN=sod-3 /TR=SW:P41977 /GB=AAB53822.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=superoxide dismutase
Cluster 6grp_high1_10_10 > 96      4grp_high_8_8 > 06      6grp_total > 86      4grp_total > 02      6grp_cgc > 67      6grp_high1_sub > In      6grp_cgc_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 838
1 2 3 4 range
A 70.4
(-3)
A 		95.1
(-2.8)
P 		110.9
(-2.7)
P 		882.8
(3)
P 		812
B 86.9
(-2.8)
A 		58.9
(-3)
A 		138.8
(-2.4)
P 		896.5
(3)
P 		838
C 69.3
(-3)
P 		101.7
(-2.7)
M 		132.9
(-2.5)
P 		835.2
(3)
P 		766
avr 75.5
(-3) 		85.2
(-2.9) 		127.5
(-2.6) 		871.5
(3) 		796

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2927
1 2 3 4 5 6 range
A 197.5
(-3)
A 		298
(-2.8)
P 		1128.1
(-0.7)
P 		1195
(-0.6)
P 		1677.5
(0.6)
P 		2640.4
(3)
P 		2443
B 183.2
(-3)
P 		323.9
(-2.7)
P 		1529.9
(-0.2)
P 		1392.8
(-0.5)
P 		2052.6
(0.9)
P 		3054.4
(3)
P 		2871
C 180
(-3)
P 		342.9
(-2.7)
P 		989.8
(-1.3)
P 		1012
(-1.3)
P 		1717.4
(0.2)
P 		3106.5
(3)
P 		2927
avr 186.9
(-3) 		321.6
(-2.7) 		1215.9
(-0.8) 		1199.9
(-0.8) 		1815.8
(0.6) 		2933.8
(3) 		2747
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 176
1 2 3 4 range
A 25.6
(-2.7)
A 		20.6
(-3)
P 		29
(-2.5)
P 		129.2
(3)
P 		109
B 27.7
(-2.6)
A 		14.6
(-3)
A 		32.2
(-2.4)
P 		191
(3)
P 		176
C 22.9
(-3)
P 		29.2
(-2.7)
M 		46.3
(-1.8)
P 		140.8
(3)
P 		118
avr 25.4
(-2.8) 		21.5
(-3) 		35.8
(-2.4) 		153.7
(3) 		132

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1103
1 2 3 4 5 6 range
A 36.4
(-3)
A 		106
(-2.3)
P 		245.7
(-0.9)
P 		303.1
(-0.4)
P 		506.2
(1.6)
P 		642.8
(3)
P 		606
B 63.7
(-3)
P 		107.8
(-2.8)
P 		371.5
(-1.3)
P 		368.9
(-1.3)
P 		833.9
(1.3)
P 		1139
(3)
P 		1075
C 66.7
(-3)
P 		104.6
(-2.8)
P 		251.9
(-1.9)
P 		203.5
(-2.2)
P 		555.7
(0)
P 		1039.9
(3)
P 		973
avr 55.6
(-3) 		106.1
(-2.7) 		289.7
(-1.4) 		291.8
(-1.4) 		631.9
(0.9) 		940.6
(3) 		885
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192617_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17322
Sequence Type Exemplar sequence
Representative Public ID C08A9.1 NCBI
Target Description C08A9.1 /REP_DB=WormBase Gene ID /WP=CE08002 /GEN=sod-3 /TR=SW:P41977 /GB=AAB53822.1 /SUBMIT=ST.LOUIS /CHR=X /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 identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_078363(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_078363 NCBI Caenorhabditis elegans SOD (superoxide dismutase) family member (sod-3) (sod-3) mRNA, complete cds. 11/11 None
SNAP00000037423 ENSEMBL cdna:SNAP chromosome:CEL140:X:17092680:17094009:1 11/11 None
GENEFINDER00000037434 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:17092680:17094073:1 11/11 None
C08A9.1 ENSEMBL cdna:known chromosome:CEL140:X:17092646:17094132:1 gene:C08A9.1 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
chrX:17092679-17094009(+) 100.0 100.0
Public Domain and Genome References
Gene Title superoxide dismutase
Gene Symbol sod-3
Ensembl C08A9.1
Entrez Gene 181748 Entrez gene
SwissProt P41977 EMBL-EBI
WormBase CE08002 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
4784 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 CAA59790 mangenese superoxide dismutase [Caenorhabditis elegans] emb|CAA54319.1| manganese superoxide dismutase [Caenorhabditis elegans] gb|AAB53822.1| Sod (superoxide dismutase) protein 3 [Caenorhabditis elegans] ref|NP_510764.1| SOD (superoxide dismutase) family member (sod-3) [Caenorhabditis elegans] sp|P41977|SODM2_CAEEL Superoxide dismutase [Mn] 2, mitochondrial precursor 1.0E-126
blast CAA59790 mangenese superoxide dismutase [Caenorhabditis elegans] emb|CAA54319.1| manganese superoxide dismutase [Caenorhabditis elegans] gb|AAB53822.1| Sod (superoxide dismutase) protein 3 [Caenorhabditis elegans] ref|NP_510764.1| SOD (superoxide dismutase) family member (sod-3) [Caenorhabditis elegans] sp|P41977|SODM2_CAEEL Superoxide dismutase [Mn] 2, mitochondrial precursor 1.0E-116
blast CAB02913 Hypothetical protein F10D11.1 [Caenorhabditis elegans] ref|NP_492290.1| SOD (superoxide dismutase) family member (sod-2) [Caenorhabditis elegans] sp|P31161|SODM1_CAEEL Superoxide dismutase [Mn] 1, mitochondrial precursor dbj|BAA12821.1| manganese superoxide dismutase [Caenorhabditis elegans] dbj|BAA02363.1| manganese superoxide dismutase precursor [Caenorhabditis elegans] 1.0E-111
blast CAE67278 Hypothetical protein CBG12726 [Caenorhabditis briggsae] 1.0E-107
Protein Domains
Database ID Description E-Value
scop a.2.11.Fe,Mn superoxide dismutase (SOD), N-terminal domain All alpha proteins; Long alpha-hairpin; Fe,Mn superoxide dismutase (SOD), N-terminal domain; Fe,Mn superoxide dismutase (SOD), N-terminal domain 2.99999991051457E-35
scop a.2.11.Fe,Mn superoxide dismutase (SOD), N-terminal domain All alpha proteins; Long alpha-hairpin; Fe,Mn superoxide dismutase (SOD), N-terminal domain; Fe,Mn superoxide dismutase (SOD), N-terminal domain 5.00000009001255E-36
Pfam IPR001189 EMBL-EBI Manganese and iron superoxide dismutase 7.6E-75
Pfam IPR001189 EMBL-EBI Manganese and iron superoxide dismutase 6.6E-52
Pfam IPR001189 EMBL-EBI Manganese and iron superoxide dismutase 4.9E-64
Sequence
Target Sequence 
>C. ELEGANS:192617_AT
ttcaaccggttgcgggagttctcgccgtccgctccaagcacactctcccagatctcccat
tcgactatgcagatttggaacctgtaatcagccatgaaatcatgcagcttcatcatcaaa
agcatcatgccacctacgtgaacaatctcaatcagatcgaggagaaacttcacgaggctg
tttcgaaagggaatctaaaagaagcaattgctctccaaccagcgctgaaattcaatggtg
gtggacacatcaatcattctatcttctggaccaacttggctaaggatggtggagaacctt
caaaggagctgatggacactattaagcgcgacttcggttccctggataacttgcaaaaac
gtctttctgacatcactattgcggttcaaggctctggctggggatggttgggatattgca
agaaagacaaaatcttgaagatcgccacctgtgcaaaccaggatcctttggaaggaatgg
tcccactttttggaattgacgtttgggagcacgcctactacttgcagtacaaaaatgtcc
gcccagactatgtcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCAACCGGTTGCGGGAGTTCTCGC 370 1 50 Antisense
AGATCTCCCATTCGACTATGCAGAT 440 65 99 Antisense
GCCACCTACGTGAACAATCTCAATC 561 279 178 Antisense
GGTGGTGGACACATCAATCATTCTA 47 501 286 Antisense
ATCATTCTATCTTCTGGACCAACTT 463 29 302 Antisense
GATGGACACTATTAAGCGCGACTTC 435 407 360 Antisense
GACTTCGGTTCCCTGGATAACTTGC 173 315 379 Antisense
CGTCTTTCTGACATCACTATTGCGG 289 247 409 Antisense
ACTATTGCGGTTCAAGGCTCTGGCT 651 101 424 Antisense
TTGAAGATCGCCACCTGTGCAAACC 664 701 484 Antisense
AAAAATGTCCGCCCAGACTATGTCC 320 129 580 Antisense
Sequence Source Affymetrix Proprietary Database