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[190771_s_at] degenerin

Description R13A1.4 /REP_DB=WormBase Gene ID /WP=CE26381 /GEN=unc-8 /TR=SW:Q21974 /GB=AAA81473.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=degenerin
Cluster 4grp_high_8_8 > 17      6grp_total > 25      4grp_total > 38      6grp_cgc > 33      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 131
1 2 3 4 range
A 241.2
(3)
P 		182.8
(-2.5)
M 		185.2
(-2.2)
A 		177
(-3)
P 		64
B 234.3
(3)
P 		143.1
(-1.6)
P 		114.9
(-3)
P 		135.8
(-1.9)
M 		119
C 211.2
(3)
P 		158.5
(-0.1)
M 		109.9
(-3)
P 		166.9
(0.4)
P 		101
avr 228.9
(3) 		161.5
(-1.4) 		136.7
(-3) 		159.9
(-1.5) 		92

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 200
1 2 3 4 5 6 range
A 285.6
(3)
P 		198.3
(-0.7)
P 		169
(-1.9)
A 		145.9
(-2.9)
A 		142.7
(-3)
A 		147.7
(-2.8)
A 		143
B 145.2
(-0.6)
P 		235.9
(3)
P 		119.4
(-1.7)
P 		142
(-0.8)
M 		137.2
(-0.9)
P 		85.8
(-3)
M 		150
C 220.9
(1.7)
P 		252.7
(3)
P 		175
(-0.2)
M 		136.2
(-1.8)
A 		108
(-3)
A 		119.2
(-2.5)
A 		145
avr 217.2
(2.4) 		229
(3) 		154.5
(-1) 		141.4
(-1.7) 		129.3
(-2.4) 		117.6
(-3) 		111
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 62
1 2 3 4 range
A 87.8
(3)
P 		39.7
(-1.7)
M 		48.4
(-0.8)
A 		25.9
(-3)
P 		62
B 74.7
(3)
P 		35.3
(-1.9)
P 		26.6
(-3)
P 		28.9
(-2.7)
M 		48
C 69.9
(3)
P 		45.6
(-0.5)
M 		38.3
(-1.5)
P 		28.1
(-3)
P 		42
avr 77.5
(3) 		40.2
(-1.5) 		37.8
(-1.8) 		27.6
(-3) 		50

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 55
1 2 3 4 5 6 range
A 52.6
(-0.1)
P 		70.5
(3)
P 		36.8
(-2.9)
A 		37
(-2.8)
A 		43.1
(-1.8)
A 		36
(-3)
A 		35
B 50.5
(-0.4)
P 		78.5
(3)
P 		29
(-3)
P 		37.6
(-2)
M 		55.7
(0.2)
P 		32
(-2.6)
M 		50
C 81.9
(3)
P 		77.1
(2.5)
P 		44.5
(-1.1)
M 		27.4
(-3)
A 		34.9
(-2.2)
A 		39.9
(-1.6)
A 		55
avr 61.7
(1) 		75.4
(3) 		36.8
(-2.6) 		34
(-3) 		44.6
(-1.5) 		36
(-2.7) 		41
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 190771_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9366
Sequence Type Exemplar sequence
Representative Public ID R13A1.4 NCBI
Target Description R13A1.4 /REP_DB=WormBase Gene ID /WP=CE26381 /GEN=unc-8 /TR=SW:Q21974 /GB=AAA81473.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=degenerin
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_068737(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068737 NCBI Caenorhabditis elegans R13A1.4 (degenerin) mRNA, complete cds. 11/11 None
SNAP00000003732 ENSEMBL cdna:SNAP chromosome:CEL140:IV:7199539:7203481:1 11/11 None
GENEFINDER00000003744 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:7197136:7203481:1 11/11 None
R13A1.4 ENSEMBL cdna:known chromosome:CEL140:IV:7198476:7203481:1 gene:R13A1.4 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
chrIV:7198481-7203487(+) 100.0 100.0
Public Domain and Genome References
Gene Title degenerin
Gene Symbol unc-8
Ensembl R13A1.4
Entrez Gene 177494 Entrez gene
SwissProt Q21974 EMBL-EBI
WormBase CE26381 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1582809_AT sodium channel, nonvoltage-gated 1 alpha cfa
CANINE_2:CFA.3515.1.S1_S_AT sodium channel, nonvoltage-gated 1 alpha cfa
CANINE_2:CFAAFFX.23375.1.S1_AT sodium channel, nonvoltage-gated 1 alpha cfa
CHICKEN:GGA.922.1.S1_A_AT sodium channel, nonvoltage-gated 1 alpha gga
CHICKEN:GGA.922.2.S1_A_AT sodium channel, nonvoltage-gated 1 alpha gga
HG-U133_PLUS_2:203453_AT sodium channel, nonvoltage-gated 1 alpha hs
HG-U133A:203453_AT sodium channel, nonvoltage-gated 1 alpha hs
HG-FOCUS:203453_AT sodium channel, nonvoltage-gated 1 alpha hs
HG-U133A_2:203453_AT sodium channel, nonvoltage-gated 1 alpha hs
HG-U133_PLUS_2:215026_X_AT sodium channel, nonvoltage-gated 1 alpha hs
HG-U133A_2:215026_X_AT sodium channel, nonvoltage-gated 1 alpha hs
HG-U133A:215026_X_AT sodium channel, nonvoltage-gated 1 alpha hs
HG-U133_PLUS_2:217264_S_AT sodium channel, nonvoltage-gated 1 alpha hs
HG-U133A_2:217264_S_AT sodium channel, nonvoltage-gated 1 alpha hs
HG-U133A:217264_S_AT sodium channel, nonvoltage-gated 1 alpha hs
HUGENEFL:X76180_AT sodium channel, nonvoltage-gated 1 alpha hs
U133_X3P:G4506814_3P_AT sodium channel, nonvoltage-gated 1 alpha hs
U133_X3P:HS.2794.2.S1_3P_X_AT sodium channel, nonvoltage-gated 1 alpha hs
U133_X3P:HS.2794.2.S1_3P_A_AT sodium channel, nonvoltage-gated 1 alpha hs
U133_X3P:HS.2794.1.S1_3P_X_AT sodium channel, nonvoltage-gated 1 alpha hs
HG-U95AV2:35207_AT sodium channel, nonvoltage-gated 1 alpha hs
MOE430A:1425088_AT sodium channel, nonvoltage-gated, type I, alpha mm
MOUSE430_2:1425088_AT sodium channel, nonvoltage-gated, type I, alpha mm
MOUSE430A_2:1425088_AT sodium channel, nonvoltage-gated, type I, alpha mm
MG-U74CV2:167199_AT sodium channel, nonvoltage-gated, type I, alpha mm
RN-U34:X70521_AT sodium channel, nonvoltage-gated, type I, alpha polypeptide rn
RG-U34A:X70521_AT sodium channel, nonvoltage-gated, type I, alpha polypeptide rn
RAE230A:1368203_AT sodium channel, nonvoltage-gated, type I, alpha polypeptide rn
RAT230_2:1368203_AT sodium channel, nonvoltage-gated, type I, alpha polypeptide rn
RAE230A:1387104_AT sodium channel, nonvoltage-gated, type I, alpha polypeptide rn
RAT230_2:1387104_AT sodium channel, nonvoltage-gated, type I, alpha polypeptide rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6811 ion transport inferred from electronic annotation QuickGO AmiGO
6814 sodium ion transport inferred from electronic annotation QuickGO AmiGO
40011 locomotion inferred from sequence similarity QuickGO AmiGO
6812 cation transport inferred from sequence similarity QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
16021 integral to membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5216 ion channel activity inferred from electronic annotation QuickGO AmiGO
5272 sodium channel activity inferred from electronic annotation QuickGO AmiGO
5261 cation channel activity inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast NP_501138 R13A1.4 [Caenorhabditis elegans] gb|AAA81473.2| Uncoordinated protein 8 [Caenorhabditis elegans] sp|Q21974|UNC8_CAEEL Degenerin unc-8 (Uncoordinated protein 8) gb|AAB39734.1| degenerin [Caenorhabditis elegans] 0.0
blast T16737 hypothetical protein R13A1.4 - Caenorhabditis elegans 0.0
blast CAE61835 Hypothetical protein CBG05805 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001873 EMBL-EBI Na+ channel, amiloride-sensitive 1.0E-126
Pfam IPR001873 EMBL-EBI Na+ channel, amiloride-sensitive 1.0E-126
Pfam IPR001873 EMBL-EBI Na+ channel, amiloride-sensitive 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_501138.1 1 128-150
R13A1.4 1 128-150
SNAP00000003732 1 88-110
GENEFINDER00000003744 1 127-149
Sequence
Target Sequence 
>C. ELEGANS:190771_S_AT
tgtggagatccaagattccctctaccatctgaagagcatagacattgtaatgcgaagtca
aaaattgatcgtcaatgtttatcaaacctaacaagtgactctggaggttaccaccatcta
cacgaacaatgtgaatgtcgtcagccatgtcatgaaaaagtatttgagactgcttactct
gcatctgcatggcccagtcaaaatttcaaaattggtaccgactgccccgccgtatcagat
attttcaacgacactgaagcttgtaccgaatattatcgtcaaaacactgcttacattgaa
atttactacgaacaattgaatttcgaatcgctgaaagaaaccgccggttacacgctcgtc
aatcttttctcagattttggaggtaatattggattatggattggattttcagtcattacg
tttgctgaatttgcagaacttttctgcgagatctgcaaactaatgtatttcaaaggaata
gtctatgtacagaaaaagatgcaaggaaaagaatacacatcatcttcattaatgcacatt
gattttcttcaacgatcgcctaaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGTGGAGATCCAAGATTCCCTCTAC 249 555 1717 Antisense
GATTCCCTCTACCATCTGAAGAGCA 620 431 1730 Antisense
TGACTCTGGAGGTTACCACCATCTA 321 571 1812 Antisense
TTTGAGACTGCTTACTCTGCATCTG 415 667 1879 Antisense
TGCATCTGCATGGCCCAGTCAAAAT 72 579 1896 Antisense
TTCAAAATTGGTACCGACTGCCCCG 297 671 1921 Antisense
GCCCCGCCGTATCAGATATTTTCAA 183 287 1940 Antisense
TCAACGACACTGAAGCTTGTACCGA 376 629 1961 Antisense
GAATCGCTGAAAGAAACCGCCGGTT 526 305 2041 Antisense
ACGCTCGTCAATCTTTTCTCAGATT 26 93 2068 Antisense
TGATTTTCTTCAACGATCGCCTAAA 684 563 2256 Antisense
Sequence Source Affymetrix Proprietary Database