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[171857_x_at] degenerin

Description CEK008H5R_rc /REP_DB=TREMBL Accession /GB=D34573 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk8h5 : 3prime end, single read.
Cluster 6grp_total > 04      4grp_total > 51      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 130
1 2 3 4 range
A 134.9
(-1.9)
P 		241.9
(3)
A 		187.3
(0.5)
P 		112.2
(-3)
A 		130
B 195.3
(3)
P 		194.7
(2.9)
A 		136
(-2.4)
P 		128.9
(-3)
P 		66
C 189.5
(3)
P 		180
(1.8)
A 		147.9
(-2.3)
P 		142.8
(-3)
A 		47
avr 173.2
(0.5) 		205.5
(3) 		157.1
(-0.7) 		128
(-3) 		78

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 220
1 2 3 4 5 6 range
A 250.1
(3)
M 		213.1
(2)
P 		118.2
(-0.6)
A 		164.3
(0.7)
P 		136.3
(-0.1)
A 		30.2
(-3)
A 		220
B 157.9
(3)
P 		111.5
(-0.5)
P 		96.7
(-1.6)
P 		134.8
(1.3)
P 		78.2
(-3)
A 		88.9
(-2.2)
M 		80
C 162.6
(3)
P 		110.2
(0.1)
A 		69.6
(-2.1)
A 		77.3
(-1.7)
A 		93.5
(-0.8)
A 		53.2
(-3)
A 		109
avr 190.2
(3) 		144.9
(1) 		94.8
(-1.3) 		125.5
(0.1) 		102.7
(-1) 		57.4
(-3) 		133
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 46
1 2 3 4 range
A 49.1
(2.4)
P 		52.5
(3)
A 		49
(2.4)
P 		16.4
(-3)
A 		36
B 62.3
(3)
P 		48.1
(0.6)
A 		31.5
(-2.3)
P 		27.5
(-3)
P 		35
C 62.7
(3)
P 		51.8
(1.3)
A 		51.5
(1.3)
P 		24.1
(-3)
A 		39
avr 58
(3) 		50.8
(1.8) 		44
(0.6) 		22.7
(-3) 		35

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 68
1 2 3 4 5 6 range
A 46.1
(0.4)
M 		75.8
(3)
P 		25.7
(-1.4)
A 		41.7
(0)
P 		41.1
(-0)
A 		7.4
(-3)
A 		68
B 54.9
(3)
P 		37.1
(-0.4)
P 		23.5
(-3)
P 		35.7
(-0.7)
P 		31.8
(-1.4)
A 		33.2
(-1.1)
M 		31
C 60.3
(3)
P 		33.6
(-0.6)
A 		17.7
(-2.7)
A 		15.6
(-3)
A 		30.3
(-1)
A 		17.8
(-2.7)
A 		45
avr 53.8
(3) 		48.8
(2.1) 		22.3
(-2.5) 		31
(-1) 		34.4
(-0.4) 		19.5
(-3) 		34
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171857_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27765
Sequence Type Exemplar sequence
Representative Public ID CEK008H5R NCBI
Target Description CEK008H5R_rc /REP_DB=TREMBL Accession /GB=D34573 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk8h5 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript Cluster.
Annotation Method Description
Annotation Description This probe set was annotated using the Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_062901
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062901 NCBI Caenorhabditis elegans T28D9.7 (degenerin) mRNA, complete cds. None
SNAP00000011375 ENSEMBL cdna:SNAP chromosome:CEL140:II:6474363:6474847:-1 None
T28D9.7 ENSEMBL cdna:known chromosome:CEL140:II:6474285:6481990:-1 gene:T28D9.7 None
GENEFINDER00000011386 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:6474363:6474721:-1 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
chrII:6474346-6474719(-) 73.1 73.1
Public Domain and Genome References
Gene Title degenerin
Ensembl T28D9.7
Entrez Gene 174069 Entrez gene
SwissProt Q10025 EMBL-EBI
WormBase CE37157 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6814 sodium ion transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5272 sodium channel activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAA68309 Hypothetical protein T28D9.7 [Caenorhabditis elegans] ref|NP_495302.2| T28D9.7 [Caenorhabditis elegans] sp|Q10025|DEGZ_CAEEL Degenerin-like protein T28D9.7 in chromosome II 0.0
blast CAE59316 Hypothetical protein CBG02656 [Caenorhabditis briggsae] 0.0
blast T16948 hypothetical protein T28D9.7 - Caenorhabditis elegans 0.0
blast T16948 hypothetical protein T28D9.7 - Caenorhabditis elegans 1.0E-44
blast AAA68309 Hypothetical protein T28D9.7 [Caenorhabditis elegans] ref|NP_495302.2| T28D9.7 [Caenorhabditis elegans] sp|Q10025|DEGZ_CAEEL Degenerin-like protein T28D9.7 in chromosome II 1.0E-43
blast CAE59316 Hypothetical protein CBG02656 [Caenorhabditis briggsae] 4.0E-26
Protein Domains
Database ID Description E-Value
Pfam IPR001873 EMBL-EBI Na+ channel, amiloride-sensitive 2.2E-4
Pfam IPR001873 EMBL-EBI Na+ channel, amiloride-sensitive 1.5E-6
Pfam IPR001873 EMBL-EBI Na+ channel, amiloride-sensitive 1.5E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_495302.2 2 95-114,742-764
T28D9.7 2 95-114,742-764
Sequence
Target Sequence 
>C. ELEGANS:171857_X_AT
gaagacccactactactacaatgaccccagctatttaacaatttcaccaccttcagatag
accaggagataacccgcgaaggatcaaacttctggatattactcgagccctcgtgctccc
accccaggcaaatcctcgtgatggaatccccaattccagataccgagccaatttcagtat
ctgagttttcagatgcacttgctccgcctcnnnnnaaaactccaccacgtggagcgacgt
acacggaaagagcaggta

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAGACCCACTACTACTACAATGAC 454 339 43 Antisense
ACTACAATGACCCCAGCTATTTAAC 702 99 57 Antisense
ATTTCACCACCTTCAGATAGACCAG 249 15 83 Antisense
GATAGACCAGGAGATAACCCGCGAA 341 421 98 Antisense
GATAACCCGCGAAGGATCAAACTTC 130 421 110 Antisense
ACTTCTGGATATTACTCGAGCCCTC 656 103 130 Antisense
AATCCTCGTGATGGAATCCCCAATT 664 167 173 Antisense
TTCCAGATACCGAGCCAATTTCAGT 197 699 196 Antisense
TGAGTTTTCAGATGCACTTGCTCCG 44 569 224 Antisense
TCCACCACGTGGAGCGACGTACACG 410 587 263 Antisense
GCGACGTACACGGAAAGAGCAGGTA 500 277 276 Antisense
Sequence Source Affymetrix Proprietary Database