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[173122_s_at]

Description AV180948_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AV180948 /DEF=Caenorhabditis elegans cDNA clone:yk614a9 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 40      6grp_high1_10_10 > 06      4grp_highest_8_8 > 08      4grp_high_8_8 > 53      6grp_highest_nonorm > 51      6grp_total > 24      4grp_total > 51      6grp_highest_sub > De      6grp_high1_sub > De      6grp_total_sub > Decrease      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 423
1 2 3 4 range
A 664.3
(1.4)
P 		708.4
(2.4)
P 		737.6
(3)
P 		464.4
(-3)
P 		273
B 509
(-1.7)
P 		840.7
(3)
P 		633.7
(0.1)
P 		417.4
(-3)
P 		423
C 602.8
(-0.6)
P 		822.4
(3)
P 		745.7
(1.7)
P 		456.6
(-3)
P 		366
avr 592
(-0.5) 		790.5
(3) 		705.7
(1.5) 		446.1
(-3) 		344

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 531
1 2 3 4 5 6 range
A 788.1
(3)
P 		718.6
(2)
P 		564.6
(-0.4)
P 		555.7
(-0.5)
P 		389.2
(-3)
P 		438.4
(-2.3)
P 		399
B 805.3
(3)
P 		606.8
(0.1)
P 		723.6
(1.8)
P 		544.2
(-0.8)
P 		483.9
(-1.7)
P 		394.7
(-3)
P 		411
C 877.9
(3)
P 		527.9
(-1)
P 		662.7
(0.6)
P 		404.7
(-2.3)
P 		590.1
(-0.2)
P 		346.5
(-3)
P 		531
avr 823.8
(3) 		617.8
(0.1) 		650.3
(0.6) 		501.5
(-1.5) 		487.7
(-1.7) 		393.2
(-3) 		431
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 192
1 2 3 4 range
A 241.9
(3)
P 		153.8
(-0)
P 		192.8
(1.3)
P 		68
(-3)
P 		174
B 162.3
(0.7)
P 		207.6
(3)
P 		146.8
(-0.1)
P 		88.9
(-3)
P 		119
C 199.6
(1)
P 		236.5
(2.2)
P 		259.9
(3)
P 		77
(-3)
P 		183
avr 201.3
(3) 		199.3
(2.9) 		199.8
(2.9) 		78
(-3) 		123

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 244
1 2 3 4 5 6 range
A 145.3
(-1.4)
P 		255.6
(3)
P 		123
(-2.3)
P 		140.9
(-1.6)
P 		117.4
(-2.6)
P 		106.7
(-3)
P 		149
B 280.2
(3)
P 		202
(-0.4)
P 		175.7
(-1.6)
P 		144.2
(-3)
P 		196.6
(-0.7)
P 		147.2
(-2.9)
P 		136
C 325.4
(3)
P 		161.1
(-1)
P 		168.7
(-0.9)
P 		81.4
(-3)
P 		190.9
(-0.3)
P 		116
(-2.1)
P 		244
avr 250.3
(3) 		206.2
(0.9) 		155.8
(-1.4) 		122.2
(-3) 		168.3
(-0.8) 		123.3
(-2.9) 		128
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173122_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.26703
Sequence Type Exemplar sequence
Representative Public ID AV180948 NCBI
Target Description AV180948_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AV180948 /DEF=Caenorhabditis elegans cDNA clone:yk614a9 : 3prime end, single read.
Cluster Evidence This cluster is supported by a EST Transcript.
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_001027135(11), NM_001027134(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001027135 NCBI Caenorhabditis elegans T04B8.5b (T04B8.5) mRNA, complete cds. 11/11 None
NM_001027134 NCBI Caenorhabditis elegans T04B8.5a (T04B8.5) mRNA, complete cds. 11/11 None
SNAP00000021876 ENSEMBL cdna:SNAP chromosome:CEL140:II:614959:620708:-1 11/11 None
GENEFINDER00000021885 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:614959:624546:-1 11/11 None
T04B8.5b ENSEMBL cdna:known chromosome:CEL140:II:614773:621321:-1 gene:T04B8.5 11/11 A 
T04B8.5a ENSEMBL cdna:known chromosome:CEL140:II:614959:624549:-1 gene:T04B8.5 11/11 A 
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:614906-615361(-) 89.58 89.58
Public Domain and Genome References
Ensembl T04B8.5
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAT81190 Hypothetical protein T04B8.5b [Caenorhabditis elegans] ref|NP_001022306.1| T04B8.5b [Caenorhabditis elegans] 0.0
blast AAB95011 Hypothetical protein T04B8.5a [Caenorhabditis elegans] ref|NP_001022305.1| T04B8.5a [Caenorhabditis elegans] 0.0
blast CAE62896 Hypothetical protein CBG07084 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR004841 EMBL-EBI Amino acid permease-associated region 1.2E-13
Pfam IPR004841 EMBL-EBI Amino acid permease-associated region 1.7E-39
Pfam IPR004841 EMBL-EBI Amino acid permease-associated region 1.2E-13
Pfam IPR004841 EMBL-EBI Amino acid permease-associated region 1.7E-39
Pfam IPR004841 EMBL-EBI Amino acid permease-associated region 1.6E-9
Pfam IPR004841 EMBL-EBI Amino acid permease-associated region 1.7E-39
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_001022306.1 12 69-91,98-120,150-172,193-215,219-238,307-326,346-368,381-403,434-453,460-479,494-513,520-539
NP_001022305.1 12 82-104,111-133,163-185,206-228,232-251,320-339,359-381,394-416,447-466,473-492,507-526,533-552
T04B8.5b 12 69-91,98-120,150-172,193-215,219-238,307-326,346-368,381-403,434-453,460-479,494-513,520-539
T04B8.5a 12 82-104,111-133,163-185,206-228,232-251,320-339,359-381,394-416,447-466,473-492,507-526,533-552
SNAP00000021876 11 7-29,39-61,81-103,108-130,197-216,236-258,271-293,324-343,350-369,384-403,410-429
GENEFINDER00000021885 12 82-104,111-133,163-185,206-228,232-251,320-339,359-381,394-416,447-466,473-492,507-526,533-552
Sequence
Target Sequence 
>C. ELEGANS:173122_S_AT
gagatactccgaagatgcggcgattactctgctgaaccttccggtacctccagataatgc
agatatagatgctgataggtacctggaaatggtgcgcaacctgactgacgcccttccacc
aactcttctagtccacggagtctcttcggttatttctacggc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGATACTCCGAAGATGCGGCGATT 263 397 13 Antisense
CGAAGATGCGGCGATTACTCTGCTG 680 251 22 Antisense
CCTTCCGGTACCTCCAGATAATGCA 236 269 49 Antisense
GGTACCTCCAGATAATGCAGATATA 351 505 55 Antisense
ATATAGATGCTGATAGGTACCTGGA 210 19 75 Antisense
GGTACCTGGAAATGGTGCGCAACCT 224 505 90 Antisense
AAATGGTGCGCAACCTGACTGACGC 206 121 99 Antisense
CCAACTCTTCTAGTCCACGGAGTCT 100 277 131 Antisense
AACTCTTCTAGTCCACGGAGTCTCT 279 141 133 Antisense
TCCACGGAGTCTCTTCGGTTATTTC 512 271 144 Antisense
GAGTCTCTTCGGTTATTTCTACGGC 672 395 150 Antisense
Sequence Source Affymetrix Proprietary Database