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[171944_x_at]

Description AV184292_rc /REP_DB=TREMBL Accession /GB=AV184292 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk662e3 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 42      6grp_high1_10_10 > 23      4grp_highest_8_8 > 56      4grp_high_8_8 > 34      6grp_highest_nonorm > 70      6grp_total > 12      4grp_total > 45      6grp_highest_sub > 02      6grp_cgc > 52      6grp_high1_sub > 02      6grp_total_sub > Hat      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 274
1 2 3 4 range
A 427.9
(3)
P 		352.7
(-0.3)
P 		353.5
(-0.3)
P 		290.8
(-3)
P 		137
B 495
(3)
P 		397.5
(0.9)
P 		220.7
(-3)
P 		265.2
(-2)
P 		274
C 417.2
(3)
P 		388.6
(2)
P 		282.3
(-1.9)
P 		253.1
(-3)
P 		164
avr 446.7
(3) 		379.6
(0.7) 		285.5
(-2.5) 		269.7
(-3) 		177

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 355
1 2 3 4 5 6 range
A 311.1
(3)
P 		222.3
(-0.3)
P 		161.1
(-2.5)
P 		174.3
(-2.1)
P 		300
(2.6)
P 		148.7
(-3)
P 		162
B 394.1
(3)
P 		379.7
(2.6)
P 		261.4
(-0.8)
P 		295.3
(0.2)
P 		278.5
(-0.3)
P 		184.9
(-3)
P 		209
C 266.4
(-1.7)
P 		503.9
(3)
P 		425.4
(1.5)
P 		385.4
(0.7)
P 		198.6
(-3)
P 		308.2
(-0.8)
P 		305
avr 323.9
(1.3) 		368.6
(3) 		282.6
(-0.3) 		285
(-0.2) 		259
(-1.3) 		213.9
(-3) 		155
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 115
1 2 3 4 range
A 155.8
(3)
P 		76.6
(-1.2)
P 		92.4
(-0.4)
P 		42.6
(-3)
P 		113
B 157.8
(3)
P 		98.2
(-0.4)
P 		51.1
(-3)
P 		56.5
(-2.7)
P 		107
C 138.1
(3)
P 		111.7
(1.3)
P 		98.4
(0.5)
P 		42.7
(-3)
P 		95
avr 150.6
(3) 		95.5
(-0.2) 		80.6
(-1.1) 		47.3
(-3) 		103

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 119
1 2 3 4 5 6 range
A 57.4
(-0.6)
P 		79.1
(1.8)
P 		35.1
(-3)
P 		44.2
(-2)
P 		90.5
(3)
P 		36.2
(-2.9)
P 		55
B 137.1
(3)
P 		126.4
(2.1)
P 		63.5
(-3)
P 		78.2
(-1.8)
P 		113.1
(1)
P 		69
(-2.6)
P 		74
C 98.8
(-0.7)
P 		153.8
(3)
P 		108.3
(-0.1)
P 		77.5
(-2.1)
P 		64.3
(-3)
P 		103.2
(-0.4)
P 		90
avr 97.8
(0.5) 		119.8
(3) 		69
(-2.7) 		66.6
(-3) 		89.3
(-0.4) 		69.5
(-2.7) 		53
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171944_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27699
Sequence Type Exemplar sequence
Representative Public ID AV184292 NCBI
Target Description AV184292_rc /REP_DB=TREMBL Accession /GB=AV184292 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk662e3 : 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_001028999, NM_001028998, NM_001029003, NM_001029001, NM_001029002
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
T28F12.2b ENSEMBL cdna:known chromosome:CEL140:V:4499290:4511257:1 gene:T28F12.2 A 
NM_001029002 NCBI Caenorhabditis elegans UNCoordinated family member (unc-62) (unc-62) mRNA, complete cds. None
NM_001029001 NCBI Caenorhabditis elegans UNCoordinated family member (unc-62) (unc-62) mRNA, complete cds. None
NM_001029003 NCBI Caenorhabditis elegans UNCoordinated family member (unc-62) (unc-62) mRNA, complete cds. None
NM_001028998 NCBI Caenorhabditis elegans UNCoordinated family member (unc-62) (unc-62) mRNA, complete cds. None
T28F12.2a.1 ENSEMBL cdna:known chromosome:CEL140:V:4497277:4511257:1 gene:T28F12.2 None
T28F12.2f ENSEMBL cdna:known chromosome:CEL140:V:4497277:4511257:1 gene:T28F12.2 A 
T28F12.2a.2 ENSEMBL cdna:known chromosome:CEL140:V:4497276:4511235:1 gene:T28F12.2 None
NM_001028999 NCBI Caenorhabditis elegans UNCoordinated family member (unc-62) (unc-62) mRNA, complete cds. None
T28F12.2e ENSEMBL cdna:known chromosome:CEL140:V:4499144:4511257:1 gene:T28F12.2 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
chrV:4510875-4511119(+) 60.62 60.62
Public Domain and Genome References
Ensembl T28F12.2
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAO61421 Uncoordinated protein 62, isoform f [Caenorhabditis elegans] ref|NP_001024174.1| UNCoordinated family member (unc-62) [Caenorhabditis elegans] gb|AAL65142.1| UNC-62 splice variant 1a-7a [Caenorhabditis elegans] 0.0
blast AAF39974 Uncoordinated protein 62, isoform a [Caenorhabditis elegans] ref|NP_001024169.1| UNCoordinated family member (unc-62) [Caenorhabditis elegans] gb|AAL65143.1| UNC-62 splice variant 1a-7b [Caenorhabditis elegans] 0.0
blast AAO61420 Uncoordinated protein 62, isoform e [Caenorhabditis elegans] ref|NP_001024173.1| UNCoordinated family member (unc-62) [Caenorhabditis elegans] gb|AAL65144.1| UNC-62 splice variant 1b-7a [Caenorhabditis elegans] 0.0
blast AAF39975 Uncoordinated protein 62, isoform b [Caenorhabditis elegans] ref|NP_001024170.1| UNCoordinated family member (unc-62) [Caenorhabditis elegans] gb|AAL65145.1| UNC-62 splice variant 1b-7b [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 9.99999999819959E-24
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 5.00000009770741E-26
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 3.99999995490641E-26
Pfam IPR001356 EMBL-EBI Homeobox 4.0E-4
Pfam IPR001356 EMBL-EBI Homeobox 4.0E-4
Pfam IPR001356 EMBL-EBI Homeobox 4.0E-4
Pfam IPR001356 EMBL-EBI Homeobox 4.0E-4
Sequence
Target Sequence 
>C. ELEGANS:171944_X_AT
gtgaccacagggttaataccacacattcaattgctctccacgatgtaatannnnnngacg
naaaatttgnaaagtgagaaactgaaactaattgattaattgccagttcatatcatatgt
atgttcttattctcctcctccagttctcctcatgtttggaactcannnnnctaatattca
ccagtctcttctctcacaaaagacc

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
GTGACCACAGGGTTAATACCACACA 650 473 81 Antisense
ATACCACACATTCAATTGCTCTCCA 422 23 96 Antisense
ATTCAATTGCTCTCCACGATGTAAT 641 11 105 Antisense
GTGAGAAACTGAAACTAATTGATTA 640 239 154 Antisense
ATTAATTGCCAGTTCATATCATATG 186 13 175 Antisense
AATTGCCAGTTCATATCATATGTAT 99 179 178 Antisense
CATATGTATGTTCTTATTCTCCTCC 206 215 194 Antisense
CTCCAGTTCTCCTCATGTTTGGAAC 668 235 218 Antisense
CAGTTCTCCTCATGTTTGGAACTCA 606 205 221 Antisense
ACCAGTCTCTTCTCTCACAAAAGAC 683 85 260 Antisense
CCAGTCTCTTCTCTCACAAAAGACC 162 273 261 Antisense
Sequence Source Affymetrix Proprietary Database