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[193341_at]

Description C38D4.6 /REP_DB=WormBase Gene ID /WP=CE27837 /GEN=pal-1 /TR=Q18513 /GB=CAA86322.2 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=homeobox protein (cad subfamily)
Cluster 6grp_highest_10_10 > 78      6grp_high1_10_10 > 88      4grp_highest_8_8 > 39      4grp_high_8_8 > 12      6grp_highest_nonorm > 92      6grp_total > 87      4grp_total > 12      6grp_highest_sub > In      6grp_cgc > 58      6grp_high1_sub > Da      6grp_cgc_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 222
1 2 3 4 range
A 213.6
(-1.1)
P 		146.4
(-3)
P 		148.7
(-2.9)
P 		357.8
(3)
P 		211
B 198
(1.8)
P 		135.7
(-3)
P 		149.8
(-1.9)
P 		212.9
(3)
P 		77
C 221.4
(-0.9)
P 		225.2
(-0.8)
P 		156.5
(-3)
P 		346.2
(3)
P 		190
avr 211
(-0.7) 		169.1
(-2.3) 		151.7
(-3) 		305.6
(3) 		154

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 441
1 2 3 4 5 6 range
A 109.6
(-3)
P 		194.7
(-1.6)
P 		245.3
(-0.8)
P 		211
(-1.4)
P 		304.6
(0.2)
P 		479.2
(3)
P 		370
B 150.1
(-3)
P 		196.1
(-2.2)
P 		243.1
(-1.5)
P 		182.9
(-2.5)
P 		341.5
(0.2)
P 		511.6
(3)
P 		362
C 183.3
(-2.3)
P 		163.5
(-2.6)
P 		137
(-3)
P 		225.3
(-1.7)
P 		334
(-0.1)
P 		550.3
(3)
P 		413
avr 147.7
(-3) 		184.8
(-2.4) 		208.5
(-2) 		206.4
(-2) 		326.7
(-0.1) 		513.7
(3) 		366
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 46
1 2 3 4 range
A 77.8
(3)
P 		31.8
(-3)
P 		38.9
(-2.1)
P 		52.4
(-0.3)
P 		46
B 63.2
(3)
P 		33.5
(-3)
P 		34.7
(-2.8)
P 		45.4
(-0.6)
P 		30
C 73.3
(3)
P 		64.8
(0.3)
P 		54.5
(-3)
P 		58.4
(-1.8)
P 		19
avr 71.4
(3) 		43.4
(-2.9) 		42.7
(-3) 		52.1
(-1) 		29

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 171
1 2 3 4 5 6 range
A 20.2
(-3)
P 		69.3
(0.1)
P 		53.4
(-0.9)
P 		53.5
(-0.9)
P 		91.9
(1.5)
P 		116.7
(3)
P 		97
B 52.2
(-2.8)
P 		65.3
(-2.3)
P 		59
(-2.6)
P 		48.5
(-3)
P 		138.8
(0.8)
P 		190.8
(3)
P 		142
C 68
(-1.7)
P 		49.9
(-2.4)
P 		34.9
(-3)
P 		45.3
(-2.6)
P 		108.1
(-0.1)
P 		184.2
(3)
P 		149
avr 46.8
(-3) 		61.5
(-2.2) 		49.1
(-2.9) 		49.1
(-2.9) 		112.9
(0.4) 		163.9
(3) 		117
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193341_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6623
Sequence Type Exemplar sequence
Representative Public ID C38D4.6 NCBI
Target Description C38D4.6 /REP_DB=WormBase Gene ID /WP=CE27837 /GEN=pal-1 /TR=Q18513 /GB=CAA86322.2 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=homeobox protein (cad subfamily)
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_001026038(11), NM_001026039(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001026038 NCBI Caenorhabditis elegans Posterior ALae in males family member (pal-1) (pal-1) mRNA, complete cds. 11/11 None
NM_001026039 NCBI Caenorhabditis elegans Posterior ALae in males family member (pal-1) (pal-1) mRNA, complete cds. 11/11 None
GENEFINDER00000018680 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:4805173:4808670:-1 11/11 None
SNAP00000018668 ENSEMBL cdna:SNAP chromosome:CEL140:III:4806658:4808056:-1 11/11 None
C38D4.6a.2 ENSEMBL cdna:known chromosome:CEL140:III:4804670:4808671:-1 gene:C38D4.6 11/11 None
C38D4.6b.1 ENSEMBL cdna:known chromosome:CEL140:III:4804676:4808673:-1 gene:C38D4.6 11/11 None
C38D4.6b.2 ENSEMBL cdna:known chromosome:CEL140:III:4804680:4808671:-1 gene:C38D4.6 11/11 None
C38D4.6a.1 ENSEMBL cdna:known chromosome:CEL140:III:4804970:4808673:-1 gene:C38D4.6 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
chrIII:4805172-4808670(-) 100.0 100.0
Public Domain and Genome References
Ensembl C38D4.6
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA86322 Hypothetical protein C38D4.6a [Caenorhabditis elegans] ref|NP_001021209.1| Posterior ALae in males family member (pal-1) [Caenorhabditis elegans] 1.0E-124
blast 1709361A pal-1 gene 1.0E-124
blast CAH19082 Hypothetical protein C38D4.6b [Caenorhabditis elegans] ref|NP_001021210.1| Posterior ALae in males family member (pal-1) [Caenorhabditis elegans] pir||T19829 hypothetical protein C38D4.6 - Caenorhabditis elegans 1.0E-122
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 4.00000018325482E-18
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 4.00000012549758E-22
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 2.99999990479657E-22
Pfam IPR001356 EMBL-EBI Homeobox 3.3E-23
Pfam IPR001356 EMBL-EBI Homeobox 2.2E-17
Pfam IPR001356 EMBL-EBI Homeobox 3.3E-23
Sequence
Target Sequence 
>C. ELEGANS:193341_AT
gatactggtttttacggacatccggatctctatccattcggccttccacaactcgctgcc
aacggacaaattccagcagtagaagccgttgatgtgaagccaccgctttcgaatggaagt
agcagtagtgatagtggaatgtatccatcaccgagtgatatgatgacaccgttcccatca
acatcatctggagctgcatcttcttcagagctttcagcagctgctgctgctgcagccaac
taccagatgagagctgccacgtgttatcagcaatctgtttggccgtttatggattatcaa
cagggattctcgtggaaaatgcctcttgga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATACTGGTTTTTACGGACATCCGG 273 421 205 Antisense
AACTCGCTGCCAACGGACAAATTCC 539 141 254 Antisense
AAGCCGTTGATGTGAAGCCACCGCT 276 147 287 Antisense
TGGAATGTATCCATCACCGAGTGAT 135 547 339 Antisense
TGATGACACCGTTCCCATCAACATC 296 567 365 Antisense
CAACATCATCTGGAGCTGCATCTTC 545 187 383 Antisense
CTGCATCTTCTTCAGAGCTTTCAGC 538 237 398 Antisense
CTGCTGCAGCCAACTACCAGATGAG 341 237 431 Antisense
AGATGAGAGCTGCCACGTGTTATCA 623 67 449 Antisense
ATCAGCAATCTGTTTGGCCGTTTAT 653 21 470 Antisense
ATTCTCGTGGAAAATGCCTCTTGGA 199 9 510 Antisense
Sequence Source Affymetrix Proprietary Database