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[193962_at] Fork head domain, eukaryotic transcription factors

Description F38A6.1 /REP_DB=WormBase Gene ID /WP=CE15998 /GEN=fkh-1 /TR=Q17381 /GB=CAB07378.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Fork head domain, eukaryotic transcription factors
Cluster 6grp_highest_10_10 > 81      6grp_high1_10_10 > 29      4grp_highest_8_8 > 47      4grp_high_8_8 > 11      6grp_highest_nonorm > 50      6grp_total > 28      4grp_total > 13      6grp_highest_sub > Cu      6grp_cgc > 05      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 848
1 2 3 4 range
A 661.6
(0.9)
P 		515
(-1.1)
P 		372.4
(-3)
P 		820.5
(3)
P 		448
B 648.3
(-1.4)
P 		480.5
(-2.7)
P 		440.5
(-3)
P 		1217
(3)
P 		777
C 684.4
(2.4)
P 		498.7
(-0.8)
P 		369.5
(-3)
P 		722.5
(3)
P 		353
avr 664.8
(0.1) 		498.1
(-1.8) 		394.1
(-3) 		920
(3) 		526

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 567
1 2 3 4 5 6 range
A 582.8
(3)
P 		488.4
(1.3)
P 		241.2
(-3)
P 		317.2
(-1.7)
P 		508.5
(1.7)
P 		580.3
(3)
P 		342
B 757.3
(3)
P 		439.9
(-1.2)
P 		375.3
(-2)
P 		299.8
(-3)
P 		366.2
(-2.1)
P 		420.2
(-1.4)
P 		458
C 808.5
(3)
P 		457.4
(-1.1)
P 		299.9
(-3)
P 		333
(-2.6)
P 		428
(-1.5)
P 		397.3
(-1.9)
P 		509
avr 716.2
(3) 		461.9
(-0.7) 		305.5
(-3) 		316.7
(-2.8) 		434.2
(-1.1) 		465.9
(-0.7) 		411
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 162
1 2 3 4 range
A 240.9
(3)
P 		111.8
(-2.4)
P 		97.3
(-3)
P 		120.1
(-2)
P 		144
B 206.7
(1)
P 		118.7
(-2.4)
P 		102.1
(-3)
P 		259.4
(3)
P 		157
C 226.5
(3)
P 		143.4
(-1.8)
P 		128.8
(-2.6)
P 		121.8
(-3)
P 		105
avr 224.7
(3) 		124.6
(-2.2) 		109.4
(-3) 		167.1
(0) 		115

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 247
1 2 3 4 5 6 range
A 107.4
(-0.3)
P 		173.7
(3)
P 		52.5
(-3)
P 		80.5
(-1.6)
P 		153.4
(2)
P 		141.3
(1.4)
P 		121
B 263.5
(3)
P 		146.4
(-0.8)
P 		91.1
(-2.6)
P 		79.4
(-3)
P 		148.8
(-0.7)
P 		156.7
(-0.5)
P 		184
C 299.7
(3)
P 		139.6
(-1.1)
P 		76.3
(-2.8)
P 		67
(-3)
P 		138.5
(-1.2)
P 		133
(-1.3)
P 		233
avr 223.5
(3) 		153.2
(0.2) 		73.3
(-3) 		75.6
(-2.9) 		146.9
(-0.1) 		143.7
(-0.2) 		150
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193962_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.14058
Sequence Type Exemplar sequence
Representative Public ID F38A6.1 NCBI
Target Description F38A6.1 /REP_DB=WormBase Gene ID /WP=CE15998 /GEN=fkh-1 /TR=Q17381 /GB=CAB07378.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Fork head domain, eukaryotic transcription factors
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_075605(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_075605 NCBI Caenorhabditis elegans defective PHArynx development family member (pha-4) (pha-4) mRNA, complete cds. 11/11 A 
SNAP00000022175 ENSEMBL cdna:SNAP chromosome:CEL140:V:20754964:20757731:1 11/11 None
GENEFINDER00000022184 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:20753362:20756868:1 11/11 None
F38A6.1 ENSEMBL cdna:known chromosome:CEL140:V:20750987:20758364:1 gene:F38A6.1 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
chrV:20751102-20757731(+) 100.0 100.0
Public Domain and Genome References
Gene Title Fork head domain, eukaryotic transcription factors
Gene Symbol pha-4
Ensembl F38A6.1
Entrez Gene 180357 Entrez gene
SwissProt Q17381 EMBL-EBI
WormBase CE15998 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6355 regulation of transcription, DNA-dependent inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3700 transcription factor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB07378 Hypothetical protein F38A6.1 [Caenorhabditis elegans] ref|NP_508006.1| defective PHArynx development family member (pha-4) [Caenorhabditis elegans] gb|AAA96319.1| CE-FKH-1 0.0
blast CAE61643 Hypothetical protein CBG05577 [Caenorhabditis briggsae] 1.0E-169
blast CAE61643 Hypothetical protein CBG05577 [Caenorhabditis briggsae] 1.0E-163
blast CAE61643 Hypothetical protein CBG05577 [Caenorhabditis briggsae] 1.0E-158
blast NP_571374 forkhead box A3 [Danio rerio] gb|AAC06362.1| fork head domain protein FKD2 [Danio rerio] 2.0E-52
blast NP_571374 forkhead box A3 [Danio rerio] gb|AAC06362.1| fork head domain protein FKD2 [Danio rerio] 3.0E-52
Protein Domains
Database ID Description E-Value
scop a.4.5.MarR-like transcriptional regulators All alpha proteins; DNA/RNA-binding 3-helical bundle; "Winged helix" DNA-binding domain; MarR-like transcriptional regulators 3.0
scop a.4.5.Forkhead DNA-binding domain All alpha proteins; DNA/RNA-binding 3-helical bundle; "Winged helix" DNA-binding domain; Forkhead DNA-binding domain 2.0000032332076E-40
scop a.4.5.Forkhead DNA-binding domain All alpha proteins; DNA/RNA-binding 3-helical bundle; "Winged helix" DNA-binding domain; Forkhead DNA-binding domain 3.000039882273E-41
Pfam IPR001766 EMBL-EBI Fork head transcription factor 2.7E-67
Pfam IPR001766 EMBL-EBI Fork head transcription factor 2.7E-67
Pfam IPR001766 EMBL-EBI Fork head transcription factor 2.7E-67
Sequence
Target Sequence 
>C. ELEGANS:193962_AT
gaaagggatccttctggactcttcacgagcactgtgggaatatgtttgagaatggatgct
acctccgtaggcagaagagattcaaggtcaaggaacgtgagccatcgagaaagaagagaa
atgccaactcccaacaattgcatcaacaacaacacattccaaaaatggaaatcaaagaag
aggatccaacatccatcacgaccacatcatcacttggtgcttattctctgatccctcaaa
tttctacaaagaaggagatcaaggaagagctgaaagctgtgcaagatgcaactgcagctg
ctgccaatcttggcctaattgacccatcgggaacgccgtcggctgttaatcacagtcaac
ctacttcagtgatctca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAAGGGATCCTTCTGGACTCTTCA 349 361 926 Antisense
TGGACTCTTCACGAGCACTGTGGGA 183 549 940 Antisense
GAGAATGGATGCTACCTCCGTAGGC 304 391 973 Antisense
AGAAATGCCAACTCCCAACAATTGC 566 71 1042 Antisense
ACGACCACATCATCACTTGGTGCTT 323 93 1123 Antisense
TATTCTCTGATCCCTCAAATTTCTA 644 663 1147 Antisense
GCAAGATGCAACTGCAGCTGCTGCC 586 319 1206 Antisense
AGCTGCTGCCAATCTTGGCCTAATT 465 81 1221 Antisense
TAATTGACCCATCGGGAACGCCGTC 67 631 1241 Antisense
GAACGCCGTCGGCTGTTAATCACAG 688 345 1256 Antisense
CAGTCAACCTACTTCAGTGATCTCA 548 207 1278 Antisense
Sequence Source Affymetrix Proprietary Database