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[188021_at]

Description F54C4.2 /REP_DB=WormBase Gene ID /WP=CE19891 /GEN=spt-4 /TR=Q9TZ93 /GB=AAC68775.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 75      6grp_high1_10_10 > 67      4grp_highest_8_8 > 28      4grp_high_8_8 > 23      6grp_highest_nonorm > 91      6grp_total > 57      4grp_total > 0      6grp_highest_sub > Cu      6grp_cgc > 47      6grp_high1_sub > Da      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 128
1 2 3 4 range
A 173.2
(-2.2)
P 		157.8
(-3)
P 		275.8
(2.9)
P 		278
(3)
P 		120
B 228.7
(2.2)
P 		149.8
(-3)
P 		240.8
(3)
P 		210.1
(1)
P 		91
C 180.9
(-0.6)
P 		157.6
(-3)
P 		200.8
(1.5)
P 		215.4
(3)
P 		58
avr 194.3
(-0.2) 		155.1
(-3) 		239.1
(3) 		234.5
(2.7) 		84

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 206
1 2 3 4 5 6 range
A 164.8
(-3)
P 		226.8
(-0.3)
P 		227.1
(-0.2)
P 		267.6
(1.5)
P 		170.7
(-2.7)
P 		300.4
(3)
P 		136
B 181.6
(-2)
P 		278.3
(1.6)
P 		220.7
(-0.6)
P 		155.9
(-3)
P 		207.6
(-1.1)
P 		315.8
(3)
P 		160
C 287.6
(1.9)
P 		203.6
(-0.5)
P 		221.7
(0)
P 		118.4
(-3)
P 		229.5
(0.2)
P 		324
(3)
P 		206
avr 211.3
(-1.6) 		236.2
(-0.5) 		223.2
(-1.1) 		180.6
(-3) 		202.6
(-2) 		313.4
(3) 		133
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 39
1 2 3 4 range
A 63
(1.6)
P 		34.3
(-3)
P 		72.1
(3)
P 		40.7
(-2)
P 		38
B 72.9
(3)
P 		37
(-3)
P 		55.8
(0.1)
P 		44.8
(-1.7)
P 		36
C 59.9
(1.2)
P 		45.3
(-1.4)
P 		70
(3)
P 		36.3
(-3)
P 		34
avr 65.3
(2.8) 		38.9
(-3) 		66
(3) 		40.6
(-2.6) 		27

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 94
1 2 3 4 5 6 range
A 30.4
(-3)
P 		80.7
(3)
P 		49.5
(-0.7)
P 		67.9
(1.5)
P 		51.5
(-0.5)
P 		73.1
(2.1)
P 		50
B 63.2
(-1.3)
P 		92.6
(1)
P 		53.6
(-2)
P 		41.3
(-3)
P 		84.3
(0.4)
P 		117.8
(3)
P 		77
C 106.6
(2.9)
P 		62.1
(-0.3)
P 		56.4
(-0.7)
P 		23.8
(-3)
P 		74.3
(0.6)
P 		108.4
(3)
P 		85
avr 66.7
(-0.6) 		78.5
(0.7) 		53.2
(-2) 		44.3
(-3) 		70
(-0.2) 		99.8
(3) 		56
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188021_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8168
Sequence Type Exemplar sequence
Representative Public ID F54C4.2 NCBI
Target Description F54C4.2 /REP_DB=WormBase Gene ID /WP=CE19891 /GEN=spt-4 /TR=Q9TZ93 /GB=AAC68775.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=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_064734(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064734 NCBI Caenorhabditis elegans SPT transcription factor family member (spt-4) (spt-4) mRNA, complete cds. 11/11 None
SNAP00000020628 ENSEMBL cdna:SNAP chromosome:CEL140:III:69225:86376:-1 10/11 None
GENEFINDER00000020633 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:69225:69737:-1 10/11 None
F54C4.2 ENSEMBL cdna:known chromosome:CEL140:III:69094:69751:-1 gene:F54C4.2 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:69224-69737(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol spt-4
Ensembl F54C4.2
Entrez Gene 175172 Entrez gene
SwissProt Q9TZ93 EMBL-EBI
WormBase CE19891 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1591602_AT similar to Transcription initiation protein SPT4 homolog 2 cfa
CANINE_2:CFA.20467.1.S1_S_AT similar to Transcription initiation protein SPT4 homolog 2 cfa
CANINE_2:CFA.20467.2.S1_A_AT similar to Transcription initiation protein SPT4 homolog 2 cfa
DROSOPHILA_2:1627131_AT dm
DROSGENOME1:151714_AT dm
DROSGENOME1:142904_AT dm
DROSGENOME1:141835_S_AT dm
HG-U133A:201483_S_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HG-U133_PLUS_2:201483_S_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HG-U133A_2:201483_S_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HG-U133A:201484_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HG-U133_PLUS_2:201484_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HG-FOCUS:201484_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HG-U133A_2:201484_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HG-U95AV2:508_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HC-G110:508_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HUGENEFL:U43923_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
U133_X3P:G4507310_3P_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
U133_X3P:G12803910_3P_A_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HU35KSUBB:RC_R10105_S_AT Suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HU35KSUBD:RC_F10720_S_AT Suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HU35KSUBD:RC_AA488989_AT Suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
U133_X3P:HS.180804.0.S2_3P_AT Suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
U133_X3P:HS.180804.0.S1_3P_AT Suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HG-U133_PLUS_2:228826_AT Suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HG-U133B:228826_AT Suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HG-U133_PLUS_2:228828_AT Suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HG-U133B:228828_AT Suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HG-U95B:58978_AT Suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HG-U133_PLUS_2:244226_S_AT Suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HG-U133B:244226_S_AT Suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HU35KSUBD:RC_H82846_AT Suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
HU35KSUBB:RC_H60543_AT Suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
U133_X3P:HS.37848.0.A1_3P_AT Suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
U133_X3P:HS.37848.1.A1_3P_AT Suppressor of Ty 4 homolog 1 (S. cerevisiae) hs
MOE430A:1422418_S_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) mm
MOUSE430A_2:1422418_S_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) mm
MOUSE430_2:1422418_S_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) mm
MU11KSUBA:U43154_S_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) mm
MU11KSUBB:MSA.3195.0_S_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) mm
MG-U74AV2:100585_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) mm
MG-U74AV2:95796_G_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) mm
MG-U74CV2:170267_F_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) mm
MG-U74CV2:169684_R_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) mm
MG-U74CV2:169517_I_AT suppressor of Ty 4 homolog 1 (S. cerevisiae) mm
MU19KSUBA:TC18478_AT Suppressor of Ty 4 homolog 1 (S. cerevisiae), mRNA (cDNA clone MGC:36170 IMAGE:5011064) mm
RG-U34B:RC_AA945746_G_AT suppressor of Ty 4 homolog 2 (S. cerevisiae) (predicted) rn
RG-U34B:RC_AA945746_AT suppressor of Ty 4 homolog 2 (S. cerevisiae) (predicted) rn
RG-U34C:RC_AI169382_AT suppressor of Ty 4 homolog 2 (S. cerevisiae) (predicted) rn
RAE230A:1398987_AT suppressor of Ty 4 homolog 2 (S. cerevisiae) (predicted) rn
RAT230_2:1398987_AT suppressor of Ty 4 homolog 2 (S. cerevisiae) (predicted) rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
45941 positive regulation of transcription 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
8159 positive transcription elongation factor activity inferred from electronic annotation QuickGO AmiGO
8270 zinc ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAC68776 Hypothetical protein F54C4.3 [Caenorhabditis elegans] ref|NP_497136.1| F54C4.3 [Caenorhabditis elegans] 0.0
blast CAE57493 Hypothetical protein CBG00463 [Caenorhabditis briggsae] 0.0
blast AAC68775 Spt transcription factor family protein 4 [Caenorhabditis elegans] ref|NP_497135.1| SPT transcription factor family member (spt-4) [Caenorhabditis elegans] 3.0E-65
blast AAC68775 Spt transcription factor family protein 4 [Caenorhabditis elegans] ref|NP_497135.1| SPT transcription factor family member (spt-4) [Caenorhabditis elegans] 3.0E-63
blast AAC68775 Spt transcription factor family protein 4 [Caenorhabditis elegans] ref|NP_497135.1| SPT transcription factor family member (spt-4) [Caenorhabditis elegans] 1.0E-61
blast CAE57492 Hypothetical protein CBG00462 [Caenorhabditis briggsae] 2.0E-55
blast CAE57492 Hypothetical protein CBG00462 [Caenorhabditis briggsae] 1.0E-53
blast EAA11938 ENSANGP00000014073 [Anopheles gambiae str. PEST] ref|XP_315434.1| ENSANGP00000014073 [Anopheles gambiae str. PEST] 1.0E-35
Protein Domains
Database ID Description E-Value
Pfam IPR009287 EMBL-EBI Transcription initiation Spt4 1.5E-66
Pfam IPR009287 EMBL-EBI Transcription initiation Spt4 1.5E-66
Pfam IPR009287 EMBL-EBI Transcription initiation Spt4 1.5E-71
Sequence
Target Sequence 
>C. ELEGANS:188021_AT
gcctactctgctcactggtaaaatcggtggaaagcttccagaaagagggctgcgagaatt
gtgaagacgtgcttcacctgaaaggcgacgaggagaaggtctatgattgtaccagtgcaa
actacgatggaatgatcgcggcgatgagcaacaacgagtcgtgggtgtgcaaatggcaga
aaatgcagcgaaaagtgaagggaatgtacgcgatcagtgtgtctggagtactgccgaaca
atattgtcagcgagctcaagagcctcggcgt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCCTACTCTGCTCACTGGTAAAATC 87 283 56 Antisense
GAAAGCTTCCAGAAAGAGGGCTGCG 583 357 85 Antisense
GCTGCGAGAATTGTGAAGACGTGCT 318 297 104 Antisense
GACGTGCTTCACCTGAAAGGCGACG 21 377 121 Antisense
GAAGGTCTATGATTGTACCAGTGCA 277 335 150 Antisense
ATGATCGCGGCGATGAGCAACAACG 204 47 187 Antisense
CGAGTCGTGGGTGTGCAAATGGCAG 111 249 210 Antisense
GAATGTACGCGATCAGTGTGTCTGG 610 331 257 Antisense
GTGTGTCTGGAGTACTGCCGAACAA 709 487 272 Antisense
GCCGAACAATATTGTCAGCGAGCTC 503 285 288 Antisense
TCAGCGAGCTCAAGAGCCTCGGCGT 416 623 302 Antisense
Sequence Source Affymetrix Proprietary Database