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[188003_s_at]

Description B0414.2 /REP_DB=WormBase Gene ID /WP=CE24772 /GEN=rnt-1 /TR=O01834 /GB=AAB57715.2 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 92      6grp_high1_10_10 > 39      4grp_high_8_8 > 12      6grp_highest_nonorm > 90      6grp_total > 18      4grp_total > 12      6grp_highest_sub > Cu      6grp_cgc > 01      6grp_high1_sub > Cu      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 279
1 2 3 4 range
A 131.9
(-0.8)
P 		80.8
(-3)
P 		115.4
(-1.5)
A 		217.7
(3)
P 		137
B 92.6
(-1.7)
P 		93.9
(-1.7)
A 		65.1
(-3)
A 		195
(3)
P 		130
C 140.9
(-1)
P 		135.7
(-1.1)
P 		48.8
(-3)
P 		327.9
(3)
P 		279
avr 121.8
(-1.4) 		103.5
(-2) 		76.4
(-3) 		246.9
(3) 		171

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 146
1 2 3 4 5 6 range
A 253.6
(3)
P 		127.7
(-2.4)
P 		114.4
(-3)
P 		181.4
(-0.1)
P 		143
(-1.8)
P 		131.9
(-2.2)
P 		139
B 167.4
(2.1)
P 		130.8
(-1)
P 		107.6
(-3)
P 		133
(-0.8)
P 		150.6
(0.7)
P 		178.1
(3)
P 		71
C 153.9
(3)
P 		150.4
(1.9)
P 		134
(-3)
P 		141.3
(-0.8)
P 		141.9
(-0.6)
P 		134.7
(-2.8)
P 		20
avr 191.6
(3) 		136.3
(-1.6) 		118.7
(-3) 		151.9
(-0.3) 		145.2
(-0.8) 		148.2
(-0.6) 		73
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 40
1 2 3 4 range
A 48
(3)
P 		17.5
(-3)
P 		30.2
(-0.5)
A 		31.9
(-0.2)
P 		31
B 29.5
(0.3)
P 		23.2
(-1.2)
A 		15.1
(-3)
A 		41.6
(3)
P 		27
C 46.6
(1.6)
P 		39
(0.4)
P 		17
(-3)
P 		55.3
(3)
P 		38
avr 41.4
(2.6) 		26.6
(-1.4) 		20.8
(-3) 		42.9
(3) 		22

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 42
1 2 3 4 5 6 range
A 46.7
(3)
P 		45.4
(2.6)
P 		24.9
(-3)
P 		46
(2.8)
P 		43.2
(2)
P 		32.1
(-1)
P 		22
B 58.2
(1.8)
P 		43.5
(-0.4)
P 		26.1
(-3)
P 		35.2
(-1.6)
P 		61.2
(2.2)
P 		66.4
(3)
P 		40
C 57.1
(3)
P 		45.9
(0.7)
P 		34.1
(-1.8)
P 		28.4
(-3)
P 		45.9
(0.7)
P 		45.1
(0.5)
P 		29
avr 54
(3) 		44.9
(0.9) 		28.4
(-3) 		36.5
(-1.1) 		50.1
(2.1) 		47.9
(1.6) 		26
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188003_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1125
Sequence Type Exemplar sequence
Representative Public ID B0414.2 NCBI
Target Description B0414.2 /REP_DB=WormBase Gene ID /WP=CE24772 /GEN=rnt-1 /TR=O01834 /GB=AAB57715.2 /SUBMIT=ST.LOUIS /CHR=1 /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_059278(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059278 NCBI Caenorhabditis elegans RuNT related family member (rnt-1) (rnt-1) mRNA, complete cds. 11/11 A 
SNAP00000011711 ENSEMBL cdna:SNAP chromosome:CEL140:I:5791977:5796525:1 11/11 None
GENEFINDER00000011719 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:5791977:5796525:1 11/11 None
B0414.2 ENSEMBL cdna:known chromosome:CEL140:I:5784233:5796744:1 gene:B0414.2 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
chrI:5791976-5796525(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol rnt-1
Ensembl B0414.2
Entrez Gene 172243 Entrez gene
SwissProt O01834 EMBL-EBI
WormBase CE24772 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1627618_AT dm
DROSGENOME1:145432_AT dm
CHICKEN:GGA.157.1.S1_AT runt-related transcription factor 2 gga
HG-U133_PLUS_2:216994_S_AT runt-related transcription factor 2 hs
HG-U133A_2:216994_S_AT runt-related transcription factor 2 hs
HG-FOCUS:216994_S_AT runt-related transcription factor 2 hs
HG-U133A:216994_S_AT runt-related transcription factor 2 hs
HG-U133_PLUS_2:232231_AT runt-related transcription factor 2 hs
HG-U133B:232231_AT runt-related transcription factor 2 hs
HG-U95AV2:39187_AT runt-related transcription factor 2 hs
HG-U95AV2:34501_AT runt-related transcription factor 2 hs
HG-U133_PLUS_2:221282_X_AT runt-related transcription factor 2 hs
HG-U133A:221282_X_AT runt-related transcription factor 2 hs
HG-U133A_2:221282_X_AT runt-related transcription factor 2 hs
HU35KSUBA:AA287840_AT runt-related transcription factor 2 hs
HU35KSUBC:RC_N67149_AT runt-related transcription factor 2 hs
HUGENEFL:L40992_AT runt-related transcription factor 2 hs
U133_X3P:G10863884_3P_A_AT runt-related transcription factor 2 hs
U133_X3P:HS.50115.0.S1_3P_AT runt-related transcription factor 2 hs
U133_X3P:HS.122116.0.A1_3P_AT runt-related transcription factor 2 hs
HG-U133_PLUS_2:236858_S_AT runt-related transcription factor 2 hs
HG-U133B:236858_S_AT runt-related transcription factor 2 hs
HG-U133_PLUS_2:236859_AT runt-related transcription factor 2 hs
HG-U133B:236859_AT runt-related transcription factor 2 hs
HG-U95AV2:34502_G_AT runt-related transcription factor 2 hs
HG-U95C:53261_AT runt-related transcription factor 2 hs
HG-U95E:73682_AT runt-related transcription factor 2 hs
HG-U133_PLUS_2:221283_AT runt-related transcription factor 2 hs
HG-U133A_2:221283_AT runt-related transcription factor 2 hs
HG-U133A:221283_AT runt-related transcription factor 2 hs
HG-U95D:87778_AT Runt-related transcription factor 2 hs
MG-U74AV2:92676_AT runt related transcription factor 2 mm
MOE430A:1424704_AT runt related transcription factor 2 mm
MOUSE430A_2:1424704_AT runt related transcription factor 2 mm
MOUSE430_2:1424704_AT runt related transcription factor 2 mm
MU11KSUBA:D14636_S_AT runt related transcription factor 2 mm
MG-U74AV2:92677_S_AT runt related transcription factor 2 mm
MG-U74AV2:161378_R_AT runt related transcription factor 2 mm
MG-U74CV2:169237_I_AT runt related transcription factor 2 mm
MOE430A:1426034_A_AT runt related transcription factor 2 mm
MOUSE430A_2:1426034_A_AT runt related transcription factor 2 mm
MOUSE430_2:1426034_A_AT runt related transcription factor 2 mm
MOE430A:1425389_A_AT runt related transcription factor 2 mm
MOUSE430A_2:1425389_A_AT runt related transcription factor 2 mm
MOUSE430_2:1425389_A_AT runt related transcription factor 2 mm
RAE230A:1376614_AT Runt related transcription factor 2 rn
RAT230_2:1376614_AT Runt related transcription factor 2 rn
RAE230B:1396592_AT Runt related transcription factor 2 rn
RAT230_2:1396592_AT Runt related transcription factor 2 rn
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
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
5524 ATP binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB57715 Runt related protein 1 [Caenorhabditis elegans] ref|NP_491679.1| RuNT related family member (rnt-1) [Caenorhabditis elegans] gb|AAD54940.1| transcription factor RUN [Caenorhabditis elegans] dbj|BAA77765.1| RNT-1 [Caenorhabditis elegans] 1.0E-145
blast CAE60460 Hypothetical protein CBG04068 [Caenorhabditis briggsae] 1.0E-112
blast AAM51942 GH02614p [Drosophila melanogaster] 3.0E-30
Protein Domains
Database ID Description E-Value
Pfam IPR000040 EMBL-EBI Acute myeloid leukemia 1 protein (AML 1)/Runt 3.0E-93
Sequence
Target Sequence 
>C. ELEGANS:188003_S_AT
ggcagaggccgaaaattccatttgacaatcgttatacattcggcgccgatgatggtggcc
accgtcaaaaatgtgatcaaggttacggttgatggaccaagggatgcgagaataccaaaa
ccacaaggatctttgaaacggcaggcagaacagcagacaatattcccaaatgatattatc
cgaacgcctggaccaccgatgccaatgacaatgattccaccaccatggtttcctttacca
atgactcaaactttccccccatcattttttccgcttatctctccaggaccacatccttct
atctcagctgcactttggaaaattcacagcgaatcgatgaaaactccgattaaacaaaaa
gttgaacaggaaaatgtatcccttaatacgtctacatgcctatcatctccatcaattttt
ataactccaacttctgatgatcggaagttaaaacgaccatcttctcctcg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGCAGAGGCCGAAAATTCCATTTGA 65 535 313 Antisense
TGACAATCGTTATACATTCGGCGCC 140 573 335 Antisense
GATGGTGGCCACCGTCAAAAATGTG 59 407 363 Antisense
GGGATGCGAGAATACCAAAACCACA 391 493 413 Antisense
TGATATTATCCGAACGCCTGGACCA 212 565 483 Antisense
ACCACCATGGTTTCCTTTACCAATG 501 85 531 Antisense
CTTCTATCTCAGCTGCACTTTGGAA 591 219 608 Antisense
ATCCCTTAATACGTCTACATGCCTA 512 37 690 Antisense
ATGCCTATCATCTCCATCAATTTTT 545 41 708 Antisense
TCAATTTTTATAACTCCAACTTCTG 401 633 724 Antisense
AGTTAAAACGACCATCTTCTCCTCG 101 63 758 Antisense
Sequence Source Affymetrix Proprietary Database