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[188690_at] Ank repeat

Description C04F12.3 /REP_DB=WormBase Gene ID /WP=CE19676 /TR=Q9U3S0 /GB=CAB62796.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Ank repeat
Cluster 6grp_highest_10_10 > 44      6grp_high1_10_10 > 43      4grp_highest_8_8 > 14      4grp_high_8_8 > 14      6grp_highest_nonorm > 62      6grp_total > 20      4grp_total > 09      6grp_highest_sub > 02      6grp_cgc > 63      6grp_high1_sub > 02      6grp_cgc_sub > 02      6grp_total_sub > Hat      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 804
1 2 3 4 range
A 366.9
(-3)
P 		534.2
(-1.7)
P 		435.7
(-2.5)
P 		1130.6
(3)
P 		764
B 371.5
(-3)
P 		422.5
(-2.4)
P 		512.2
(-1.4)
P 		914.6
(3)
P 		543
C 327
(-3)
P 		483.1
(-1.7)
P 		455.8
(-1.9)
P 		1023.1
(3)
P 		696
avr 355.1
(-3) 		479.9
(-1.9) 		467.9
(-2) 		1022.8
(3) 		668

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 323
1 2 3 4 5 6 range
A 448
(-0.3)
P 		564.3
(1.9)
P 		623.8
(3)
P 		512.6
(0.9)
P 		473.3
(0.2)
P 		302.1
(-3)
P 		322
B 490.1
(-0.2)
P 		616.1
(3)
P 		378.7
(-3)
P 		520.1
(0.6)
P 		534.9
(0.9)
P 		447.2
(-1.3)
P 		237
C 314.7
(-2.9)
P 		625.2
(3)
P 		587.2
(2.3)
P 		556.2
(1.7)
P 		307.7
(-3)
P 		463.3
(-0.1)
P 		318
avr 417.6
(-2.6) 		601.9
(3) 		529.9
(0.8) 		529.6
(0.8) 		438.6
(-2) 		404.2
(-3) 		198
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 91
1 2 3 4 range
A 133.6
(-0.7)
P 		116
(-2.8)
P 		113.9
(-3)
P 		165.5
(3)
P 		52
B 118.5
(-2.1)
P 		104.3
(-3)
P 		118.7
(-2)
P 		194.9
(3)
P 		91
C 108.2
(-3)
P 		138.9
(-0.1)
P 		158.8
(1.7)
P 		172.5
(3)
P 		64
avr 120.1
(-3) 		119.7
(-3) 		130.5
(-1.9) 		177.6
(3) 		58

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 144
1 2 3 4 5 6 range
A 82.6
(-2.6)
P 		200.7
(3)
P 		135.9
(-0.1)
P 		130
(-0.3)
P 		142.8
(0.3)
P 		73.6
(-3)
P 		127
B 170.5
(0.8)
P 		205.1
(2.4)
P 		92
(-3)
P 		137.8
(-0.8)
P 		217.3
(3)
P 		166.8
(0.6)
P 		125
C 116.6
(-1.9)
P 		190.8
(3)
P 		149.4
(0.3)
P 		111.9
(-2.2)
P 		99.6
(-3)
P 		155.1
(0.7)
P 		91
avr 123.2
(-3) 		198.9
(3) 		125.8
(-2.8) 		126.6
(-2.7) 		153.2
(-0.6) 		131.8
(-2.3) 		76
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188690_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1819
Sequence Type Exemplar sequence
Representative Public ID C04F12.3 NCBI
Target Description C04F12.3 /REP_DB=WormBase Gene ID /WP=CE19676 /TR=Q9U3S0 /GB=CAB62796.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Ank repeat
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_060174(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060174 NCBI Caenorhabditis elegans I Kappa B homolog family member (ikb-1) (ikb-1) mRNA, complete cds. 11/11 None
SNAP00000037401 ENSEMBL cdna:SNAP chromosome:CEL140:I:9693675:9696713:1 11/11 None
GENEFINDER00000037416 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:9693675:9696817:1 11/11 None
C04F12.3 ENSEMBL cdna:known chromosome:CEL140:I:9693603:9696764:1 gene:C04F12.3 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
chrI:9693605-9696644(+) 100.0 100.0
Public Domain and Genome References
Gene Title Ank repeat
Gene Symbol ikb-1
Ensembl C04F12.3
Entrez Gene 172817 Entrez gene
SwissProt Q9U3S0 EMBL-EBI
WormBase CE19676 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
7165 signal transduction inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB62796 Hypothetical protein C04F12.3 [Caenorhabditis elegans] ref|NP_492575.1| I Kappa B homolog family member (ikb-1) [Caenorhabditis elegans] gb|AAK37547.1| IKB-1 [Caenorhabditis elegans] 0.0
blast CAE60207 Hypothetical protein CBG03770 [Caenorhabditis briggsae] 0.0
blast XP_214856 PREDICTED: similar to BCL3 [Rattus norvegicus] 6.0E-22
Protein Domains
Database ID Description E-Value
Pfam IPR000488 EMBL-EBI Death domain 6.9E-20
Pfam IPR002110 EMBL-EBI Ankyrin 0.017
Pfam IPR002110 EMBL-EBI Ankyrin 8.9E-9
Pfam IPR002110 EMBL-EBI Ankyrin 1.1
Pfam IPR002110 EMBL-EBI Ankyrin 4.6E-6
Pfam IPR002110 EMBL-EBI Ankyrin 8.2E-4
Pfam IPR002110 EMBL-EBI Ankyrin 7.9E-8
Pfam IPR000488 EMBL-EBI Death domain 6.1E-20
Pfam IPR002110 EMBL-EBI Ankyrin 0.017
Pfam IPR002110 EMBL-EBI Ankyrin 8.9E-9
Pfam IPR002110 EMBL-EBI Ankyrin 1.1
Pfam IPR002110 EMBL-EBI Ankyrin 4.6E-6
Pfam IPR002110 EMBL-EBI Ankyrin 8.2E-4
Pfam IPR002110 EMBL-EBI Ankyrin 7.9E-8
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000037416 1 27-49
Sequence
Target Sequence 
>C. ELEGANS:188690_AT
tggagatagacccgaactacccaagaaagaagcttttggtgttcctaatgatttagctat
ttctagatctcccttatttgggagatctcatccagatcaggctccaggtgaagagagtgg
gcggcacagagttgtgaagagatctagagaagaaatattaaatgacgctcaaactcttct
cgctgaaactgactccatggctccacgtgtttcgagaatatccacatctgaatctgaaga
tgagcaacagccgggaccctcaacatcgtcgggaacacgaaggcgtcgaagtgaatggga
tcggaatccgaagcttagtgattcggtctgcaatttagattatttgacccgaattcgcgt
tgcaaaaatatttgatgatcagtgcaaatggcaaagattggcacaacaactcaattgtga
tcacatggtggaacttatttctatttgctcatcgggagacgattcaagcccgactatgat
tcttttggaccaatttgaacaacttgaagactcatcaatttcccgattgcgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGAGATAGACCCGAACTACCCAAG 417 525 1209 Antisense
CTATTTCTAGATCTCCCTTATTTGG 447 221 1265 Antisense
TCATCCAGATCAGGCTCCAGGTGAA 80 621 1296 Antisense
TAAATGACGCTCAAACTCTTCTCGC 429 641 1367 Antisense
CCATGGCTCCACGTGTTTCGAGAAT 53 273 1403 Antisense
TGAAGATGAGCAACAGCCGGGACCC 283 575 1443 Antisense
AAGCTTAGTGATTCGGTCTGCAATT 67 151 1519 Antisense
TATTTGACCCGAATTCGCGTTGCAA 384 661 1549 Antisense
GGAACTTATTTCTATTTGCTCATCG 529 529 1638 Antisense
GACGATTCAAGCCCGACTATGATTC 222 379 1666 Antisense
AGACTCATCAATTTCCCGATTGCGC 514 71 1716 Antisense
Sequence Source Affymetrix Proprietary Database