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[188960_s_at] sushi repeats

Description C54G4.4 /REP_DB=WormBase Gene ID /WP=CE15735 /TR=Q18849 /GB=CAA99822.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=sushi repeats
Cluster 6grp_high1_10_10 > 24      4grp_high_8_8 > 38      6grp_total > 02      4grp_total > 41      6grp_high1_sub > 02      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 222
1 2 3 4 range
A 114.6
(-3)
A 		287.8
(3)
P 		278.5
(2.7)
P 		228.6
(0.9)
A 		173
B 133.4
(-2.8)
P 		239.5
(3)
P 		214.3
(1.6)
P 		130.1
(-3)
A 		109
C 91.8
(-3)
M 		313.7
(3)
P 		287.7
(2.3)
P 		205.9
(0.1)
P 		222
avr 113.3
(-3) 		280.3
(3) 		260.2
(2.3) 		188.2
(-0.3) 		167

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 266
1 2 3 4 5 6 range
A 235.9
(1.4)
P 		262
(3)
P 		223.3
(0.7)
P 		182.6
(-1.8)
P 		249.8
(2.3)
P 		162.4
(-3)
P 		100
B 266.3
(1.7)
P 		310.4
(3)
P 		105.6
(-3)
P 		264.4
(1.7)
P 		198.1
(-0.3)
P 		165.5
(-1.2)
P 		205
C 242.1
(-0.1)
P 		371.5
(3)
P 		145
(-2.5)
P 		122.5
(-3)
A 		218.4
(-0.7)
P 		175.4
(-1.7)
P 		249
avr 248.1
(0.5) 		314.6
(3) 		158
(-3) 		189.8
(-1.8) 		222.1
(-0.5) 		167.8
(-2.6) 		157
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 73
1 2 3 4 range
A 41.7
(-1.7)
A 		62.5
(1.4)
P 		72.8
(3)
P 		33.5
(-3)
A 		39
B 42.5
(-0.2)
P 		59.1
(3)
P 		49.7
(1.2)
P 		27.7
(-3)
A 		31
C 30.4
(-3)
M 		90.2
(2.1)
P 		100.3
(3)
P 		34.7
(-2.6)
P 		70
avr 38.2
(-2.1) 		70.6
(2.5) 		74.3
(3) 		32
(-3) 		42

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 89
1 2 3 4 5 6 range
A 43.5
(-2.6)
P 		93.2
(3)
P 		48.6
(-2)
P 		46.3
(-2.2)
P 		75.4
(1)
P 		39.5
(-3)
P 		54
B 92.7
(2.2)
P 		103.3
(3)
P 		25.6
(-3)
P 		70
(0.4)
P 		80.5
(1.2)
P 		61.7
(-0.2)
P 		78
C 89.8
(1.4)
P 		113.4
(3)
P 		36.9
(-2.2)
P 		24.6
(-3)
A 		70.7
(0.1)
P 		58.7
(-0.7)
P 		89
avr 75.3
(0.5) 		103.3
(3) 		37
(-3) 		47
(-2.1) 		75.5
(0.5) 		53.3
(-1.5) 		66
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188960_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1898
Sequence Type Exemplar sequence
Representative Public ID C54G4.4 NCBI
Target Description C54G4.4 /REP_DB=WormBase Gene ID /WP=CE15735 /TR=Q18849 /GB=CAA99822.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=sushi repeats
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_059800(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059800 NCBI Caenorhabditis elegans C54G4.4 (C54G4.4) mRNA, complete cds. 11/11 None
GENEFINDER00000028905 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:8004892:8012729:-1 11/11 None
SNAP00000028896 ENSEMBL cdna:SNAP chromosome:CEL140:I:8004932:8010915:-1 11/11 None
C54G4.4 ENSEMBL cdna:known chromosome:CEL140:I:8004854:8011305:-1 gene:C54G4.4 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:8004862-8011236(-) 100.0 100.0
Public Domain and Genome References
Gene Title sushi repeats
Ensembl C54G4.4
Entrez Gene 172579 Entrez gene
SwissProt Q18849 EMBL-EBI
WormBase CE15735 Wormbase
Functional Annotations
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
5529 sugar binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA99822 Hypothetical protein C54G4.4 [Caenorhabditis elegans] ref|NP_492201.1| C54G4.4 [Caenorhabditis elegans] 0.0
blast CAE63715 Hypothetical protein CBG08236 [Caenorhabditis briggsae] 0.0
blast XP_396985 PREDICTED: similar to CG1500-PA [Apis mellifera] 3.0E-49
Protein Domains
Database ID Description E-Value
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 2.5E-11
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 3.1E-7
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 2.2E-8
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 8.7E-15
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 5.0E-7
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 3.1E-7
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 2.2E-8
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 8.7E-15
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 2.5E-11
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 3.1E-7
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 2.2E-8
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 8.7E-15
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_492201.1 1 115-137
C54G4.4 1 115-137
Sequence
Target Sequence 
>C. ELEGANS:188960_S_AT
aatggctgttcttgcatcagttattgttgcaattttatgttatggtattacaaagtttgc
aaaatcgacgaatcactcaaatggagatttatcaatatctcgtgataaattgaatgcatc
aaatgctgcaatttatgcaacgccgtcaattccaccacaaagaccagattcagtaattta
ctatgctccaactgttgctcatatggaggtaccaccccatctacttcaacttcaacaatt
accaaatggaaacatccacgtcacacttccaattggtcgtcaaatgggtcgtccttcact
tcccccttcaatgttattcaatccatccataccaccaccatcaccgactccatctcaaat
attgtactcattcgaccacgaaccgatttatgacactccacctgatacgataccgtatca
accagaaagtgtatacgaacgtcttcccgatcga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AATGGCTGTTCTTGCATCAGTTATT 184 163 2073 Antisense
TTTATGCAACGCCGTCAATTCCACC 575 673 2204 Antisense
GTAATTTACTATGCTCCAACTGTTG 348 461 2245 Antisense
TCATATGGAGGTACCACCCCATCTA 142 619 2271 Antisense
TCCACGTCACACTTCCAATTGGTCG 282 589 2327 Antisense
TTGGTCGTCAAATGGGTCGTCCTTC 479 677 2345 Antisense
TTCCCCCTTCAATGTTATTCAATCC 447 695 2372 Antisense
TCACCGACTCCATCTCAAATATTGT 19 627 2413 Antisense
AATATTGTACTCATTCGACCACGAA 649 173 2430 Antisense
TTATGACACTCCACCTGATACGATA 111 681 2460 Antisense
TGTATACGAACGTCTTCCCGATCGA 687 557 2502 Antisense
Sequence Source Affymetrix Proprietary Database