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[193131_at]

Description F38B2.1 /REP_DB=WormBase Gene ID /WP=CE24961 /GEN=ifa-1 /TR=Q17599 /GB=CAA90365.2 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=intermediate filament protein
Cluster 6grp_highest_10_10 > 40      6grp_high1_10_10 > 05      4grp_highest_8_8 > 48      4grp_high_8_8 > 42      6grp_highest_nonorm > 03      6grp_total > 05      4grp_total > 54      6grp_highest_sub > De      6grp_cgc > 22      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 7430
1 2 3 4 range
A 7657.2
(3)
P 		5015.6
(0.6)
P 		3056.4
(-1.2)
P 		1112.7
(-3)
P 		6545
B 8343.5
(3)
P 		4543.1
(-0.2)
P 		2803.8
(-1.6)
P 		1136.1
(-3)
P 		7207
C 6973.2
(3)
P 		4314.9
(0.4)
P 		2679.5
(-1.3)
P 		913.3
(-3)
P 		6060
avr 7658
(3) 		4624.5
(0.2) 		2846.6
(-1.4) 		1054
(-3) 		6604

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5377
1 2 3 4 5 6 range
A 6343.2
(3)
P 		4865.8
(1.3)
P 		2475.9
(-1.5)
P 		2295.2
(-1.7)
P 		2062.3
(-2)
P 		1161
(-3)
P 		5182
B 5724.4
(3)
P 		4431.4
(1.4)
P 		2566.6
(-1)
P 		2065.3
(-1.6)
P 		1927.1
(-1.8)
P 		978.6
(-3)
P 		4746
C 5417.1
(3)
P 		4304.7
(1.5)
P 		3488
(0.4)
P 		2133.9
(-1.4)
P 		2315.5
(-1.2)
P 		966.4
(-3)
P 		4451
avr 5828.2
(3) 		4534
(1.4) 		2843.5
(-0.7) 		2164.8
(-1.6) 		2101.6
(-1.7) 		1035.3
(-3) 		4793
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2634
1 2 3 4 range
A 2788
(3)
P 		1088.8
(-0.9)
P 		799
(-1.5)
P 		162.9
(-3)
P 		2625
B 2660.7
(3)
P 		1122
(-0.8)
P 		649.7
(-2)
P 		242.1
(-3)
P 		2419
C 2308.3
(3)
P 		1240.6
(0)
P 		933.9
(-0.8)
P 		154
(-3)
P 		2154
avr 2585.7
(3) 		1150.5
(-0.6) 		794.2
(-1.5) 		186.3
(-3) 		2399

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1725
1 2 3 4 5 6 range
A 1169.3
(0.7)
P 		1730.5
(3)
P 		539.2
(-1.9)
P 		582.1
(-1.8)
P 		622.3
(-1.6)
P 		282.7
(-3)
P 		1448
B 1991.8
(3)
P 		1475
(1.1)
P 		623.2
(-2)
P 		547
(-2.3)
P 		782.9
(-1.5)
P 		364.9
(-3)
P 		1627
C 2007.9
(3)
P 		1313.5
(0.5)
P 		887.8
(-1)
P 		429.1
(-2.6)
P 		749.3
(-1.5)
P 		323.5
(-3)
P 		1684
avr 1723
(3) 		1506.3
(2.1) 		683.4
(-1.5) 		519.4
(-2.2) 		718.2
(-1.3) 		323.7
(-3) 		1399
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193131_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17205
Sequence Type Exemplar sequence
Representative Public ID F38B2.1 NCBI
Target Description F38B2.1 /REP_DB=WormBase Gene ID /WP=CE24961 /GEN=ifa-1 /TR=Q17599 /GB=CAA90365.2 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=intermediate filament protein
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_171777(11), NM_171778(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_171777 NCBI Caenorhabditis elegans Intermediate Filament, A family member (ifa-1) (ifa-1) mRNA, complete cds. 11/11 None
NM_171778 NCBI Caenorhabditis elegans Intermediate Filament, A family member (ifa-1) (ifa-1) mRNA, complete cds. 11/11 None
SNAP00000008606 ENSEMBL cdna:SNAP chromosome:CEL140:X:11274094:11275267:1 11/11 None
GENEFINDER00000008620 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:11274282:11275267:1 11/11 None
F38B2.1a ENSEMBL cdna:known chromosome:CEL140:X:11271108:11275402:1 gene:F38B2.1 11/11 None
F38B2.1b ENSEMBL cdna:known chromosome:CEL140:X:11271477:11275267:1 gene:F38B2.1 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
chrX:11271171-11275267(+) 100.0 100.0
Public Domain and Genome References
Ensembl F38B2.1
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA97777 Hypothetical protein F38B2.1a [Caenorhabditis elegans] emb|CAA90365.3| Hypothetical protein F38B2.1a [Caenorhabditis elegans] ref|NP_741902.1| Intermediate Filament, A family member (ifa-1) [Caenorhabditis elegans] sp|P90901|IFA1_CAEEL Intermediate filament protein ifa-1 (Intermediate filament protein A1) (IF-A1) (Cel IF A1) 0.0
blast CAD44093 Hypothetical protein F38B2.1b [Caenorhabditis elegans] emb|CAD44129.1| Hypothetical protein F38B2.1b [Caenorhabditis elegans] ref|NP_741903.1| Intermediate Filament, A family member (ifa-1) [Caenorhabditis elegans] 0.0
blast CAA50182 Cytoplasmic intermediate filament (IF) protein [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001664 EMBL-EBI Intermediate filament protein 2.1E-21
Pfam IPR001664 EMBL-EBI Intermediate filament protein 5.4E-75
Pfam IPR001322 EMBL-EBI Intermediate filament, C-terminal 1.2E-77
Pfam IPR001664 EMBL-EBI Intermediate filament protein 2.4E-66
Pfam IPR001322 EMBL-EBI Intermediate filament, C-terminal 1.2E-77
Pfam IPR001664 EMBL-EBI Intermediate filament protein 3.8E-43
Pfam IPR001322 EMBL-EBI Intermediate filament, C-terminal 1.2E-77
Sequence
Target Sequence 
>C. ELEGANS:193131_AT
gatcttatgaagcagccctcaacgacagagattcccaaatccgcaaaatgcgtgaggaat
gccaagcccttatggtcgaattgcaaatgctcctggataccaaacaaactttggatgccg
aaatcgccatctacagaaagatgctcgaaggagaagagaaccgtgctggactcaagcaac
ttgtcgaacaggttgtcaagacccatgctatcacacaggaaaccgataccgagacgatga
gagtcgtcaagggcgaaactgcatcccgtcaatcgttccagcgttctgcaaagggaaatg
tttctatccacgaggcatcgccggatggaaagttcatcgtcctccagaacacacatcgtg
ccaaggacgaggctatcggtgagtggaagttgaagagacgtatcgacggaaaacgtgaga
atgtctacacgcttccaagagactttgtccttcgtgccggaaagaccctcaaaatcttcg
cccgtaaccaaggagttg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATCTTATGAAGCAGCCCTCAACGA 98 421 1163 Antisense
GGAATGCCAAGCCCTTATGGTCGAA 224 533 1218 Antisense
GAACCGTGCTGGACTCAAGCAACTT 221 345 1320 Antisense
GTTGTCAAGACCCATGCTATCACAC 704 437 1354 Antisense
GTCAAGGGCGAAACTGCATCCCGTC 444 461 1408 Antisense
TCAATCGTTCCAGCGTTCTGCAAAG 266 633 1431 Antisense
TATCCACGAGGCATCGCCGGATGGA 245 657 1467 Antisense
TCCTCCAGAACACACATCGTGCCAA 534 593 1502 Antisense
GTGAGAATGTCTACACGCTTCCAAG 405 483 1577 Antisense
TCCAAGAGACTTTGTCCTTCGTGCC 633 587 1596 Antisense
ATCTTCGCCCGTAACCAAGGAGTTG 307 31 1636 Antisense
Sequence Source Affymetrix Proprietary Database