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[173919_s_at] Transthyretin-like family

Description AV199129_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C56A3.2 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV199129 /WB_GENE_ID=C56A3.2 /WP=CE09030 /CHR=5 /FEA=Genomic Cluster /DEF=Transthyretin-like family; Caenorhabditis elegans cDNA clone:yk541a5 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 39      6grp_high1_10_10 > 82      4grp_highest_8_8 > 33      4grp_high_8_8 > 50      6grp_highest_nonorm > 39      6grp_total > 73      4grp_total > 61      6grp_highest_sub > 04      6grp_high1_sub > 04      6grp_total_sub > Hat      6grp_rule_based > S4      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2460
1 2 3 4 range
A 3831.8
(3)
P 		3406.2
(1.7)
P 		3215.8
(1.1)
P 		1849.3
(-3)
P 		1983
B 3947.7
(3)
P 		3426.5
(1.6)
P 		3590.7
(2.1)
P 		1674.9
(-3)
P 		2273
C 3991.4
(3)
P 		3559.9
(1.9)
P 		3496.8
(1.8)
P 		1531.8
(-3)
P 		2460
avr 3923.6
(3) 		3464.2
(1.8) 		3434.4
(1.7) 		1685.3
(-3) 		2238

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 6851
1 2 3 4 5 6 range
A 2907.1
(-3)
P 		4715.2
(-1.4)
P 		8328.9
(1.8)
P 		9674.7
(3)
P 		9153.4
(2.5)
P 		6339.3
(0)
P 		6768
B 3460.8
(-3)
P 		5140.1
(-1.2)
P 		8327.9
(2.2)
P 		8103.9
(2)
P 		9056.4
(3)
P 		7154.4
(1)
P 		5596
C 3088.2
(-3)
P 		4966.7
(-1.3)
P 		7402.6
(0.9)
P 		9758
(3)
P 		8319.3
(1.7)
P 		6600.5
(0.2)
P 		6670
avr 3152
(-3) 		4940.7
(-1.2) 		8019.8
(1.8) 		9178.9
(3) 		8843
(2.7) 		6698.1
(0.5) 		6027
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1137
1 2 3 4 range
A 1395.2
(3)
P 		739.4
(-0.5)
P 		840.7
(0)
P 		270.7
(-3)
P 		1125
B 1258.9
(3)
P 		846.3
(0.3)
P 		832
(0.2)
P 		356.9
(-3)
P 		902
C 1321.3
(3)
P 		1023.5
(1.3)
P 		1218.8
(2.4)
P 		258.3
(-3)
P 		1063
avr 1325.1
(3) 		869.7
(0.3) 		963.8
(0.9) 		295.3
(-3) 		1030

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3144
1 2 3 4 5 6 range
A 535.9
(-3)
P 		1677
(0.1)
P 		1813.9
(0.4)
P 		2453.7
(2.2)
P 		2762.1
(3)
P 		1543.4
(-0.3)
P 		2226
B 1204.2
(-3)
P 		1710.9
(-1.8)
P 		2022.3
(-1)
P 		2146.4
(-0.7)
P 		3679.5
(3)
P 		2667.9
(0.5)
P 		2475
C 1144.7
(-3)
P 		1515.5
(-1.6)
P 		1884.1
(-0.1)
P 		1962.3
(0.2)
P 		2692
(3)
P 		2209.6
(1.1)
P 		1547
avr 961.6
(-3) 		1634.5
(-1.1) 		1906.8
(-0.3) 		2187.5
(0.5) 		3044.5
(3) 		2140.3
(0.4) 		2083
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173919_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.25480
Sequence Type Exemplar sequence
Representative Public ID AV199129 NCBI
Target Description AV199129_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C56A3.2 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV199129 /WB_GENE_ID=C56A3.2 /WP=CE09030 /CHR=5 /FEA=Genomic Cluster /DEF=Transthyretin-like family; Caenorhabditis elegans cDNA clone:yk541a5 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_073951(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073951 NCBI Caenorhabditis elegans C56A3.2 (C56A3.2) mRNA, complete cds. 11/11 None
SNAP00000001393 ENSEMBL cdna:SNAP chromosome:CEL140:V:13532329:13533331:-1 11/11 None
GENEFINDER00000001404 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:13532329:13533331:-1 11/11 None
C56A3.2.3 ENSEMBL cdna:known chromosome:CEL140:V:13531759:13533782:-1 gene:C56A3.2 11/11 None
C56A3.2.1 ENSEMBL cdna:known chromosome:CEL140:V:13532153:13533782:-1 gene:C56A3.2 11/11 None
C56A3.2.2 ENSEMBL cdna:known chromosome:CEL140:V:13532155:13533335:-1 gene:C56A3.2 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
chrV:13532255-13533332(-) 100.0 100.0
Public Domain and Genome References
Gene Title Transthyretin-like family
Ensembl C56A3.2
Entrez Gene 179835 Entrez gene
SwissProt Q18878 EMBL-EBI
WormBase CE09030 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAB01136 Hypothetical protein C56A3.2 [Caenorhabditis elegans] ref|NP_506352.1| C56A3.2 [Caenorhabditis elegans] 8.0E-87
blast CAE62570 Hypothetical protein CBG06683 [Caenorhabditis briggsae] 2.0E-67
Protein Domains
Database ID Description E-Value
Pfam IPR001534 EMBL-EBI Transthyretin-like 5.5E-72
Sequence
Target Sequence 
>C. ELEGANS:173919_S_AT
gttagctcttttttcattggcgatggtccaagcaatgcgagatcagtcgattgctgtcaa
gggacgtctgatctgtggagacaagccagcagccaatgtcagaataaagttgtgggagga
ggattcgggaccagatccagatgatcttttggaggctggatacactgacagcaacggaga
gttccaattgtccggaggagaagctgagttgacaccaattgatcctatcttcaaagtcta
tcacgattgtgatgataagtacatgcccggccaccgcaaagtaaaatttctaattccaaa
gtcgtatattacccaaggaaagacaccaaagaagacatttgatcttggagttctcaacct
ggaaactattttcccaaaagaagaaagagagctcattgtctccagaaaacgccgtcatca
cccaaaacagtacatc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTTAGCTCTTTTTTCATTGGCGATG 82 447 28 Antisense
GGCGATGGTCCAAGCAATGCGAGAT 162 541 46 Antisense
GCGAGATCAGTCGATTGCTGTCAAG 53 289 64 Antisense
GCTGTCAAGGGACGTCTGATCTGTG 525 295 80 Antisense
ACAAGCCAGCAGCCAATGTCAGAAT 458 113 108 Antisense
GATTCGGGACCAGATCCAGATGATC 93 427 149 Antisense
GGAGAGTTCCAATTGTCCGGAGGAG 544 517 203 Antisense
GATCCTATCTTCAAAGTCTATCACG 104 417 248 Antisense
TGATCTTGGAGTTCTCAACCTGGAA 192 565 367 Antisense
TGTCTCCAGAAAACGCCGTCATCAC 466 557 424 Antisense
CCGTCATCACCCAAAACAGTACATC 434 265 439 Antisense
Sequence Source Affymetrix Proprietary Database