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[190467_at] Transthyretin-like family

Description R90.4 /REP_DB=WormBase Gene ID /WP=CE06328 /TR=Q22034 /GB=CAA99912.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Transthyretin-like family
Cluster 6grp_highest_10_10 > 29      6grp_high1_10_10 > 81      4grp_highest_8_8 > 31      4grp_high_8_8 > 13      6grp_highest_nonorm > 62      6grp_total > 81      4grp_total > 11      6grp_highest_sub > 04_05      6grp_high1_sub > 04      6grp_total_sub > Hat      6grp_rule_based > S4      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 721
1 2 3 4 range
A 179.9
(-2)
P 		206.6
(-1.7)
P 		95.4
(-3)
P 		618.6
(3)
P 		523
B 194.8
(-2.4)
P 		223.2
(-2.1)
P 		138.1
(-3)
P 		706.6
(3)
P 		569
C 262.1
(-1.8)
P 		220.3
(-2.2)
P 		125
(-3)
P 		816.3
(3)
P 		691
avr 212.3
(-2.1) 		216.7
(-2) 		119.5
(-3) 		713.8
(3) 		594

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1091
1 2 3 4 5 6 range
A 256.6
(-2.7)
P 		355.9
(-2.1)
P 		498
(-1.3)
P 		1287.6
(3)
P 		468.5
(-1.5)
P 		197.1
(-3)
P 		1091
B 327.7
(-2.3)
P 		387.3
(-1.6)
P 		396.4
(-1.4)
P 		771.2
(3)
P 		604.3
(1)
P 		265.1
(-3)
P 		506
C 395.5
(-1.9)
P 		325.4
(-2.7)
P 		348.8
(-2.5)
P 		682
(1.3)
P 		839.3
(3)
P 		299.6
(-3)
P 		540
avr 326.6
(-2.3) 		356.2
(-2.1) 		414.4
(-1.5) 		913.6
(3) 		637.4
(0.5) 		253.9
(-3) 		660
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 126
1 2 3 4 range
A 65.5
(0.7)
P 		44.9
(-1.2)
P 		24.9
(-3)
P 		90.6
(3)
P 		66
B 62.1
(-1.5)
P 		55.1
(-1.8)
P 		32
(-3)
P 		150.6
(3)
P 		119
C 86.7
(-0.2)
P 		63.3
(-1.7)
P 		43.6
(-3)
P 		137.6
(3)
P 		94
avr 71.4
(-0.5) 		54.4
(-1.6) 		33.5
(-3) 		126.3
(3) 		93

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 279
1 2 3 4 5 6 range
A 47.3
(-3)
P 		126.6
(-1.3)
P 		108.4
(-1.7)
P 		326.6
(3)
P 		141.4
(-1)
P 		48
(-3)
P 		279
B 114
(-2.3)
P 		128.9
(-1.7)
P 		96.3
(-3)
P 		204.3
(1.3)
P 		245.5
(3)
P 		98.9
(-2.9)
P 		149
C 146.6
(-1.1)
P 		99.3
(-2.7)
P 		88.8
(-3)
P 		137.2
(-1.4)
P 		271.6
(3)
P 		100.3
(-2.6)
P 		183
avr 102.6
(-2.1) 		118.3
(-1.5) 		97.8
(-2.3) 		222.7
(3) 		219.5
(2.9) 		82.4
(-3) 		140
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190467_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13931
Sequence Type Exemplar sequence
Representative Public ID R90.4 NCBI
Target Description R90.4 /REP_DB=WormBase Gene ID /WP=CE06328 /TR=Q22034 /GB=CAA99912.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Transthyretin-like family
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_073826(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073826 NCBI Caenorhabditis elegans R90.4 (R90.4) mRNA, complete cds. 11/11 None
SNAP00000036529 ENSEMBL cdna:SNAP chromosome:CEL140:V:12908773:12909321:-1 11/11 None
GENEFINDER00000036532 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:12908773:12909222:-1 11/11 None
R90.4 ENSEMBL cdna:known chromosome:CEL140:V:12908718:12909336:-1 gene:R90.4 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
chrV:12908772-12909222(-) 100.0 100.0
Public Domain and Genome References
Gene Title Transthyretin-like family
Ensembl R90.4
Entrez Gene 187890 Entrez gene
SwissProt Q22034 EMBL-EBI
WormBase CE06328 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA99912 Hypothetical protein R90.4 [Caenorhabditis elegans] ref|NP_506227.1| R90.4 [Caenorhabditis elegans] 3.0E-63
blast CAE64720 Hypothetical protein CBG09506 [Caenorhabditis briggsae] 7.0E-54
blast CAE64720 Hypothetical protein CBG09506 [Caenorhabditis briggsae] 9.0E-54
blast CAA99913 Hypothetical protein R90.3 [Caenorhabditis elegans] ref|NP_506226.1| R90.3 [Caenorhabditis elegans] 2.0E-51
Protein Domains
Database ID Description E-Value
Pfam IPR001534 EMBL-EBI Transthyretin-like 3.9E-73
Pfam IPR001534 EMBL-EBI Transthyretin-like 3.9E-73
Sequence
Target Sequence 
>C. ELEGANS:190467_AT
aggctgtagctgtttctggaagactaatctgtaatggacgaccagctacaaatattaaga
tcaaactgtatgaaaatgagattctgtttgatcgactcatggaagaaagccgtacagatt
caaatggacaattcagagtttctggctcaaaacgagaaatttcaaggattgacccaaaag
tcaacgtttatcacaaatgcaattataatgggttgtgctccaaaaaattcactataaaaa
ttccaaaggattatatcaaccgtggtagtcaagcagaacgaacatacgatataggaacac
taaacttggcaaaca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGGCTGTAGCTGTTTCTGGAAGACT 401 53 17 Antisense
GAAGACTAATCTGTAATGGACGACC 381 337 35 Antisense
ATGGACGACCAGCTACAAATATTAA 636 51 50 Antisense
GAGATTCTGTTTGATCGACTCATGG 416 397 94 Antisense
GATCGACTCATGGAAGAAAGCCGTA 399 415 106 Antisense
AAAGCCGTACAGATTCAAATGGACA 419 123 122 Antisense
GACAATTCAGAGTTTCTGGCTCAAA 29 365 143 Antisense
GACCCAAAAGTCAACGTTTATCACA 25 381 187 Antisense
GCAATTATAATGGGTTGTGCTCCAA 210 323 215 Antisense
ATCAACCGTGGTAGTCAAGCAGAAC 642 25 271 Antisense
ATAGGAACACTAAACTTGGCAAACA 262 19 307 Antisense
Sequence Source Affymetrix Proprietary Database