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[190828_at] Transthyretin-like family

Description T04H1.3 /REP_DB=WormBase Gene ID /WP=CE13171 /TR=Q22176 /GB=CAB01580.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Transthyretin-like family
Cluster 6grp_total > 15      4grp_total > 53      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 217
1 2 3 4 range
A 165
(0.9)
P 		236.4
(3)
A 		128.7
(-0.1)
A 		28.7
(-3)
A 		208
B 245.4
(3)
P 		156.2
(0.5)
A 		153.3
(0.4)
A 		30.6
(-3)
A 		215
C 229
(3)
P 		149
(0.1)
A 		92.8
(-2)
A 		64.6
(-3)
A 		164
avr 213.1
(3) 		180.5
(1.9) 		124.9
(-0.1) 		41.3
(-3) 		172

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 750
1 2 3 4 5 6 range
A 795.2
(3)
P 		653
(1.8)
P 		473.8
(0.2)
P 		203.1
(-2.2)
P 		106.5
(-3)
P 		109
(-3)
A 		689
B 662.3
(3)
P 		488.8
(1.3)
P 		266.4
(-1)
P 		279.4
(-0.8)
P 		136.8
(-2.3)
P 		65.5
(-3)
A 		597
C 408
(0.9)
P 		598.5
(3)
P 		170.1
(-1.6)
P 		210.8
(-1.2)
P 		109.4
(-2.3)
A 		44.8
(-3)
A 		554
avr 621.8
(3) 		580.1
(2.5) 		303.4
(-0.5) 		231.1
(-1.3) 		117.6
(-2.5) 		73.1
(-3) 		549
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 74
1 2 3 4 range
A 60.1
(3)
P 		51.3
(2.1)
A 		33.7
(0.2)
A 		4.2
(-3)
A 		56
B 78.3
(3)
P 		38.6
(-0.3)
A 		35.5
(-0.6)
A 		6.5
(-3)
A 		72
C 75.8
(3)
P 		42.8
(-0.1)
A 		32.3
(-1)
A 		10.9
(-3)
A 		65
avr 71.4
(3) 		44.2
(0.5) 		33.8
(-0.5) 		7.2
(-3) 		64

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 217
1 2 3 4 5 6 range
A 146.6
(0.5)
P 		232.2
(3)
P 		103.2
(-0.8)
P 		51.5
(-2.3)
P 		32.1
(-2.8)
P 		26.5
(-3)
A 		206
B 230.4
(3)
P 		162.7
(1)
P 		64.7
(-1.8)
P 		74
(-1.6)
P 		55.6
(-2.1)
P 		24.4
(-3)
A 		206
C 151.2
(1.9)
P 		182.6
(3)
P 		43.3
(-2)
P 		42.4
(-2)
P 		35.4
(-2.3)
A 		15
(-3)
A 		168
avr 176.1
(2.4) 		192.5
(3) 		70.4
(-1.3) 		56
(-1.8) 		41
(-2.3) 		22
(-3) 		171
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190828_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12727
Sequence Type Exemplar sequence
Representative Public ID T04H1.3 NCBI
Target Description T04H1.3 /REP_DB=WormBase Gene ID /WP=CE13171 /TR=Q22176 /GB=CAB01580.1 /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_073667(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073667 NCBI Caenorhabditis elegans T04H1.3 (T04H1.3) mRNA, complete cds. 11/11 None
SNAP00000026399 ENSEMBL cdna:SNAP chromosome:CEL140:V:12244018:12244500:1 11/11 None
GENEFINDER00000026411 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:12239483:12244500:1 11/11 None
T04H1.3 ENSEMBL cdna:known chromosome:CEL140:V:12244018:12244500:1 gene:T04H1.3 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
chrV:12244017-12244500(+) 100.0 100.0
Public Domain and Genome References
Gene Title Transthyretin-like family
Ensembl T04H1.3
Entrez Gene 188071 Entrez gene
SwissProt Q22176 EMBL-EBI
WormBase CE13171 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAB01579 Hypothetical protein T04H1.1 [Caenorhabditis elegans] ref|NP_506066.1| T04H1.1 [Caenorhabditis elegans] 0.0
blast AAB69904 Hypothetical protein T02B11.6 [Caenorhabditis elegans] ref|NP_503350.1| T02B11.6 [Caenorhabditis elegans] 9.0E-87
blast CAB01586 Hypothetical protein T04H1.10 [Caenorhabditis elegans] ref|NP_506067.1| Serpentine Receptor, class W family member (srw-80) [Caenorhabditis elegans] 3.0E-85
blast CAB01580 Hypothetical protein T04H1.3 [Caenorhabditis elegans] ref|NP_506068.1| T04H1.3 [Caenorhabditis elegans] 4.0E-69
blast CAE75425 Hypothetical protein CBG23418 [Caenorhabditis briggsae] 5.0E-55
blast CAB02900 Hypothetical protein F09F3.6 [Caenorhabditis elegans] ref|NP_506433.1| F09F3.6 [Caenorhabditis elegans] 3.0E-50
Protein Domains
Database ID Description E-Value
Pfam IPR001534 EMBL-EBI Transthyretin-like 1.3E-62
Pfam IPR001534 EMBL-EBI Transthyretin-like 1.3E-62
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_506068.1 1 4-26
T04H1.3 1 4-26
SNAP00000026399 1 4-26
GENEFINDER00000026411 13 10-32,64-86,106-125,172-194,204-226,239-261,266-288,301-323,333-355,395-417,461-483,510-532,595-617
Sequence
Target Sequence 
>C. ELEGANS:190828_AT
tatattgctctttctgttttctttttgattcattgctccgatgctttactcaatgttatc
ggaagcactcaaagtgttactgtaacgggaaaattggtttgtgaaggacagccagccagt
ggagttctcgtgaagatgtatgacgatggaacgatatatgactcgaaattaggttcgacg
accacctcatctgatggaacattttctgtttctggaacatatacagatattttaacattg
gatccaaaagtgaatatatatcatagttgtaattacaatggaccatgttcaaagaaagtg
acaatcaatattcctgattatgcagttgcatctggaagtagctcgactgataattatgat
attggaactttgaacttagctaatcagt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TATATTGCTCTTTCTGTTTTCTTTT 541 661 28 Antisense
GTTTTCTTTTTGATTCATTGCTCCG 61 449 43 Antisense
TTCATTGCTCCGATGCTTTACTCAA 441 689 56 Antisense
TACTCAATGTTATCGGAAGCACTCA 77 645 74 Antisense
GGTTTGTGAAGGACAGCCAGCCAGT 684 505 123 Antisense
CAGCCAGCCAGTGGAGTTCTCGTGA 296 203 136 Antisense
AATTAGGTTCGACGACCACCTCATC 553 175 194 Antisense
GACGACCACCTCATCTGATGGAACA 458 379 204 Antisense
GGAACATTTTCTGTTTCTGGAACAT 516 529 223 Antisense
CAGTTGCATCTGGAAGTAGCTCGAC 274 207 350 Antisense
GGAACTTTGAACTTAGCTAATCAGT 355 529 391 Antisense
Sequence Source Affymetrix Proprietary Database