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[192674_s_at] cuticle collagen SQT-1

Description B0491.2 /REP_DB=WormBase Gene ID /WP=CE02104 /GEN=sqt-1 /TR=SW:P12114 /GB=CAA90084.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=cuticle collagen SQT-1
Cluster 6grp_highest_10_10 > 44      6grp_high1_10_10 > 43      6grp_highest_nonorm > 34      6grp_total > 10      4grp_total > 49      6grp_highest_sub > 02      6grp_cgc > 63      6grp_high1_sub > 02      6grp_cgc_sub > 02      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 6383
1 2 3 4 range
A 45.7
(-3)
A 		6384.2
(3)
P 		4982.8
(1.7)
P 		42.1
(-3)
A 		6342
B 32.2
(-3)
A 		5220.5
(3)
P 		5105.5
(2.9)
P 		3.3
(-3)
A 		5217
C 39
(-3)
A 		5417.6
(3)
P 		5026
(2.6)
P 		1.7
(-3)
A 		5416
avr 39
(-3) 		5674.1
(3) 		5038.1
(2.3) 		15.7
(-3) 		5658

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 4419
1 2 3 4 5 6 range
A 432.7
(-3)
P 		4797.4
(3)
P 		2372.4
(-0.3)
P 		2618.4
(0)
P 		1250.8
(-1.9)
P 		573.4
(-2.8)
P 		4365
B 596.4
(-2.8)
P 		4072.7
(3)
P 		2662.1
(0.7)
P 		1728.8
(-0.9)
P 		1383.4
(-1.5)
P 		469.7
(-3)
P 		3603
C 931.9
(-2)
P 		3552.4
(3)
P 		3228.1
(2.4)
P 		1571.3
(-0.7)
P 		3014.6
(2)
P 		378.4
(-3)
P 		3174
avr 653.7
(-2.7) 		4140.8
(3) 		2754.2
(0.7) 		1972.8
(-0.5) 		1882.9
(-0.7) 		473.8
(-3) 		3667
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1751
1 2 3 4 range
A 16.6
(-3)
A 		1385.8
(3)
P 		1302.6
(2.6)
P 		6.2
(-3)
A 		1380
B 10.3
(-3)
A 		1289.3
(3)
P 		1183.1
(2.5)
P 		0.7
(-3)
A 		1289
C 12.9
(-3)
A 		1557.6
(2.3)
P 		1751.7
(3)
P 		0.3
(-3)
A 		1751
avr 13.3
(-3) 		1410.9
(3) 		1412.5
(3) 		2.4
(-3) 		1410

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1626
1 2 3 4 5 6 range
A 79.8
(-3)
P 		1706.2
(3)
P 		516.7
(-1.4)
P 		664.1
(-0.8)
P 		377.4
(-1.9)
P 		139.6
(-2.8)
P 		1626
B 207.5
(-2.8)
P 		1355.6
(3)
P 		646.4
(-0.6)
P 		457.9
(-1.6)
P 		562
(-1)
P 		175.1
(-3)
P 		1181
C 345.4
(-1.6)
P 		1084
(3)
P 		821.6
(1.4)
P 		316
(-1.8)
P 		975.5
(2.3)
P 		126.7
(-3)
P 		957
avr 210.9
(-2.7) 		1381.9
(3) 		661.6
(-0.5) 		479.3
(-1.4) 		638.3
(-0.6) 		147.1
(-3) 		1235
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192674_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3295
Sequence Type Exemplar sequence
Representative Public ID B0491.2 NCBI
Target Description B0491.2 /REP_DB=WormBase Gene ID /WP=CE02104 /GEN=sqt-1 /TR=SW:P12114 /GB=CAA90084.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=cuticle collagen SQT-1
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_064020(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064020 NCBI Caenorhabditis elegans SQuaT family member (sqt-1) (sqt-1) mRNA, complete cds. 11/11 None
SNAP00000040217 ENSEMBL cdna:SNAP chromosome:CEL140:II:11336634:11337655:-1 11/11 None
GENEFINDER00000040232 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:11336634:11337655:-1 11/11 None
B0491.2.1 ENSEMBL cdna:known chromosome:CEL140:II:11336626:11337740:-1 gene:B0491.2 11/11 None
B0491.2.2 ENSEMBL cdna:known chromosome:CEL140:II:11336628:11337737:-1 gene:B0491.2 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
chrII:11336630-11337652(-) 100.0 100.0
Public Domain and Genome References
Gene Title cuticle collagen SQT-1
Gene Symbol sqt-1
Ensembl B0491.2
Entrez Gene 174731 Entrez gene
SwissProt P12114 EMBL-EBI
WormBase CE02104 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6817 phosphate transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5737 cytoplasm inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
42302 structural constituent of cuticle inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA90084 Hypothetical protein B0491.2 [Caenorhabditis elegans] ref|NP_496421.1| SQuaT family member (sqt-1) [Caenorhabditis elegans] 2.0E-99
blast P12114 Cuticle collagen sqt-1 (Squat-1 protein) gb|AAA65468.1| collagen 7.0E-99
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.7E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.6E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.6E-10
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_496421.1 1 7-29
B0491.2.1 1 7-29
B0491.2.2 1 7-29
SNAP00000040217 1 7-29
GENEFINDER00000040232 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:192674_S_AT
tgcaatgctgataacaagtgcccagctggaccatccggaccaaagggagttccaggagtt
ccaggactcgacggagttccaggacttgacggtgttccaggagttggagctgatgatatc
gctccacaacgcgagtctgtcggatgcttcacttgcccacaaggaccagttggaccacca
ggagctcttggaagaccaggaccacgtggacttccaggaccaagaggacaaaatggaaac
ccaggaagagatggacaaccaggacatccaggagagcaaggatcatccggtcaaatcgga
aagatcggagagccaggaccaccaggagagaagggacgcgacgccgagcatccaatcgga
agaccaggaccaaagggaccaagaggagatcaaggaccaacaggaccagctggacagaac
ggtcttcacggac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGCAATGCTGATAACAAGTGCCCAG 51 577 364 Antisense
GAGTTCCAGGACTCGACGGAGTTCC 3 397 419 Antisense
AGTTCCAGGACTTGACGGTGTTCCA 527 61 438 Antisense
GACTTGACGGTGTTCCAGGAGTTGG 521 371 446 Antisense
AGCTGATGATATCGCTCCACAACGC 549 79 471 Antisense
ACAACGCGAGTCTGTCGGATGCTTC 293 113 489 Antisense
CAGGAGCTCTTGGAAGACCAGGACC 14 209 542 Antisense
GAGCAAGGATCATCCGGTCAAATCG 335 391 637 Antisense
CAGGAGAGAAGGGACGCGACGCCGA 375 209 686 Antisense
GACGCCGAGCATCCAATCGGAAGAC 582 379 703 Antisense
GCTGGACAGAACGGTCTTCACGGAC 455 293 772 Antisense
Sequence Source Affymetrix Proprietary Database