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[174910_at] collagen

Description CEK091CZR_rc /REP_DB=TREMBL Accession /GB=D72194 /CHR=5 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk91c12 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 08      6grp_high1_10_10 > 80      6grp_highest_nonorm > 28      6grp_total > 72      4grp_total > 49      6grp_cgc > 74      6grp_high1_sub > 02_03_04_05      6grp_cgc_sub > 02_03_04_05      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 21535
1 2 3 4 range
A 126.8
(-3)
A 		21629.8
(3)
P 		20177.9
(2.6)
P 		1524.5
(-2.6)
P 		21503
B 95.1
(-3)
A 		18946.2
(2.4)
P 		21055.4
(3)
P 		1773.3
(-2.5)
P 		20960
C 126.1
(-3)
A 		18506.8
(3)
P 		17355.3
(2.6)
P 		1575.7
(-2.5)
P 		18381
avr 116
(-3) 		19694.3
(3) 		19529.5
(2.9) 		1624.5
(-2.5) 		19578

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 8540
1 2 3 4 5 6 range
A 4887.8
(-3)
P 		12640
(2.9)
P 		12776.8
(3)
P 		10918.9
(1.6)
P 		10374.7
(1.2)
P 		6549.4
(-1.7)
P 		7889
B 6463.8
(-3)
P 		12533.4
(2.2)
P 		13427.4
(3)
P 		12376.2
(2.1)
P 		9065.7
(-0.8)
P 		7933.6
(-1.7)
P 		6964
C 5221.6
(-3)
P 		12027.4
(3)
P 		9586.3
(0.8)
P 		11230.8
(2.3)
P 		11910.9
(2.9)
P 		6794.5
(-1.6)
P 		6806
avr 5524.4
(-3) 		12400.3
(3) 		11930.2
(2.6) 		11508.6
(2.2) 		10450.4
(1.3) 		7092.5
(-1.6) 		6876
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 6019
1 2 3 4 range
A 46.2
(-3)
A 		4695.2
(2.3)
P 		5274.9
(3)
P 		223.2
(-2.8)
P 		5229
B 30.3
(-3)
A 		4679.3
(2.8)
P 		4879
(3)
P 		377.9
(-2.6)
P 		4849
C 41.7
(-3)
A 		5320.8
(2.3)
P 		6048.9
(3)
P 		265.7
(-2.8)
P 		6007
avr 39.4
(-3) 		4898.4
(2.4) 		5400.9
(3) 		288.9
(-2.7) 		5362

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3594
1 2 3 4 5 6 range
A 901
(-3)
P 		4495.4
(3)
P 		2782.5
(0.1)
P 		2769.3
(0.1)
P 		3130.6
(0.7)
P 		1594.6
(-1.8)
P 		3594
B 2249.1
(-3)
P 		4171.9
(3)
P 		3260.6
(0.2)
P 		3278
(0.2)
P 		3683.3
(1.5)
P 		2958.4
(-0.8)
P 		1923
C 1935.4
(-3)
P 		3669.9
(2.4)
P 		2439.9
(-1.4)
P 		2258.5
(-2)
P 		3854.2
(3)
P 		2274.5
(-1.9)
P 		1919
avr 1695.2
(-3) 		4112.4
(3) 		2827.7
(-0.2) 		2768.6
(-0.3) 		3556
(1.6) 		2275.8
(-1.6) 		2417
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174910_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21886
Sequence Type Exemplar sequence
Representative Public ID CEK091CZR NCBI
Target Description CEK091CZR_rc /REP_DB=TREMBL Accession /GB=D72194 /CHR=5 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk91c12 : 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_073694(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073694 NCBI Caenorhabditis elegans F23H12.4 (collagen) mRNA, complete cds. 10/11 None
F23H12.4.2 ENSEMBL cdna:known chromosome:CEL140:V:12355582:12357069:1 gene:F23H12.4 10/11 A 
F23H12.4.1 ENSEMBL cdna:known chromosome:CEL140:V:12355582:12356902:1 gene:F23H12.4 10/11 A 
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:12356563-12356872(+) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol sqt-3
Ensembl F23H12.4
Entrez Gene 179693 Entrez gene
SwissProt P08124 EMBL-EBI
WormBase CE05707 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 CAA98942 Hypothetical protein F23H12.4 [Caenorhabditis elegans] ref|NP_506095.1| F23H12.4 [Caenorhabditis elegans] pir||T21314 hypothetical protein F23H12.4 - Caenorhabditis elegans 1.0E-54
blast CAE75463 Hypothetical protein CBG23461 [Caenorhabditis briggsae] 1.0E-53
blast P08124 Cuticle collagen 1 precursor (Squat-3 protein) (Dumpy-15 protein) emb|CAA23463.1| unnamed protein product [Caenorhabditis elegans] gb|AAA27988.1| collagen 7.0E-50
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 6.9E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0015
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.7E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.2E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_506095.1 1 12-34
F23H12.4.2 1 12-34
F23H12.4.1 1 12-34
Sequence
Target Sequence 
>C. ELEGANS:174910_AT
aatatttcaggtattgcgctctcgatggaggagtcttcttcgaggacggaaccagacgat
aaacatacatcgtcaatggatcgcggtagacgatgttcaacttctgcgtcgcaccgttat
gattcaatcattcctcaatcatatcctctctcttttttgtttcaactttacttctttctt
ctcacagtccaaacctcatcatcatctcgttgttgtgtatagtcgcgttgacagac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AATATTTCAGGTATTGCGCTCTCGA 65 175 56 Antisense
AACATACATCGTCAATGGATCGCGG 490 135 117 Antisense
ACATCGTCAATGGATCGCGGTAGAC 676 105 122 Antisense
GCGGTAGACGATGTTCAACTTCTGC 229 293 138 Antisense
GACGATGTTCAACTTCTGCGTCGCA 579 377 144 Antisense
AACTTCTGCGTCGCACCGTTATGAT 423 137 154 Antisense
GCGTCGCACCGTTATGATTCAATCA 574 291 161 Antisense
GTTATGATTCAATCATTCCTCAATC 337 447 171 Antisense
CTCATCATCATCTCGTTGTTGTGTA 143 229 250 Antisense
ATCTCGTTGTTGTGTATAGTCGCGT 347 33 259 Antisense
GTTGTGTATAGTCGCGTTGACAGAC 563 437 267 Antisense
Sequence Source Affymetrix Proprietary Database