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[188276_s_at] collagen

Description C50B6.4 /REP_DB=WormBase Gene ID /WP=CE08873 /TR=O17686 /GB=CAB02849.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 84      4grp_total > 49      6grp_cgc > 65      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 6905
1 2 3 4 range
A 53.5
(-3)
A 		6707.1
(3)
P 		6184.3
(2.5)
P 		127.3
(-2.9)
A 		6654
B 30.3
(-3)
A 		5993
(2.2)
P 		6934.9
(3)
P 		58.4
(-3)
A 		6905
C 55.8
(-3)
A 		6048.6
(2.4)
P 		6715.4
(3)
P 		161
(-2.9)
A 		6660
avr 46.5
(-3) 		6249.6
(2.7) 		6611.5
(3) 		115.6
(-2.9) 		6565

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 6517
1 2 3 4 5 6 range
A 4.5
(-3)
A 		5739
(3)
P 		4123.8
(1.3)
P 		4626.6
(1.8)
P 		5324
(2.6)
P 		4731.9
(1.9)
P 		5735
B 43.7
(-3)
A 		5464.9
(2)
P 		3293
(0)
P 		4891.2
(1.5)
P 		5518.3
(2.1)
P 		6521
(3)
P 		6477
C 5.1
(-3)
A 		4991
(2.6)
P 		3504.1
(0.9)
P 		4608.3
(2.2)
P 		5356.1
(3)
P 		4448.5
(2)
P 		5351
avr 17.8
(-3) 		5398.3
(3) 		3640.3
(1) 		4708.7
(2.2) 		5399.5
(3) 		5233.8
(2.8) 		5382
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2331
1 2 3 4 range
A 19.5
(-3)
A 		1455.9
(2.4)
P 		1616.7
(3)
P 		18.6
(-3)
A 		1598
B 9.7
(-3)
A 		1480.1
(2.5)
P 		1607
(3)
P 		12.4
(-3)
A 		1597
C 18.5
(-3)
A 		1739
(1.4)
P 		2340.5
(3)
P 		27.1
(-3)
A 		2322
avr 15.9
(-3) 		1558.3
(2) 		1854.7
(3) 		19.4
(-3) 		1839

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2431
1 2 3 4 5 6 range
A 0.8
(-3)
A 		2041.1
(3)
P 		898.1
(-0.4)
P 		1173.4
(0.4)
P 		1606.6
(1.7)
P 		1152.1
(0.4)
P 		2040
B 15.2
(-3)
A 		1819.1
(1.5)
P 		799.6
(-1.1)
P 		1295.5
(0.2)
P 		2242
(2.5)
P 		2431.7
(3)
P 		2417
C 1.9
(-3)
A 		1522.9
(2.3)
P 		891.9
(0.1)
P 		926.7
(0.2)
P 		1733.2
(3)
P 		1489.2
(2.2)
P 		1731
avr 6
(-3) 		1794.4
(2.8) 		863.2
(-0.2) 		1131.9
(0.6) 		1860.6
(3) 		1691
(2.5) 		1855
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188276_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.14169
Sequence Type Exemplar sequence
Representative Public ID C50B6.4 NCBI
Target Description C50B6.4 /REP_DB=WormBase Gene ID /WP=CE08873 /TR=O17686 /GB=CAB02849.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=collagen
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_073899(11), NM_073933(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073899 NCBI Caenorhabditis elegans C50B6.4 (collagen) mRNA, complete cds. 11/11 None
NM_073933 NCBI Caenorhabditis elegans COLlagen family member (col-162) (col-162) mRNA, complete cds. 11/11 None
SNAP00000011265 ENSEMBL cdna:SNAP chromosome:CEL140:V:13319667:13320589:-1 11/11 None
GENEFINDER00000011290 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:13319667:13320589:-1 11/11 None
SNAP00000011428 ENSEMBL cdna:SNAP chromosome:CEL140:V:13444558:13445962:1 11/11 None
GENEFINDER00000011431 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:13444558:13445962:1 11/11 None
C50B6.4 ENSEMBL cdna:known chromosome:CEL140:V:13319620:13320589:-1 gene:C50B6.4 11/11 None
Y2H9A.3 ENSEMBL cdna:known chromosome:CEL140:V:13444558:13445993:1 gene:Y2H9A.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:13444557-13445962(+) 93.26 97.72
chrV:13319666-13320589(-) 86.53 100.0
Public Domain and Genome References
Gene Title collagen

Gene Symbol col-161
col-162
Ensembl C50B6.4
Y2H9A.3
Entrez Gene 179812 Entrez gene
179825 Entrez gene
SwissProt O17686 EMBL-EBI
Q9U2P5 EMBL-EBI
WormBase CE08873 Wormbase
CE21291 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 CAB02849 Hypothetical protein C50B6.4 [Caenorhabditis elegans] ref|NP_506300.1| C50B6.4 [Caenorhabditis elegans] 2.0E-53
blast CAA16275 Hypothetical protein Y2H9A.3 [Caenorhabditis elegans] ref|NP_506334.1| COLlagen family member (col-162) [Caenorhabditis elegans] 2.0E-53
blast CAA16275 Hypothetical protein Y2H9A.3 [Caenorhabditis elegans] ref|NP_506334.1| COLlagen family member (col-162) [Caenorhabditis elegans] 5.0E-53
blast CAB02849 Hypothetical protein C50B6.4 [Caenorhabditis elegans] ref|NP_506300.1| C50B6.4 [Caenorhabditis elegans] 5.0E-53
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 7.9E-27
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.5E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.8E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.4E-12
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.8E-27
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_506300.1 1 7-29
NP_506334.1 1 7-29
C50B6.4 1 7-29
Y2H9A.3 1 7-29
SNAP00000011265 1 7-29
GENEFINDER00000011290 1 7-29
SNAP00000011428 1 7-29
GENEFINDER00000011431 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188276_S_AT
gatggacatgctggagaagctggaaagccaggaaccgccggtgttgctgttggtattgtt
tcggagggtggaccatgcatcaagtgcccagctggtgagccaggaccagccggagaggca
ggagctccaggaccagccggaccagacggacaaccaggacaagatggacaaggaggacag
ccaggaccagcaggaccagccggaccagccggagatgccggagcaccaggagcaccagga
caagatggacagccaggagccccaggacaagatggacaaagatctactggaaccccagga
gctgccggagcaccaggaccagctggaccagcaggacaagatggacaaccaggatctgat
ggaggaccaggagaggcaggagctccaggagcaccaggaccagacggacaaccaggacaa
ccaggacaagacggagaagctggagctccaggacaagatggacaaccaggatccgatgct
gcttattgtccatgcccagcaagatctgttgctgttcaacgcagtgtttctcgt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATGGACATGCTGGAGAAGCTGGAA 440 407 325 Antisense
GAAAGCCAGGAACCGCCGGTGTTGC 258 359 347 Antisense
CCAGGAACCGCCGGTGTTGCTGTTG 577 271 352 Antisense
GGTGTTGCTGTTGGTATTGTTTCGG 242 501 364 Antisense
GCTGTTGGTATTGTTTCGGAGGGTG 457 295 370 Antisense
GTTTCGGAGGGTGGACCATGCATCA 658 449 382 Antisense
AGGGTGGACCATGCATCAAGTGCCC 134 59 389 Antisense
GATCTACTGGAACCCCAGGAGCTGC 425 419 605 Antisense
TTGTCCATGCCCAGCAAGATCTGTT 183 707 810 Antisense
GCAAGATCTGTTGCTGTTCAACGCA 446 321 823 Antisense
TGCTGTTCAACGCAGTGTTTCTCGT 202 579 834 Antisense
Sequence Source Affymetrix Proprietary Database