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[188335_at] collagen

Description T05A1.2 /REP_DB=WormBase Gene ID /WP=CE03622 /TR=Q22183 /GB=CAA92476.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 93      4grp_total > 56      6grp_cgc > 99      6grp_total_sub > Hat      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 86
1 2 3 4 range
A 15.2
(-3)
A 		32.5
(-1.6)
A 		80.9
(2.5)
A 		87.1
(3)
A 		72
B 31.8
(-1.1)
A 		37
(-0.7)
A 		90.4
(3)
A 		4
(-3)
A 		86
C 39.3
(0.5)
A 		36.7
(0.1)
A 		57.1
(3)
A 		15.1
(-3)
A 		42
avr 28.8
(-3) 		35.4
(-2.2) 		76.1
(3) 		35.4
(-2.2) 		47

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 15535
1 2 3 4 5 6 range
A 73.8
(-3)
A 		44.1
(-3)
A 		31.2
(-3)
A 		536.1
(-2.7)
P 		12071.2
(3)
P 		3759
(-1.1)
P 		12040
B 65.1
(-3)
A 		37.8
(-3)
A 		37.2
(-3)
A 		434.1
(-2.8)
P 		11197.6
(3)
P 		2897.5
(-1.5)
P 		11160
C 79.2
(-3)
A 		9.2
(-3)
A 		38
(-3)
A 		449.1
(-2.8)
P 		15544.1
(3)
P 		2019.1
(-2.2)
P 		15535
avr 72.7
(-3) 		30.4
(-3) 		35.5
(-3) 		473.1
(-2.8) 		12937.6
(3) 		2891.9
(-1.7) 		12907
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 20
1 2 3 4 range
A 5.5
(-3)
A 		7.1
(-2.4)
A 		21.1
(3)
A 		12.8
(-0.2)
A 		16
B 10.1
(-0.3)
A 		9.1
(-0.6)
A 		21
(3)
A 		0.9
(-3)
A 		20
C 13
(0.6)
A 		10.5
(-0.3)
A 		19.9
(3)
A 		2.6
(-3)
A 		17
avr 9.5
(-1.4) 		8.9
(-1.6) 		20.7
(3) 		5.4
(-3) 		15

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5027
1 2 3 4 5 6 range
A 13.6
(-3)
A 		15.7
(-3)
A 		6.8
(-3)
A 		136
(-2.8)
P 		3642.6
(3)
P 		915.2
(-1.5)
P 		3636
B 22.6
(-3)
A 		12.6
(-3)
A 		9
(-3)
A 		115
(-2.9)
P 		4549.4
(3)
P 		1080.5
(-1.6)
P 		4540
C 29.3
(-3)
A 		2.8
(-3)
A 		9.7
(-3)
A 		90.3
(-2.9)
P 		5029.8
(3)
P 		675.9
(-2.2)
P 		5027
avr 21.8
(-3) 		10.4
(-3) 		8.5
(-3) 		113.8
(-2.9) 		4407.3
(3) 		890.5
(-1.8) 		4399
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188335_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9517
Sequence Type Exemplar sequence
Representative Public ID T05A1.2 NCBI
Target Description T05A1.2 /REP_DB=WormBase Gene ID /WP=CE03622 /TR=Q22183 /GB=CAA92476.1 /SUBMIT=HINXTON /CHR=4 /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_069299(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069299 NCBI Caenorhabditis elegans T05A1.2 (collagen) mRNA, complete cds. 11/11 None
SNAP00000033943 ENSEMBL cdna:SNAP chromosome:CEL140:IV:9563329:9564373:1 11/11 None
GENEFINDER00000033946 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:9563365:9564373:1 11/11 None
T05A1.2 ENSEMBL cdna:known chromosome:CEL140:IV:9563342:9564418:1 gene:T05A1.2 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
chrIV:9563370-9564379(+) 85.6 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-122
Ensembl T05A1.2
Entrez Gene 177789 Entrez gene
SwissProt Q22183 EMBL-EBI
WormBase CE03622 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 CAA92476 Hypothetical protein T05A1.2 [Caenorhabditis elegans] ref|NP_501700.1| T05A1.2 [Caenorhabditis elegans] 1.0E-56
blast CAE72779 Hypothetical protein CBG20034 [Caenorhabditis briggsae] 1.0E-53
blast CAE56383 Hypothetical protein CBG24065 [Caenorhabditis briggsae] emb|CAE57041.1| Hypothetical protein CBG24927 [Caenorhabditis briggsae] 6.0E-23
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 4.6E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.5E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.6E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-13
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 4.6E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.5E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.6E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_501700.1 1 13-35
T05A1.2 1 13-35
SNAP00000033943 1 23-45
GENEFINDER00000033946 1 13-35
Sequence
Target Sequence 
>C. ELEGANS:188335_AT
caggagcacaatagctgcgacggatgctgcttgccaggagccgctggatcagtcggagct
gccggacgcccaggaactccaggacgcccaggtgcaccaggagccccaggacacccagga
aagccaccacagtcaccatgtgaaccattaaccccaccaccatgcccagcttgcccacca
gggccaccaggagctccaggagcaccaggaaagccaggatccgagggaccaccaggacca
ccagggcacgatggaccaaatggaggaccaggacaaccaggacaaccaggaccacacgga
ccaaacggacacccaggaaagccaggatcccaaggaccaccaggaccaccaggacactcc
gacgagccaaagccaggacaac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAGGAGCACAATAGCTGCGACGGAT 402 209 286 Antisense
GCACAATAGCTGCGACGGATGCTGC 259 317 291 Antisense
AATAGCTGCGACGGATGCTGCTTGC 207 171 295 Antisense
CCAGGAGCCGCTGGATCAGTCGGAG 65 273 319 Antisense
CGCTGGATCAGTCGGAGCTGCCGGA 91 255 327 Antisense
CCACAGTCACCATGTGAACCATTAA 336 275 412 Antisense
GTCACCATGTGAACCATTAACCCCA 432 465 417 Antisense
TCACCATGTGAACCATTAACCCCAC 312 625 418 Antisense
GGAAAGCCAGGATCCGAGGGACCAC 123 527 493 Antisense
CTCCGACGAGCCAAAGCCAGGACAA 599 231 642 Antisense
TCCGACGAGCCAAAGCCAGGACAAC 380 587 643 Antisense
Sequence Source Affymetrix Proprietary Database