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[188132_at] collagen

Description M110.1 /REP_DB=WormBase Gene ID /WP=CE02274 /TR=Q21528 /GB=CAA90258.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 39      6grp_high1_10_10 > 93      4grp_high_8_8 > 38      6grp_highest_nonorm > 74      6grp_total > 84      4grp_total > 41      6grp_highest_sub > 04      6grp_cgc > 77      6grp_high1_sub > 04      6grp_cgc_sub > 04_05_06      6grp_total_sub > Hat      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1084
1 2 3 4 range
A 328.4
(-3)
P 		1390.6
(3)
P 		1054.8
(1.1)
P 		777.1
(-0.5)
P 		1062
B 310.4
(-3)
A 		1143.7
(3)
P 		1108.6
(2.7)
P 		740.5
(0.1)
P 		833
C 306.2
(-3)
M 		1026.4
(2.7)
P 		1069.4
(3)
P 		721.7
(0.3)
P 		763
avr 315
(-3) 		1186.9
(3) 		1077.6
(2.2) 		746.4
(-0) 		872

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 415
1 2 3 4 5 6 range
A 588.2
(-2.2)
P 		772.3
(1.4)
P 		546
(-3)
P 		845.6
(2.9)
P 		699.8
(0)
P 		852.5
(3)
P 		307
B 505.6
(-2.1)
P 		544
(-1)
P 		475.9
(-3)
P 		646
(2)
P 		679.3
(3)
P 		613.5
(1.1)
P 		203
C 618.4
(-2.2)
P 		576.2
(-3)
P 		890.6
(3)
P 		863.3
(2.5)
P 		776.2
(0.8)
P 		637.8
(-1.8)
P 		314
avr 570.7
(-3) 		630.8
(-1.3) 		637.5
(-1.1) 		785
(3) 		718.4
(1.1) 		701.3
(0.7) 		214
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 274
1 2 3 4 range
A 119.6
(-2.8)
P 		301.9
(3)
P 		275.8
(2.2)
P 		113.8
(-3)
P 		188
B 99
(-3)
A 		282.5
(3)
P 		256.9
(2.2)
P 		157.8
(-1.1)
P 		184
C 101.4
(-3)
M 		295.1
(1.3)
P 		372.7
(3)
P 		121.7
(-2.6)
P 		271
avr 106.7
(-3) 		293.2
(2.7) 		301.8
(3) 		131.1
(-2.2) 		195

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 168
1 2 3 4 5 6 range
A 108.4
(-3)
P 		274.7
(3)
P 		118.9
(-2.6)
P 		214.5
(0.8)
P 		211.2
(0.7)
P 		207.6
(0.6)
P 		166
B 175.9
(-0.7)
P 		181.1
(-0.5)
P 		115.6
(-3)
P 		171.1
(-0.9)
P 		276
(3)
P 		228.8
(1.2)
P 		160
C 229.2
(1.3)
P 		175.8
(-2.8)
P 		226.7
(1.1)
P 		173.6
(-3)
P 		251.2
(3)
P 		213.5
(0.1)
P 		78
avr 171.2
(-1.9) 		210.5
(0.7) 		153.7
(-3) 		186.4
(-0.9) 		246.1
(3) 		216.6
(1.1) 		92
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188132_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3057
Sequence Type Exemplar sequence
Representative Public ID M110.1 NCBI
Target Description M110.1 /REP_DB=WormBase Gene ID /WP=CE02274 /TR=Q21528 /GB=CAA90258.1 /SUBMIT=HINXTON /CHR=2 /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_063325(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063325 NCBI Caenorhabditis elegans M110.1 (collagen) mRNA, complete cds. 11/11 None
GENEFINDER00000006409 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:8201834:8207286:1 11/11 None
M110.1 ENSEMBL cdna:known chromosome:CEL140:II:8204261:8207391:1 gene:M110.1 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000006396 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:8204203-8207283(+) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-76
Ensembl M110.1
Entrez Gene 174320 Entrez gene
SwissProt Q21528 EMBL-EBI
WormBase CE35898 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 CAA90258 Hypothetical protein M110.1 [Caenorhabditis elegans] ref|NP_495726.2| M110.1 [Caenorhabditis elegans] 0.0
blast CAE57709 Hypothetical protein CBG00716 [Caenorhabditis briggsae] 1.0E-155
blast CAA91313 Hypothetical protein T05C12.10 [Caenorhabditis elegans] emb|CAA90265.2| Hypothetical protein T05C12.10 [Caenorhabditis elegans] ref|NP_495725.2| QUAhog (hedgehog related) family member (qua-1) [Caenorhabditis elegans] 1.0E-135
blast AAC48094 Dumpy : shorter than wild-type protein 9 [Caenorhabditis elegans] ref|NP_499889.2| DumPY : shorter than wild-type family member (dpy-9) [Caenorhabditis elegans] 1.0E-24
Protein Domains
Database ID Description E-Value
Pfam IPR001767 EMBL-EBI Peptidase C46, hedgehog protein, hint region 6.7E-40
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.4E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.1E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.9E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.0E-14
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.4E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.1E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.9E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.0E-14
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_495726.2 1 12-34
M110.1 1 12-34
GENEFINDER00000006409 1 411-433
Sequence
Target Sequence 
>C. ELEGANS:188132_AT
gagagttctctaatcaacagcctgcttcctacgaagagcaacctcccgtaatcaccacta
ccactacggagactgcaccagtttatactaatccaccagctcatcagccagtgcatcggt
ctttcccttcagctgaaccacggcaatctcataaaaattccccttcggtcccagtgccac
aagaacaatacaactctgcaaattctgaagtaattcccaagacaatcaactaccctgaca
ccataaatcaccaatcctataaacatgatggtgatgtaagtgtcgccggaactactgatg
atagtgaagacgttaacgtcatcccagctggacaatattctagccgacagtacgcttcaa
agacgaacaaaattggaaaagccgttcatttcggttattccaatgatcaactctcctctt
ttgtcccaatgggag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGAGTTCTCTAATCAACAGCCTGC 465 395 944 Antisense
ACAGCCTGCTTCCTACGAAGAGCAA 397 109 960 Antisense
GTTTATACTAATCCACCAGCTCATC 645 449 1024 Antisense
TCAGCTGAACCACGGCAATCTCATA 406 625 1072 Antisense
TTCGGTCCCAGTGCCACAAGAACAA 110 695 1107 Antisense
AACTACCCTGACACCATAAATCACC 238 139 1171 Antisense
GTAAGTGTCGCCGGAACTACTGATG 439 461 1219 Antisense
TTAACGTCATCCCAGCTGGACAATA 695 681 1256 Antisense
TATTCTAGCCGACAGTACGCTTCAA 533 663 1279 Antisense
TTATTCCAATGATCAACTCTCCTCT 257 679 1338 Antisense
CTCTCCTCTTTTGTCCCAATGGGAG 199 231 1354 Antisense
Sequence Source Affymetrix Proprietary Database