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[190446_s_at] collagen alpha (weak)

Description C31H2.2 /REP_DB=WormBase Gene ID /WP=CE04130 /TR=Q18345 /GB=AAA83336.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=collagen alpha (weak)
Cluster 6grp_highest_10_10 > 10      6grp_high1_10_10 > 23      6grp_highest_nonorm > 32      6grp_total > 03      4grp_total > 50      6grp_cgc > 51      6grp_high1_sub > 02      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 4940
1 2 3 4 range
A 56.5
(-3)
A 		4972.9
(3)
P 		3209.6
(0.9)
P 		38.5
(-3)
A 		4934
B 50.9
(-3)
A 		4395.6
(3)
P 		3477.9
(1.7)
P 		60.3
(-3)
A 		4345
C 78.1
(-2.9)
A 		4157.8
(3)
P 		3265.2
(1.7)
P 		33.2
(-3)
A 		4125
avr 61.8
(-3) 		4508.8
(3) 		3317.6
(1.4) 		44
(-3) 		4465

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1724
1 2 3 4 5 6 range
A 1269.4
(0.5)
P 		1933.1
(3)
P 		808.7
(-1.2)
P 		1646.1
(1.9)
P 		945.3
(-0.7)
P 		311.2
(-3)
P 		1622
B 961.2
(1.1)
P 		1141.7
(2.1)
P 		747.8
(-0)
P 		1297.6
(3)
P 		787.9
(0.2)
P 		209.5
(-3)
P 		1088
C 1507.1
(3)
P 		955.9
(0.4)
P 		1149.1
(1.3)
P 		1059.2
(0.9)
P 		1359
(2.3)
P 		215.8
(-3)
P 		1291
avr 1245.9
(2.5) 		1343.6
(3) 		901.9
(0.6) 		1334.3
(2.9) 		1030.7
(1.3) 		245.5
(-3) 		1098
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1190
1 2 3 4 range
A 20.6
(-2.9)
A 		1079.5
(3)
P 		839.1
(1.7)
P 		5.6
(-3)
A 		1074
B 16.2
(-3)
A 		1085.6
(3)
P 		805.9
(1.4)
P 		12.9
(-3)
A 		1073
C 25.9
(-2.9)
A 		1195.4
(3)
P 		1138
(2.7)
P 		5.6
(-3)
A 		1190
avr 20.9
(-2.9) 		1120.2
(3) 		927.7
(2) 		8
(-3) 		1112

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 615
1 2 3 4 5 6 range
A 234
(-1.4)
P 		687.5
(3)
P 		176.1
(-2)
P 		417.5
(0.4)
P 		285.2
(-0.9)
P 		75.8
(-3)
P 		612
B 334.5
(2.1)
P 		380
(3)
P 		181.6
(-0.9)
P 		343.7
(2.3)
P 		320.1
(1.8)
P 		78.1
(-3)
P 		302
C 558.6
(3)
P 		291.7
(-0.3)
P 		292.5
(-0.3)
P 		213
(-1.3)
P 		439.7
(1.5)
P 		72.2
(-3)
P 		486
avr 375.7
(1.8) 		453.1
(3) 		216.7
(-0.8) 		324.7
(1) 		348.3
(1.3) 		75.4
(-3) 		378
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 190446_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16004
Sequence Type Exemplar sequence
Representative Public ID C31H2.2 NCBI
Target Description C31H2.2 /REP_DB=WormBase Gene ID /WP=CE04130 /TR=Q18345 /GB=AAA83336.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=collagen alpha (weak)
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_076472(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076472 NCBI Caenorhabditis elegans DumPY : shorter than wild-type family member (dpy-8) (dpy-8) mRNA, complete cds. 11/11 None
SNAP00000008495 ENSEMBL cdna:SNAP chromosome:CEL140:X:5148881:5150399:-1 11/11 None
GENEFINDER00000008500 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:5148881:5150399:-1 11/11 None
C31H2.2 ENSEMBL cdna:known chromosome:CEL140:X:5148819:5150443:-1 gene:C31H2.2 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
chrX:5148881-5150400(-) 97.13 100.0
Public Domain and Genome References
Gene Title collagen alpha (weak)
Gene Symbol dpy-8
Ensembl C31H2.2
Entrez Gene 180785 Entrez gene
SwissProt Q18345 EMBL-EBI
WormBase CE04130 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 AAA83336 Dumpy : shorter than wild-type protein 8 [Caenorhabditis elegans] ref|NP_508873.1| DumPY : shorter than wild-type family member (dpy-8) [Caenorhabditis elegans] 9.0E-83
blast CAE68699 Hypothetical protein CBG14618 [Caenorhabditis briggsae] 4.0E-56
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 4.8E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0010
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.3E-9
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_508873.1 1 7-29
C31H2.2 1 7-29
SNAP00000008495 1 7-29
GENEFINDER00000008500 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:190446_S_AT
ggagatcctggaatgccagcctcatactgtccatctgactgcggagttcaaccgattctc
actgaaatgttcccaacaccattcaccccaactgccggatattctaacatgcaaagacca
gctgctccatctcgtccacttgctcacccagaatacgctgacggatctgctccagctcac
cttccacattctggagcttctgattctgccgctgcttctgaggtagatgctccagcacca
catcaacatcgcaaaagccatcgtcttagaccttcccatcagcaacaatatggagatgag
caaaataacgctgtcgccgacgccggccgctcagtaaatgctccagaatacggagacgga
tctgccccatcccacatgccaagtcacagagcacatcatcatccaaattcagcttctca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAGATCCTGGAATGCCAGCCTCAT 490 517 811 Antisense
CTCATACTGTCCATCTGACTGCGGA 226 229 831 Antisense
ACTGCGGAGTTCAACCGATTCTCAC 293 97 848 Antisense
TGAAATGTTCCCAACACCATTCACC 81 573 873 Antisense
CCCCAACTGCCGGATATTCTAACAT 25 261 896 Antisense
ACTTGCTCACCCAGAATACGCTGAC 233 105 948 Antisense
CATTCTGGAGCTTCTGATTCTGCCG 241 217 997 Antisense
TGCCGCTGCTTCTGAGGTAGATGCT 430 585 1017 Antisense
GCAAAAGCCATCGTCTTAGACCTTC 406 317 1061 Antisense
CATCCCACATGCCAAGTCACAGAGC 670 211 1178 Antisense
ATCATCATCCAAATTCAGCTTCTCA 191 31 1205 Antisense
Sequence Source Affymetrix Proprietary Database