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[172895_x_at] cuticular collagen

Description F30B5.1 /REP_DB=WormBase Gene ID /WP=CE04462 /GEN=dpy-13 /TR=SW:P17657 /GB=AAA83499.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_highest_10_10 > 25      6grp_high1_10_10 > 40      4grp_highest_8_8 > 17      4grp_high_8_8 > 61      6grp_highest_nonorm > 09      6grp_total > 52      4grp_total > 59      6grp_highest_sub > 03      6grp_cgc > 92      6grp_high1_sub > 03      6grp_cgc_sub > 03      6grp_total_sub > Hat      6grp_rule_based > S3      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 41830
1 2 3 4 range
A 24335.6
(0.3)
P 		42818.7
(3)
P 		37915.6
(2.3)
P 		1344.2
(-3)
P 		41475
B 18935.7
(0)
P 		28347.8
(1.6)
P 		36590.2
(3)
P 		988.8
(-3)
P 		35601
C 21759.6
(1.4)
P 		27715.7
(2.6)
P 		29401.1
(3)
P 		1139.3
(-3)
P 		28262
avr 21677
(0.7) 		32960.7
(2.7) 		34635.6
(3) 		1157.4
(-3) 		33478

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 25195
1 2 3 4 5 6 range
A 28503.4
(-2)
P 		34557
(-0.3)
P 		45914.7
(3)
P 		31409.3
(-1.2)
P 		27358
(-2.3)
P 		24971.9
(-3)
P 		20943
B 27507.9
(-1.3)
P 		30619.8
(-0.5)
P 		44709.8
(3)
P 		37929.7
(1.3)
P 		23091.7
(-2.4)
P 		20720
(-3)
P 		23990
C 26140.6
(-1)
P 		24729.2
(-1.5)
P 		36008.3
(3)
P 		31461
(1.2)
P 		28311.4
(-0.1)
P 		21022.6
(-3)
P 		14986
avr 27384
(-1.5) 		29968.7
(-0.7) 		42210.9
(3) 		33600
(0.4) 		26253.7
(-1.8) 		22238.2
(-3) 		19973
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 10055
1 2 3 4 range
A 8860.6
(2.4)
P 		9294.8
(2.6)
P 		9911.9
(3)
P 		196.8
(-3)
P 		9715
B 6038.4
(1.2)
P 		7001.3
(1.9)
P 		8478.8
(3)
P 		210.7
(-3)
P 		8268
C 7203
(1.2)
P 		7968.4
(1.6)
P 		10247.2
(3)
P 		192.1
(-3)
P 		10055
avr 7367.3
(1.6) 		8088.2
(2.1) 		9546
(3) 		199.9
(-3) 		9346

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7036
1 2 3 4 5 6 range
A 5254.4
(-3)
P 		12290.2
(3)
P 		9999.2
(1)
P 		7966.1
(-0.7)
P 		8255.5
(-0.4)
P 		6079.9
(-2.3)
P 		7036
B 9571.4
(0.5)
P 		10192
(1.7)
P 		10856.9
(3)
P 		10046.3
(1.4)
P 		9381.9
(0.2)
P 		7726.4
(-3)
P 		3131
C 9689.2
(3)
P 		7545.6
(-0.8)
P 		9164.7
(2.1)
P 		6326.8
(-3)
P 		9161.2
(2.1)
P 		7037.5
(-1.7)
P 		3362
avr 8171.7
(-0.6) 		10009.3
(3) 		10006.9
(3) 		8113.1
(-0.7) 		8932.9
(0.9) 		6947.9
(-3) 		3061
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172895_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11009
Sequence Type Exemplar sequence
Representative Public ID F30B5.1 NCBI
Target Description F30B5.1 /REP_DB=WormBase Gene ID /WP=CE04462 /GEN=dpy-13 /TR=SW:P17657 /GB=AAA83499.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cuticular 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_068118(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068118 NCBI Caenorhabditis elegans DumPY : shorter than wild-type family member (dpy-13) (dpy-13) mRNA, complete cds. 11/11 None
SNAP00000023158 ENSEMBL cdna:SNAP chromosome:CEL140:IV:4235624:4236640:1 11/11 None
GENEFINDER00000023159 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:4235624:4236640:1 11/11 None
F30B5.1 ENSEMBL cdna:known chromosome:CEL140:IV:4235607:4236694:1 gene:F30B5.1 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_067008 1/11 Cross Hyb Matching Probes A 
NM_067009 1/11 Cross Hyb Matching Probes A 
NM_063961 1/11 Cross Hyb Matching Probes A 
NM_067007 1/11 Cross Hyb Matching Probes A 
NM_001027492 1/11 Cross Hyb Matching Probes None
NM_001027491 1/11 Cross Hyb Matching Probes None
SNAP00000020589 1/11 Cross Hyb Matching Probes None
GENEFINDER00000020590 1/11 Cross Hyb Matching Probes None
SNAP00000036390 1/11 Cross Hyb Matching Probes None
GENEFINDER00000036401 1/11 Cross Hyb Matching Probes None
SNAP00000036391 1/11 Cross Hyb Matching Probes None
GENEFINDER00000036400 1/11 Cross Hyb Matching Probes None
SNAP00000036392 1/11 Cross Hyb Matching Probes None
GENEFINDER00000036395 1/11 Cross Hyb Matching Probes None
SNAP00000032557 1/11 Cross Hyb Matching Probes None
GENEFINDER00000032568 1/11 Cross Hyb Matching Probes None
F38A3.2 1/11 Cross Hyb Matching Probes A 
K04H4.1b 1/11 Cross Hyb Matching Probes A 
K04H4.1a 1/11 Cross Hyb Matching Probes A 
W05B2.6 1/11 Cross Hyb Matching Probes A 
W05B2.5 1/11 Cross Hyb Matching Probes A 
W05B2.1 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:4235629-4236646(+) 100.0 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol dpy-13
Ensembl F30B5.1
Entrez Gene 177187 Entrez gene
SwissProt P17657 EMBL-EBI
WormBase CE04462 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 NP_500519 DumPY : shorter than wild-type family member (dpy-13) [Caenorhabditis elegans] sp|P17657|DPY13_CAEEL Cuticle collagen dpy-13 (Dumpy-13 protein) gb|AAA83499.1| Dumpy : shorter than wild-type protein 13 [Caenorhabditis elegans] gb|AAA27994.1| collagen 1.0E-69
blast CAE61461 Hypothetical protein CBG05353 [Caenorhabditis briggsae] 2.0E-63
blast CAE61462 Hypothetical protein CBG05354 [Caenorhabditis briggsae] 4.0E-31
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.7E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.2E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.0E-12
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_500519.1 1 12-34
F30B5.1 1 12-34
SNAP00000023158 1 12-34
GENEFINDER00000023159 1 12-34
Sequence
Target Sequence 
>C. ELEGANS:172895_X_AT
aacttcgattccggatgcgagggatgctgccagccagggccacaaggagcgccaggagca
ccaggaaagccaggacgtccaggaaagccaggagcaccaggattcccaggaaacccagga
aaggccccacagaagccttgcgaggagatcaccccaccaccatgcaagccatgcccacaa
ggaccaccaggagccccaggacttccaggagaccagggagacaagggagaggccggacaa
ccaggacagccaggatctgacgccgctccaggagagcaaggaccaaagggaccaaacgga
gcaccaggaaagccaggagcaccaggagcaccaggagacgagggacttccagctgtctgc
gagccagtccaaaagggagagccaggatccaccggagagccaggaccagtcggaccacca
ggaccatccggacaaccaggaaacgacggaaccccaggacaacctggaccaaagggacca
ccaggaccagacggcaagccaggagccgacggaaacccaggacagccaggaccagtcgga
ccaccaggaaccccaggagagcgtggaatctgtccaaagtactgcgccatcgatgg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACTTCGATTCCGGATGCGAGGGAT 620 137 292 Antisense
GGAGCACCAGGAAAGCCAGGACGTC 616 519 346 Antisense
AAAGCCAGGAGCACCAGGATTCCCA 306 123 375 Antisense
GCCCCACAGAAGCCTTGCGAGGAGA 643 285 415 Antisense
CGGACAACCAGGACAGCCAGGATCT 369 243 525 Antisense
AGGAGACGAGGGACTTCCAGCTGTC 214 57 624 Antisense
ACCGGAGAGCCAGGACCAGTCGGAC 288 87 682 Antisense
AGGACCAGACGGCAAGCCAGGAGCC 41 57 774 Antisense
GCCAGGAGCCGACGGAAACCCAGGA 555 277 789 Antisense
CCACCAGGAACCCCAGGAGAGCGTG 252 271 832 Antisense
GTCCAAAGTACTGCGCCATCGATGG 558 475 863 Antisense
Sequence Source Affymetrix Proprietary Database