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[188368_at] collagen

Description ZK836.1 /REP_DB=WormBase Gene ID /WP=CE15415 /TR=Q23628 /GB=CAB01588.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_high1_10_10 > 80      6grp_total > 72      4grp_total > 57      6grp_cgc > 74      6grp_high1_sub > 02_03_04_05      6grp_cgc_sub > 02_03_04_05      6grp_total_sub > Hat      6grp_rule_based > S4      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2746
1 2 3 4 range
A 96.4
(-2.8)
P 		2238.8
(2.4)
P 		2472.8
(3)
P 		5.5
(-3)
A 		2467
B 68.5
(-2.9)
A 		2017.3
(1.4)
P 		2749.9
(3)
P 		4.7
(-3)
A 		2745
C 133.8
(-2.7)
P 		2090.2
(2.4)
P 		2342.2
(3)
P 		3.7
(-3)
A 		2339
avr 99.6
(-2.8) 		2115.4
(2) 		2521.6
(3) 		4.6
(-3) 		2517

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 819
1 2 3 4 5 6 range
A 190.4
(-2.8)
P 		910.6
(3)
P 		830.6
(2.4)
P 		836.7
(2.4)
P 		652.6
(0.9)
P 		164.1
(-3)
P 		747
B 219.5
(-1.9)
P 		636.4
(1.8)
P 		742.4
(2.8)
P 		766.3
(3)
P 		733.8
(2.7)
P 		91.5
(-3)
A 		675
C 222.7
(-2)
P 		719.5
(2.2)
P 		694.9
(2)
P 		706.6
(2.1)
P 		817
(3)
P 		108.2
(-3)
A 		709
avr 210.9
(-2.2) 		755.5
(2.9) 		756
(2.9) 		769.9
(3) 		734.5
(2.7) 		121.3
(-3) 		649
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 816
1 2 3 4 range
A 35.1
(-2.7)
P 		486
(1.5)
P 		646.4
(3)
P 		0.8
(-3)
A 		646
B 21.8
(-2.8)
A 		498.2
(1.7)
P 		637.2
(3)
P 		1
(-3)
A 		636
C 44.3
(-2.7)
P 		601
(1.4)
P 		816.3
(3)
P 		0.6
(-3)
A 		816
avr 33.7
(-2.7) 		528.4
(1.5) 		700
(3) 		0.8
(-3) 		699

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 290
1 2 3 4 5 6 range
A 35.1
(-3)
P 		323.9
(3)
P 		180.9
(0)
P 		212.2
(0.7)
P 		196.9
(0.4)
P 		39.9
(-2.9)
P 		289
B 76.4
(-2)
P 		211.8
(1)
P 		180.3
(0.3)
P 		203
(0.8)
P 		298.1
(3)
P 		34.1
(-3)
A 		264
C 82.5
(-1.8)
P 		219.5
(1.8)
P 		176.9
(0.7)
P 		142.1
(-0.2)
P 		264.4
(3)
P 		36.2
(-3)
A 		228
avr 64.7
(-2.2) 		251.7
(3) 		179.4
(1) 		185.8
(1.1) 		253.1
(3) 		36.7
(-3) 		216
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188368_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.14334
Sequence Type Exemplar sequence
Representative Public ID ZK836.1 NCBI
Target Description ZK836.1 /REP_DB=WormBase Gene ID /WP=CE15415 /TR=Q23628 /GB=CAB01588.1 /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_073660(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073660 NCBI Caenorhabditis elegans ZK836.1 (collagen) mRNA, complete cds. 11/11 None
SNAP00000005774 ENSEMBL cdna:SNAP chromosome:CEL140:V:12200098:12201156:-1 11/11 None
GENEFINDER00000005781 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:12200098:12201156:-1 11/11 None
ZK836.1 ENSEMBL cdna:known chromosome:CEL140:V:12200023:12201213:-1 gene:ZK836.1 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:12200097-12201156(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol lon-3
Ensembl ZK836.1
Entrez Gene 179673 Entrez gene
SwissProt Q23628 EMBL-EBI
WormBase CE15415 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 CAB01588 Hypothetical protein ZK836.1 [Caenorhabditis elegans] ref|NP_506061.1| ZK836.1 [Caenorhabditis elegans] gb|AAL08218.1| cuticle collagen protein LON-3 [Caenorhabditis elegans] gb|AAL76993.1| cuticle collagen LON-3 [Caenorhabditis elegans] sp|Q23628|LON3_CAEEL Cuticle collagen lon-3 precursor 1.0E-102
blast CAE75417 Hypothetical protein CBG23407 [Caenorhabditis briggsae] 8.0E-95
blast CAE59721 Hypothetical protein CBG03154 [Caenorhabditis briggsae] 6.0E-50
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.5E-22
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0013
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.8E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.4E-9
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_506061.1 1 7-29
ZK836.1 1 7-29
SNAP00000005774 1 7-29
GENEFINDER00000005781 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188368_AT
tacttgcccaacaggaccagacggagaagaaggagaacaaggtccagatggacaagatgg
agtggatggagtacctggatttgatggacaagattgcccagatgttgagcaacaaccatc
ccaaggatgcttcacctgcccacaaggccttccaggaccacaaggatcgcagggagctcc
aggaattcggggaatgcgtggagctcgtgggcagccaggatatccaggaagagatggtca
gccaggcatgcctggagagatgggaccgactggagccccaggagatgatggtgctccagg
agcttctggaatgaagggagacgatgcagagaaaccagttggcagacaaggacaacgtgg
acaaccaggagagcaaggaccggatggtgaagaaggaccagcaggaaaagacgcattcga
aggacctccaggtgttgaaggagaggtcggagttccaggataccaaggatctgccggacc
agatggagaggaaggaccacgtggaccatctggacttccaggaaaggatgctgagtactg
taagtgcccaacgcgtgacgacggaggcaacagcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TACTTGCCCAACAGGACCAGACGGA 461 639 375 Antisense
ACCATCCCAAGGATGCTTCACCTGC 210 85 489 Antisense
GGACCACAAGGATCGCAGGGAGCTC 364 523 529 Antisense
GGAGCTCGTGGGCAGCCAGGATATC 480 521 574 Antisense
AGATGGTCAGCCAGGCATGCCTGGA 449 67 606 Antisense
GAGAGATGGGACCGACTGGAGCCCC 395 393 629 Antisense
AGACGCATTCGAAGGACCTCCAGGT 145 71 783 Antisense
GAGAGGTCGGAGTTCCAGGATACCA 667 395 815 Antisense
CAGGATACCAAGGATCTGCCGGACC 382 207 830 Antisense
GTACTGTAAGTGCCCAACGCGTGAC 299 459 909 Antisense
ACGCGTGACGACGGAGGCAACAGCC 391 79 925 Antisense
Sequence Source Affymetrix Proprietary Database