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[194205_x_at] collagen

Description CEK120E2F /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F15H10.1 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D70537 /WB_GENE_ID=F15H10.1 /WP=CE05638 /CHR=5 /FEA=Genomic Cluster /GEN=col-12 /DEF=collagen; C.elegans cDNA clone yk120e2 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 08      6grp_high1_10_10 > 43      4grp_highest_8_8 > 10      4grp_high_8_8 > 54      6grp_highest_nonorm > 29      6grp_total > 10      4grp_total > 57      6grp_cgc > 65      6grp_high1_sub > 02      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 22019
1 2 3 4 range
A 4200.6
(-2)
P 		21903.8
(2.9)
P 		22274.3
(3)
P 		445.1
(-3)
P 		21829
B 4335.1
(-1.9)
P 		19200.7
(2.1)
P 		22440.5
(3)
P 		421.2
(-3)
P 		22019
C 4210.5
(-1.7)
P 		17403.7
(2.7)
P 		18183.4
(3)
P 		499
(-3)
P 		17684
avr 4248.7
(-1.9) 		19502.7
(2.6) 		20966.1
(3) 		455.1
(-3) 		20511

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 12457
1 2 3 4 5 6 range
A 6567.4
(-3)
P 		18031.4
(3)
P 		15313.6
(1.6)
P 		16118.8
(2)
P 		15626
(1.7)
P 		13596.2
(0.7)
P 		11464
B 5574.7
(-3)
P 		17196
(3)
P 		16986.2
(2.9)
P 		13784.6
(1.2)
P 		13795.7
(1.2)
P 		12336.8
(0.5)
P 		11621
C 7171.1
(-3)
P 		17831
(3)
P 		15636
(1.8)
P 		15069.7
(1.4)
P 		16701.7
(2.4)
P 		9917
(-1.5)
P 		10660
avr 6437.7
(-3) 		17686.1
(3) 		15978.6
(2.1) 		14991
(1.6) 		15374.5
(1.8) 		11950
(-0.1) 		11248
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 6272
1 2 3 4 range
A 1529.5
(-1.5)
P 		4754.7
(1.9)
P 		5822.9
(3)
P 		65.1
(-3)
P 		5758
B 1382.4
(-1.5)
P 		4742.1
(2.5)
P 		5200
(3)
P 		89.8
(-3)
P 		5110
C 1393.8
(-1.7)
P 		5003.7
(1.7)
P 		6337.5
(3)
P 		84.1
(-3)
P 		6253
avr 1435.2
(-1.6) 		4833.5
(2) 		5786.8
(3) 		79.7
(-3) 		5707

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5202
1 2 3 4 5 6 range
A 1210.6
(-3)
P 		6412.9
(3)
P 		3335
(-0.5)
P 		4088.1
(0.3)
P 		4715.2
(1)
P 		3310.2
(-0.6)
P 		5202
B 1939.7
(-3)
P 		5723.8
(3)
P 		4124.8
(0.5)
P 		3651.1
(-0.3)
P 		5605
(2.8)
P 		4600.3
(1.2)
P 		3784
C 2658
(-3)
P 		5440.8
(3)
P 		3979.6
(-0.2)
P 		3030.5
(-2.2)
P 		5404.4
(2.9)
P 		3319.8
(-1.6)
P 		2783
avr 1936.1
(-3) 		5859.2
(3) 		3813.1
(-0.1) 		3589.9
(-0.5) 		5241.5
(2.1) 		3743.4
(-0.2) 		3923
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 194205_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.25138
Sequence Type Exemplar sequence
Representative Public ID CEK120E2F NCBI
Target Description CEK120E2F /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F15H10.1 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D70537 /WB_GENE_ID=F15H10.1 /WP=CE05638 /CHR=5 /FEA=Genomic Cluster /GEN=col-12 /DEF=collagen; C.elegans cDNA clone yk120e2 : 5prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_073277(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073277 NCBI Caenorhabditis elegans F15H10.1 (collagen) mRNA, complete cds. 11/11 A 
F15H10.1.2 ENSEMBL cdna:known chromosome:CEL140:V:10426489:10427598:-1 gene:F15H10.1 11/11 A 
F15H10.1.1 ENSEMBL cdna:known chromosome:CEL140:V:10426489:10427674:-1 gene:F15H10.1 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_073276 7/11 Cross Hyb Matching Probes A 
NM_067504 2/11 Cross Hyb Matching Probes A 
NM_073882 1/11 Cross Hyb Matching Probes A 
NM_073883 2/11 Cross Hyb Matching Probes A 
NM_072673 1/11 Cross Hyb Matching Probes A 
SNAP00000015232 2/11 Cross Hyb Matching Probes None
GENEFINDER00000015234 2/11 Cross Hyb Matching Probes None
SNAP00000002816 7/11 Cross Hyb Matching Probes None
SNAP00000002817 8/11 Cross Hyb Matching Probes None
GENEFINDER00000002822 8/11 Cross Hyb Matching Probes None
GENEFINDER00000002824 7/11 Cross Hyb Matching Probes None
SNAP00000007051 1/11 Cross Hyb Matching Probes None
SNAP00000007052 2/11 Cross Hyb Matching Probes None
GENEFINDER00000007058 1/11 Cross Hyb Matching Probes None
GENEFINDER00000007063 2/11 Cross Hyb Matching Probes None
SNAP00000025313 1/11 Cross Hyb Matching Probes None
GENEFINDER00000025319 1/11 Cross Hyb Matching Probes None
K02D7.3 2/11 Cross Hyb Matching Probes A 
ZC513.8 1/11 Cross Hyb Matching Probes A 
F15H10.2 7/11 Cross Hyb Matching Probes A 
F57B1.3 1/11 Cross Hyb Matching Probes A 
F57B1.4.1 2/11 Cross Hyb Matching Probes A 
F57B1.4.3 2/11 Cross Hyb Matching Probes None
F57B1.4.2 2/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:10426499-10427593(-) 92.23 100.0
chrV:10423461-10424468(-) 83.49 91.27
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-12
Ensembl F15H10.1
Entrez Gene 179453 Entrez gene
SwissProt P20630 EMBL-EBI
WormBase CE05638 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 CAA98257 Hypothetical protein F15H10.1 [Caenorhabditis elegans] ref|NP_505678.1| F15H10.1 [Caenorhabditis elegans] sp|P20630|COL12_CAEEL Cuticle collagen 12 precursor emb|CAA35954.1| collagen [Caenorhabditis elegans] 4.0E-60
blast CAE64818 Hypothetical protein CBG09612 [Caenorhabditis briggsae] gb|AAB41793.1| cuticle collagen [Caenorhabditis briggsae] 2.0E-58
blast CAA98258 Hypothetical protein F15H10.2 [Caenorhabditis elegans] ref|NP_505677.1| F15H10.2 [Caenorhabditis elegans] sp|P20631|COL13_CAEEL Cuticle collagen 13 precursor emb|CAA35955.1| collagen [Caenorhabditis elegans] 2.0E-58
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.3E-14
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.6E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.0E-13
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.0E-7
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505678.1 1 19-41
F15H10.1.2 1 19-41
F15H10.1.1 1 19-41
Sequence
Target Sequence 
>C. ELEGANS:194205_X_AT
accagacagcttctgcttcgattgcccagctggaccaccaggaccatcaggagcaccagg
acaaaagggaccatcaggagctccaggagccccaggacaatctggaggagctgctcttcc
aggaccaccaggaccagctggaccaccaggaccagccggacaaccaggatccaacggaaa
cgccggagctccaggagccccaggacaagtcgtcgatgttccaggaactccaggaccagc
tggaccaccaggatcaccaggaccagccggagctccaggacaaccaggacaagccggatc
ttcccaaccaggaggcccaggaccacaaggagatgccggagcaccaggagccccaggagc
cccaggacaagctggagcaccaggacaagatggagagagtggatccgagggagcttgcga
tcactgcccaccaccacgtaccgctccaggatattaagcgcttcaatgacatctcatttg
attatctctgctttatctcatttgta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACCAGACAGCTTCTGCTTCGATTGC 182 87 508 Antisense
GACAATCTGGAGGAGCTGCTCTTCC 190 365 603 Antisense
GATCCAACGGAAACGCCGGAGCTCC 456 383 675 Antisense
GCCCCAGGACAAGTCGTCGATGTTC 625 285 704 Antisense
ATGTTCCAGGAACTCCAGGACCAGC 345 47 723 Antisense
GACAACCAGGACAAGCCGGATCTTC 503 365 786 Antisense
GAGGCCCAGGACCACAAGGAGATGC 270 405 819 Antisense
ACCACGTACCGCTCCAGGATATTAA 230 83 940 Antisense
ATTAAGCGCTTCAATGACATCTCAT 170 13 960 Antisense
GACATCTCATTTGATTATCTCTGCT 670 369 975 Antisense
TTATCTCTGCTTTATCTCATTTGTA 264 681 989 Antisense
Sequence Source Affymetrix Proprietary Database