[Home] | [Total List]

[173518_s_at]

Description C69682 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C34D4.15 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C69682 /WB_GENE_ID=C34D4.15 /WP=CE17509 /CHR=4 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk368c2 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 99      6grp_high1_10_10 > 91      6grp_highest_nonorm > 74      6grp_total > 93      4grp_total > 49      6grp_cgc > 88      6grp_high1_sub > 05      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 805
1 2 3 4 range
A 33.6
(-3)
A 		553.8
(1.8)
P 		678.3
(3)
P 		47.1
(-2.9)
A 		645
B 107.1
(-2.5)
A 		838.8
(3)
P 		831.4
(2.9)
P 		44.1
(-3)
A 		795
C 54.3
(-3)
A 		767.2
(3)
P 		645.6
(2)
P 		58.9
(-3)
A 		713
avr 65
(-2.9) 		719.9
(3) 		718.4
(3) 		50
(-3) 		670

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 922
1 2 3 4 5 6 range
A 382.4
(-3)
P 		618.5
(-0.9)
P 		520
(-1.8)
P 		671.5
(-0.4)
P 		1048.9
(3)
P 		673.5
(-0.4)
P 		667
B 533.1
(-2.6)
P 		576.3
(-2.2)
P 		493.8
(-3)
P 		610.4
(-1.9)
P 		1149.9
(3)
P 		630
(-1.8)
P 		656
C 742.4
(-0.6)
P 		561.4
(-1.8)
P 		377
(-3)
P 		525.3
(-2)
P 		1298.9
(3)
P 		631.8
(-1.3)
P 		922
avr 552.6
(-2.2) 		585.4
(-2) 		463.6
(-3) 		602.4
(-1.8) 		1165.9
(3) 		645.1
(-1.4) 		702
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 218
1 2 3 4 range
A 12.2
(-2.8)
A 		120.2
(1)
P 		177.3
(3)
P 		6.9
(-3)
A 		170
B 34.1
(-2.3)
A 		207.2
(3)
P 		192.7
(2.6)
P 		9.4
(-3)
A 		198
C 18
(-2.8)
A 		220.6
(2.9)
P 		225
(3)
P 		9.9
(-3)
A 		215
avr 21.4
(-2.6) 		182.7
(2.5) 		198.3
(3) 		8.7
(-3) 		190

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 397
1 2 3 4 5 6 range
A 70.5
(-3)
P 		220
(0.6)
P 		113.2
(-2)
P 		170.3
(-0.6)
P 		316.5
(3)
P 		164
(-0.7)
P 		246
B 185.5
(-1.9)
P 		191.8
(-1.8)
P 		119.9
(-3)
P 		161.7
(-2.3)
P 		467.2
(3)
P 		234.9
(-1)
P 		347
C 275.2
(0.3)
P 		171.3
(-1.6)
P 		95.9
(-3)
P 		105.6
(-2.8)
P 		420.3
(3)
P 		211.5
(-0.9)
P 		324
avr 177.1
(-1.6) 		194.4
(-1.3) 		109.7
(-3) 		145.9
(-2.3) 		401.3
(3) 		203.5
(-1.1) 		292
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173518_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24819
Sequence Type Exemplar sequence
Representative Public ID C69682 NCBI
Target Description C69682 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C34D4.15 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C69682 /WB_GENE_ID=C34D4.15 /WP=CE17509 /CHR=4 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk368c2 : 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_068722(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068722 NCBI Caenorhabditis elegans COLlagen family member (col-113) (col-113) mRNA, complete cds. 11/11 None
SNAP00000003805 ENSEMBL cdna:SNAP chromosome:CEL140:IV:7150677:7152473:-1 11/11 None
GENEFINDER00000003812 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:7150677:7152473:-1 11/11 None
C34D4.15 ENSEMBL cdna:known chromosome:CEL140:IV:7150658:7152473:-1 gene:C34D4.15 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
chrIV:7150683-7152480(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol col-113
Ensembl C34D4.15
Entrez Gene 177487 Entrez gene
SwissProt Q18450 EMBL-EBI
WormBase CE17509 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 AAB00702 Collagen protein 113 [Caenorhabditis elegans] ref|NP_501123.1| COLlagen family member (col-113) [Caenorhabditis elegans] 1.0E-132
blast CAE61814 Hypothetical protein CBG05782 [Caenorhabditis briggsae] 1.0E-126
blast CAE69231 Hypothetical protein CBG15273 [Caenorhabditis briggsae] 2.0E-23
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.3E-20
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.9E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.9E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.8E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.1E-4
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_501123.1 1 9-31
C34D4.15 1 9-31
SNAP00000003805 1 9-31
GENEFINDER00000003812 1 9-31
Sequence
Target Sequence 
>C. ELEGANS:173518_S_AT
acccgtgaccattgatccaacgaaaggatgcagagtgtgcccgaacggaccacgtggacc
aactggaccacctggagaaactgggccatctggaccagaaggaccaccaggaaacccagg
aagaattggagaacatggacgtgaaggatatccaggacaacaaggaattcctggtgaacc
agggaagcctggaaaacttggagaagctggaccaaatggaagagatggaacacgtggaca
aaagggaccaattggaccaaaaggagattcaggaccaccaggacaaaagggtccatctgg
atatccaggtagagatggacaacgaggtaatgacggagaaagtgggccagttggaccatc
aggacaattgggaatgccaggagagccaggacaaattggaatggttggagcaccaggagc
accaggacaagatgccagttattgtaaatgtccagagagaaatgctggagtcaacaagtt
tgagcctccaccaattgagcaaccgagttatgagccacaaccgtcaacttctcagccggc
cacctacgctccagctccagcaactccaggaccagacgcagctgttgaagctccacgatc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACCCGTGACCATTGATCCAACGAAA 261 91 430 Antisense
AAGGATGCAGAGTGTGCCCGAACGG 89 161 453 Antisense
ACCTGGAGAAACTGGGCCATCTGGA 230 85 499 Antisense
AAAGGGTCCATCTGGATATCCAGGT 439 121 715 Antisense
AAGTGGGCCAGTTGGACCATCAGGA 172 159 769 Antisense
GATGCCAGTTATTGTAAATGTCCAG 309 413 860 Antisense
GAGTCAACAAGTTTGAGCCTCCACC 36 401 897 Antisense
AAGTTTGAGCCTCCACCAATTGAGC 407 155 905 Antisense
GAGCAACCGAGTTATGAGCCACAAC 172 391 926 Antisense
CTCCAGGACCAGACGCAGCTGTTGA 523 235 993 Antisense
ACGCAGCTGTTGAAGCTCCACGATC 631 91 1005 Antisense
Sequence Source Affymetrix Proprietary Database