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[171768_x_at]

Description CEK056F9R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=B0222.6 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D65444 /WB_GENE_ID=B0222.6 /WP=CE06697 /CHR=5 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk56f9 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 15      6grp_high1_10_10 > 40      4grp_highest_8_8 > 16      4grp_high_8_8 > 52      6grp_highest_nonorm > 09      6grp_total > 51      4grp_total > 59      6grp_highest_sub > 03      6grp_cgc > 82      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 50780
1 2 3 4 range
A 34917.7
(0.9)
P 		52184.8
(3)
P 		52371.6
(3)
P 		2044.1
(-3)
P 		50328
B 36045.7
(1)
P 		45713.6
(2.2)
P 		52569.2
(3)
P 		1789.4
(-3)
P 		50780
C 34102.3
(2)
P 		40773.6
(3)
P 		37633.3
(2.5)
P 		2396.6
(-3)
P 		38377
avr 35021.9
(1.3) 		46224
(2.8) 		47524.7
(3) 		2076.7
(-3) 		45448

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 26697
1 2 3 4 5 6 range
A 47710.8
(0.7)
P 		42148.2
(-1.1)
P 		55311.5
(3)
P 		44506.3
(-0.3)
P 		35900.1
(-3)
P 		37500.3
(-2.5)
P 		19411
B 36802.1
(-1.1)
P 		40794.7
(0.1)
P 		51185.9
(3)
P 		44212.8
(1)
P 		31030.5
(-2.7)
P 		29883.4
(-3)
P 		21303
C 34360.4
(-1.4)
P 		44024.5
(1.3)
P 		49987.4
(3)
P 		46934.9
(2.1)
P 		36708.2
(-0.7)
P 		28614.5
(-3)
P 		21373
avr 39624.4
(-0.7) 		42322.5
(0.1) 		52161.6
(3) 		45218
(0.9) 		34546.3
(-2.2) 		31999.4
(-3) 		20162
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 13392
1 2 3 4 range
A 12713.5
(2.6)
P 		11327.9
(1.9)
P 		13690.9
(3)
P 		299.2
(-3)
P 		13392
B 11494.7
(2.7)
P 		11290.2
(2.5)
P 		12181.5
(3)
P 		381.3
(-3)
P 		11800
C 11288.8
(2.1)
P 		11722.6
(2.3)
P 		13116.4
(3)
P 		404.1
(-3)
P 		12712
avr 11832.3
(2.4) 		11446.9
(2.3) 		12996.3
(3) 		361.5
(-3) 		12635

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 6195
1 2 3 4 5 6 range
A 8795.1
(-3)
P 		14990
(3)
P 		12045.7
(0.1)
P 		11287.9
(-0.6)
P 		10833.1
(-1)
P 		9130.1
(-2.7)
P 		6195
B 12805.3
(1.1)
P 		13578.8
(3)
P 		12429.5
(0.2)
P 		11710.4
(-1.6)
P 		12607.3
(0.6)
P 		11143.4
(-3)
P 		2435
C 12735.9
(2)
P 		13433.2
(3)
P 		12722.6
(1.9)
P 		9438.6
(-3)
P 		11878.2
(0.7)
P 		9578.9
(-2.8)
P 		3995
avr 11445.4
(-0.8) 		14000.7
(3) 		12399.3
(0.6) 		10812.3
(-1.7) 		11772.9
(-0.3) 		9950.8
(-3) 		4050
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171768_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.25125
Sequence Type Exemplar sequence
Representative Public ID CEK056F9R NCBI
Target Description CEK056F9R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=B0222.6 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D65444 /WB_GENE_ID=B0222.6 /WP=CE06697 /CHR=5 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk56f9 : 3prime 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_072973(11), NM_072975(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072973 NCBI Caenorhabditis elegans COLlagen family member (col-144) (col-144) mRNA, complete cds. 11/11 A 
NM_072975 NCBI Caenorhabditis elegans COLlagen family member (col-10) (col-10) mRNA, complete cds. 11/11 A 
SNAP00000023008 ENSEMBL cdna:SNAP chromosome:CEL140:V:9162280:9163212:-1 10/11 None
SNAP00000023010 ENSEMBL cdna:SNAP chromosome:CEL140:V:9166941:9167875:-1 10/11 None
GENEFINDER00000023016 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:9166941:9167875:-1 10/11 None
GENEFINDER00000023019 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:9162280:9163248:-1 10/11 None
B0222.6 ENSEMBL cdna:known chromosome:CEL140:V:9162221:9163248:-1 gene:B0222.6 11/11 A 
B0222.8 ENSEMBL cdna:known chromosome:CEL140:V:9166882:9167892:-1 gene:B0222.8 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_066413 1/11 Cross Hyb Matching Probes A 
NM_069125 1/11 Cross Hyb Matching Probes A 
NM_069126 1/11 Cross Hyb Matching Probes A 
NM_072974 1/11 Cross Hyb Matching Probes A 
NM_069971 1/11 Cross Hyb Matching Probes A 
NM_001029723 1/11 Cross Hyb Matching Probes None
NM_182455 1/11 Cross Hyb Matching Probes A 
NM_171268 1/11 Cross Hyb Matching Probes A 
NM_182305 1/11 Cross Hyb Matching Probes A 
NM_067693 1/11 Cross Hyb Matching Probes None
NM_059194 1/11 Cross Hyb Matching Probes A 
NM_073933 1/11 Cross Hyb Matching Probes A 
NM_001027491 1/11 Cross Hyb Matching Probes None
NM_077559 1/11 Cross Hyb Matching Probes A 
NM_077620 1/11 Cross Hyb Matching Probes A 
NM_062478 1/11 Cross Hyb Matching Probes A 
SNAP00000014505 1/11 Cross Hyb Matching Probes None
GENEFINDER00000014522 1/11 Cross Hyb Matching Probes None
SNAP00000005485 1/11 Cross Hyb Matching Probes None
GENEFINDER00000005498 1/11 Cross Hyb Matching Probes None
SNAP00000034500 1/11 Cross Hyb Matching Probes None
GENEFINDER00000034516 1/11 Cross Hyb Matching Probes None
SNAP00000032557 1/11 Cross Hyb Matching Probes None
GENEFINDER00000032568 1/11 Cross Hyb Matching Probes None
SNAP00000005654 1/11 Cross Hyb Matching Probes None
SNAP00000005655 1/11 Cross Hyb Matching Probes None
GENEFINDER00000005663 1/11 Cross Hyb Matching Probes None
GENEFINDER00000005664 1/11 Cross Hyb Matching Probes None
SNAP00000027314 1/11 Cross Hyb Matching Probes None
GENEFINDER00000027318 1/11 Cross Hyb Matching Probes None
SNAP00000036194 1/11 Cross Hyb Matching Probes None
GENEFINDER00000036201 1/11 Cross Hyb Matching Probes None
SNAP00000043808 1/11 Cross Hyb Matching Probes None
GENEFINDER00000043818 1/11 Cross Hyb Matching Probes None
SNAP00000011428 1/11 Cross Hyb Matching Probes None
GENEFINDER00000011431 1/11 Cross Hyb Matching Probes None
SNAP00000023009 1/11 Cross Hyb Matching Probes None
GENEFINDER00000023017 1/11 Cross Hyb Matching Probes None
GENEFINDER00000028425 1/11 Cross Hyb Matching Probes None
SNAP00000029185 1/11 Cross Hyb Matching Probes None
GENEFINDER00000029188 1/11 Cross Hyb Matching Probes None
SNAP00000037973 1/11 Cross Hyb Matching Probes None
GENEFINDER00000037983 1/11 Cross Hyb Matching Probes None
SNAP00000031753 1/11 Cross Hyb Matching Probes None
GENEFINDER00000031755 1/11 Cross Hyb Matching Probes None
F27C1.8 1/11 Cross Hyb Matching Probes A 
F11G11.11.2 1/11 Cross Hyb Matching Probes None
F09G8.6 1/11 Cross Hyb Matching Probes A 
K04H4.1a 1/11 Cross Hyb Matching Probes A 
Y77E11A.15 1/11 Cross Hyb Matching Probes A 
C34H4.4a 1/11 Cross Hyb Matching Probes None
C34H4.4b 1/11 Cross Hyb Matching Probes A 
T28C6.4 1/11 Cross Hyb Matching Probes A 
T28C6.6 1/11 Cross Hyb Matching Probes A 
F08G5.4 1/11 Cross Hyb Matching Probes A 
B0222.7 1/11 Cross Hyb Matching Probes A 
Y2H9A.3 1/11 Cross Hyb Matching Probes A 
T07H6.3b.3 1/11 Cross Hyb Matching Probes None
T10E10.5 1/11 Cross Hyb Matching Probes A 
C44C10.1 1/11 Cross Hyb Matching Probes A 
W03G11.1 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:9162242-9163250(-) 85.7 99.55
chrV:9166903-9167896(-) 81.12 94.97
Public Domain and Genome References
Gene Title

Gene Symbol col-144
col-10
Ensembl B0222.6
B0222.8
Entrez Gene 179296 Entrez gene
179298 Entrez gene
SwissProt Q17458 EMBL-EBI
Q17460 EMBL-EBI
WormBase CE30585 Wormbase
CE06699 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 AAA92325 Collagen protein 10 [Caenorhabditis elegans] ref|NP_505376.1| COLlagen family member (col-10) [Caenorhabditis elegans] 4.0E-58
blast CAE72121 Hypothetical protein CBG19217 [Caenorhabditis briggsae] 6.0E-56
blast AAA92324 Collagen protein 145 [Caenorhabditis elegans] ref|NP_505375.1| COLlagen family member (col-145) [Caenorhabditis elegans] 1.0E-55
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 5.6E-29
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.7E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.0E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.5E-9
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 7.7E-29
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.7E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.0E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.5E-9
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 5.6E-29
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505374.2 1 16-38
NP_505376.1 1 5-27
B0222.6 1 16-38
B0222.8 1 5-27
SNAP00000023008 1 5-27
SNAP00000023010 1 5-27
GENEFINDER00000023016 1 5-27
GENEFINDER00000023019 1 16-38
Sequence
Target Sequence 
>C. ELEGANS:171768_X_AT
gactgcgtcaagtgcccagaaggaccagctggaccagccggaccagaaggaccagccgga
ccagccggaccagacggacaaccaggagcaccaggaaacgctggaaacccaggatccgac
ggacaaccaggagccccaggagacaacggacaagacggagccccaggacaagacggacaa
ccaggagccccaggacaagacggacaacgtggatccggagccccaggaggaccaggagcc
ccaggaaacgctggaccagctggaccagccggacaagacggagccccaggacaagacgga
caaccaggaccagccggaccagctggacaagatggagccccaggaaacgctggatccgat
ggacaaccaggagccccaggaggaccaggacttccaggaaacgatgccgcttattgcgct
tgcccaccaagatccgctgtcttcgtctcccgccattagattggttcaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACTGCGTCAAGTGCCCAGAAGGAC 603 373 407 Antisense
GAAGGACCAGCTGGACCAGCCGGAC 187 333 425 Antisense
GGACCAGACGGACAACCAGGAGCAC 394 523 473 Antisense
AGGATCCGACGGACAACCAGGAGCC 226 57 517 Antisense
AACGCTGGACCAGCTGGACCAGCCG 272 145 653 Antisense
ACAAGACGGACAACCAGGACCAGCC 183 113 697 Antisense
GGACCAGCCGGACCAGCTGGACAAG 456 523 713 Antisense
GGATCCGATGGACAACCAGGAGCCC 209 511 758 Antisense
CCCAGGAGGACCAGGACTTCCAGGA 232 259 781 Antisense
AAACGATGCCGCTTATTGCGCTTGC 361 127 805 Antisense
GTCTCCCGCCATTAGATTGGTTCAA 493 469 851 Antisense
Sequence Source Affymetrix Proprietary Database