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[172746_x_at] collagen /// collagen

Description T07H6.3 /REP_DB=WormBase Gene ID /WP=CE04913 /TR=Q22326 /GB=AAA96223.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 24      6grp_high1_10_10 > 41      4grp_high_8_8 > 61      6grp_highest_nonorm > 09      6grp_total > 31      4grp_total > 59      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 39078
1 2 3 4 range
A 20149.6
(-0)
P 		39713.4
(3)
P 		37430.5
(2.6)
P 		762.7
(-3)
A 		38951
B 21093.8
(0.2)
P 		33215.6
(2)
P 		39518.5
(3)
P 		635
(-3)
P 		38884
C 19419.6
(0.7)
P 		31170.5
(3)
P 		30588.9
(2.9)
P 		839
(-3)
P 		30332
avr 20221
(0.3) 		34699.8
(2.8) 		35846
(3) 		745.6
(-3) 		35100

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 26456
1 2 3 4 5 6 range
A 25782.1
(0.2)
P 		30070.4
(1.2)
P 		37343.1
(3)
P 		27575.5
(0.6)
P 		12822.8
(-3)
P 		13531.5
(-2.8)
P 		24520
B 22731.1
(-0)
P 		27271.3
(1.3)
P 		33550
(3)
P 		26179
(1)
P 		13694.5
(-2.5)
P 		11962.1
(-3)
P 		21588
C 21308.6
(-0.3)
P 		30340.6
(2.1)
P 		33729.5
(3)
P 		24072
(0.5)
P 		19091.1
(-0.8)
P 		10887
(-3)
P 		22843
avr 23273.9
(-0.1) 		29227.4
(1.5) 		34874.2
(3) 		25942.2
(0.6) 		15202.8
(-2.2) 		12126.9
(-3) 		22747
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 10550
1 2 3 4 range
A 7336.5
(1.5)
P 		8620.7
(2.3)
P 		9785.1
(3)
P 		111.6
(-3)
A 		9674
B 6726.6
(1.4)
P 		8203.5
(2.4)
P 		9157.3
(3)
P 		135.3
(-3)
P 		9022
C 6428.4
(0.6)
P 		8961.7
(2)
P 		10661.2
(3)
P 		141.5
(-3)
P 		10520
avr 6830.5
(1.1) 		8595.3
(2.2) 		9867.9
(3) 		129.5
(-3) 		9738

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7400
1 2 3 4 5 6 range
A 4752.7
(-1.8)
P 		10694.5
(3)
P 		8132.5
(0.9)
P 		6993.8
(-0)
P 		3869.4
(-2.5)
P 		3294.5
(-3)
P 		7400
B 7909.3
(1.5)
P 		9077.5
(3)
P 		8147
(1.8)
P 		6933.9
(0.2)
P 		5563.9
(-1.6)
P 		4460.6
(-3)
P 		4617
C 7898.2
(1.5)
P 		9257.8
(3)
P 		8584.7
(2.3)
P 		4840.9
(-1.7)
P 		6177.6
(-0.3)
P 		3644.5
(-3)
P 		5613
avr 6853.4
(0.1) 		9676.6
(3) 		8288.1
(1.6) 		6256.2
(-0.5) 		5203.6
(-1.6) 		3799.9
(-3) 		5877
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172746_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16385
Sequence Type Exemplar sequence
Representative Public ID T07H6.3 NCBI
Target Description T07H6.3 /REP_DB=WormBase Gene ID /WP=CE04913 /TR=Q22326 /GB=AAA96223.1 /SUBMIT=ST.LOUIS /CHR=X /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_182467(9), NM_001029722(11), NM_001029723(11), NM_182455(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_182467 NCBI Caenorhabditis elegans T10E10.6 (collagen) mRNA, complete cds. 9/11 A 
NM_001029722 NCBI Caenorhabditis elegans COLlagen family member (col-166) (col-166) mRNA, complete cds. 11/11 None
NM_001029723 NCBI Caenorhabditis elegans COLlagen family member (col-166) (col-166) mRNA, complete cds. 11/11 None
NM_182455 NCBI Caenorhabditis elegans T10E10.5 (collagen) mRNA, complete cds. 9/11 A 
SNAP00000029185 ENSEMBL cdna:SNAP chromosome:CEL140:X:6329116:6330018:1 9/11 None
GENEFINDER00000029188 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:6329116:6330018:1 9/11 None
SNAP00000029186 ENSEMBL cdna:SNAP chromosome:CEL140:X:6331665:6332567:1 9/11 None
GENEFINDER00000029192 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:6331665:6332567:1 9/11 None
SNAP00000003213 ENSEMBL cdna:SNAP chromosome:CEL140:X:6279973:6280878:1 11/11 None
GENEFINDER00000003228 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:6279973:6280878:1 11/11 None
T07H6.3a ENSEMBL cdna:known chromosome:CEL140:X:6279632:6281028:1 gene:T07H6.3 11/11 None
T07H6.3b.3 ENSEMBL cdna:known chromosome:CEL140:X:6279789:6280878:1 gene:T07H6.3 11/11 None
T07H6.3b.2 ENSEMBL cdna:known chromosome:CEL140:X:6279972:6280878:1 gene:T07H6.3 11/11 None
T10E10.5 ENSEMBL cdna:known chromosome:CEL140:X:6329116:6330100:1 gene:T10E10.5 9/11 A 
T10E10.6 ENSEMBL cdna:known chromosome:CEL140:X:6331665:6332567:1 gene:T10E10.6 9/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_182468 1/11 Cross Hyb Matching Probes None
NM_069466 1/11 Cross Hyb Matching Probes A 
NM_067504 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_059385 1/11 Cross Hyb Matching Probes A 
NM_076658 8/11 Cross Hyb Matching Probes A 
NM_076659 7/11 Cross Hyb Matching Probes A 
NM_069706 1/11 Cross Hyb Matching Probes A 
NM_077559 1/11 Cross Hyb Matching Probes A 
NM_077873 1/11 Cross Hyb Matching Probes A 
NM_063181 1/11 Cross Hyb Matching Probes None
NM_182112 1/11 Cross Hyb Matching Probes B 
GENEFINDER00000044434 1/11 Cross Hyb Matching Probes None
SNAP00000044426 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
SNAP00000015232 1/11 Cross Hyb Matching Probes None
GENEFINDER00000015234 1/11 Cross Hyb Matching Probes None
SNAP00000037122 1/11 Cross Hyb Matching Probes None
GENEFINDER00000037126 1/11 Cross Hyb Matching Probes None
SNAP00000043526 1/11 Cross Hyb Matching Probes None
GENEFINDER00000043530 1/11 Cross Hyb Matching Probes None
SNAP00000025313 1/11 Cross Hyb Matching Probes None
GENEFINDER00000025319 1/11 Cross Hyb Matching Probes None
SNAP00000029183 8/11 Cross Hyb Matching Probes None
GENEFINDER00000029193 8/11 Cross Hyb Matching Probes None
SNAP00000029184 7/11 Cross Hyb Matching Probes None
GENEFINDER00000029190 7/11 Cross Hyb Matching Probes None
SNAP00000029187 1/11 Cross Hyb Matching Probes None
GENEFINDER00000029189 1/11 Cross Hyb Matching Probes None
SNAP00000037973 1/11 Cross Hyb Matching Probes None
GENEFINDER00000037983 1/11 Cross Hyb Matching Probes None
SNAP00000008288 1/11 Cross Hyb Matching Probes None
GENEFINDER00000008299 1/11 Cross Hyb Matching Probes None
T05E7.2 1/11 Cross Hyb Matching Probes A 
ZK1290.3a 1/11 Cross Hyb Matching Probes A B 
ZK1290.3b 1/11 Cross Hyb Matching Probes B 
K02D7.3 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 
C24F3.6 1/11 Cross Hyb Matching Probes None
C29F4.1.2 1/11 Cross Hyb Matching Probes None
C29F4.1.1 1/11 Cross Hyb Matching Probes None
T10E10.2.1 8/11 Cross Hyb Matching Probes A 
T10E10.1 7/11 Cross Hyb Matching Probes A 
T10E10.7 1/11 Cross Hyb Matching Probes None
C44C10.1 1/11 Cross Hyb Matching Probes A 
F54B11.2 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:6279631-6280878(+) 96.43 100.0
chrX:6323442-6324349(+) 77.01 80.59
chrX:6326403-6327249(+) 72.25 75.82
chrX:6329160-6330018(+) 72.53 76.1
Public Domain and Genome References
Gene Title collagen
collagen
Gene Symbol col-169
col-170
Ensembl T07H6.3
T10E10.5
T10E10.6
Entrez Gene 180909 Entrez gene
353462 Entrez gene
SwissProt Q86NE4 EMBL-EBI
Q86NE3 EMBL-EBI
WormBase CE25990 Wormbase
CE23972 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 AAA96223 Collagen protein 166, isoform a [Caenorhabditis elegans] ref|NP_001024893.1| COLlagen family member (col-166) [Caenorhabditis elegans] 1.0E-82
blast AAO44906 Collagen protein 169 [Caenorhabditis elegans] ref|NP_872255.1| T10E10.5 [Caenorhabditis elegans] 4.0E-50
blast AAO44907 Collagen protein 170 [Caenorhabditis elegans] ref|NP_872267.1| T10E10.6 [Caenorhabditis elegans] 4.0E-49
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.1E-17
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.6E-14
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.2E-12
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.1E-17
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.6E-14
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.2E-12
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.9E-17
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.7E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.6E-14
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.2E-12
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 8.6E-17
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_872267.1 1 17-39
NP_001024893.1 1 80-102
NP_001024894.1 1 17-39
NP_872255.1 1 17-39
T07H6.3a 1 80-102
T07H6.3b.3 1 17-39
T07H6.3b.2 1 17-39
T10E10.5 1 17-39
T10E10.6 1 17-39
SNAP00000029185 1 17-39
GENEFINDER00000029188 1 17-39
SNAP00000029186 1 17-39
GENEFINDER00000029192 1 17-39
SNAP00000003213 1 17-39
GENEFINDER00000003228 1 17-39
Sequence
Target Sequence 
>C. ELEGANS:172746_X_AT
gatgctgcggatgtggagtctctgctgctggaccaccaggagccccaggatccgatggag
aagatggagctgatggacaaccaggagcaccaggaaacgacggaccagatggaccagccg
ccaccccagccccagctcacgagttctgcttcgactgcccagccggaccaccaggaccag
ccggaccagctggaccaaagggaccaaacggaaactcaggatccgacggacagccaggag
ccccaggaaacaacggaaacgccggaggaccaggagccccaggacaagccggacaagacg
gacatccaggaaacgccggagctccaggagccccaggaaaggtcaacgaggttccaggcc
cagccggagccccaggagccccaggaccagacggaccagctggaccagccggatccccag
gagccccaggaaacccaggatcccaaggaccacaaggaccagccggagacaacggaggag
ctggatccccaggacagccaggagccaacggagacaatggagccgatggagagaccggag
ccc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATGCTGCGGATGTGGAGTCTCTGC 191 415 512 Antisense
GAGCCCCAGGATCCGATGGAGAAGA 81 387 551 Antisense
ACGACGGACCAGATGGACCAGCCGC 641 89 608 Antisense
GCCGGACCAGCTGGACCAAAGGGAC 376 283 691 Antisense
GGAAACTCAGGATCCGACGGACAGC 124 527 721 Antisense
GCTCCAGGAGCCCCAGGAAAGGTCA 445 297 832 Antisense
AGGACCAGACGGACCAGCTGGACCA 29 57 894 Antisense
ACCACAAGGACCAGCCGGAGACAAC 360 85 960 Antisense
GAGACAACGGAGGAGCTGGATCCCC 396 393 977 Antisense
GACAGCCAGGAGCCAACGGAGACAA 464 367 1004 Antisense
GGAGCCGATGGAGAGACCGGAGCCC 708 521 1030 Antisense
Sequence Source Affymetrix Proprietary Database