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[172735_x_at] collagen /// collagen /// collagen

Description T10E10.1 /REP_DB=WormBase Gene ID /WP=CE23970 /TR=Q22380 /GB=AAA80357.2 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 25      6grp_high1_10_10 > 41      4grp_highest_8_8 > 17      4grp_high_8_8 > 61      6grp_highest_nonorm > 09      6grp_total > 42      4grp_total > 59      6grp_highest_sub > 03      6grp_cgc > 81      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 45776
1 2 3 4 range
A 23772
(-0)
P 		46663.7
(3)
P 		45032.2
(2.8)
P 		1029.5
(-3)
P 		45634
B 25592.6
(0.4)
P 		37329.8
(2.1)
P 		44081.5
(3)
P 		887.7
(-3)
P 		43194
C 22944.2
(0.9)
P 		34444.5
(3)
P 		33161.4
(2.8)
P 		930.6
(-3)
P 		33514
avr 24102.9
(0.5) 		39479.3
(2.8) 		40758.4
(3) 		949.3
(-3) 		39809

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 32002
1 2 3 4 5 6 range
A 33414.8
(0.7)
P 		34065.6
(0.9)
P 		39932.8
(3)
P 		33100.6
(0.6)
P 		23413.6
(-2.8)
P 		22875.9
(-3)
P 		17057
B 25851
(-1.4)
P 		32341.6
(-0)
P 		47152.7
(3)
P 		29788.3
(-0.6)
P 		20839.3
(-2.4)
P 		17970.3
(-3)
P 		29182
C 25918.7
(-0.5)
P 		34475.7
(1.4)
P 		41478
(3)
P 		32160.8
(0.9)
P 		26066.7
(-0.5)
P 		15151.1
(-3)
P 		26327
avr 28394.8
(-0.6) 		33627.6
(0.7) 		42854.5
(3) 		31683.2
(0.2) 		23439.9
(-1.8) 		18665.8
(-3) 		24189
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 11622
1 2 3 4 range
A 8655.4
(1.4)
P 		10129.4
(2.2)
P 		11772.3
(3)
P 		150.7
(-3)
P 		11622
B 8161.3
(1.8)
P 		9219.6
(2.4)
P 		10214.7
(3)
P 		189.2
(-3)
P 		10026
C 7595.2
(0.9)
P 		9903
(2.1)
P 		11557.8
(3)
P 		156.9
(-3)
P 		11401
avr 8137.3
(1.3) 		9750.7
(2.2) 		11181.6
(3) 		165.6
(-3) 		11016

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7043
1 2 3 4 5 6 range
A 6159.8
(-2.5)
P 		12115.4
(3)
P 		8696.5
(-0.1)
P 		8395.1
(-0.4)
P 		7065.2
(-1.6)
P 		5569.6
(-3)
P 		6546
B 8994.9
(-0.1)
P 		10765.2
(2.1)
P 		11450.1
(3)
P 		7889.9
(-1.5)
P 		8466.7
(-0.8)
P 		6701
(-3)
P 		4749
C 9606.9
(2)
P 		10519.6
(3)
P 		10556.9
(3)
P 		6467.6
(-1.5)
P 		8434.8
(0.7)
P 		5072
(-3)
P 		5485
avr 8253.9
(-0.2) 		11133.4
(3) 		10234.5
(2) 		7584.2
(-1) 		7988.9
(-0.5) 		5780.9
(-3) 		5353
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172735_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16343
Sequence Type Exemplar sequence
Representative Public ID T10E10.1 NCBI
Target Description T10E10.1 /REP_DB=WormBase Gene ID /WP=CE23970 /TR=Q22380 /GB=AAA80357.2 /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_076658(11), NM_076659(11)
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_076658 NCBI Caenorhabditis elegans T10E10.2 (collagen) mRNA, complete cds. 11/11 A 
NM_076659 NCBI Caenorhabditis elegans T10E10.1 (collagen) mRNA, complete cds. 11/11 A 
SNAP00000029183 ENSEMBL cdna:SNAP chromosome:CEL140:X:6323444:6324349:1 11/11 None
GENEFINDER00000029193 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:6323444:6324349:1 11/11 None
SNAP00000029184 ENSEMBL cdna:SNAP chromosome:CEL140:X:6326344:6327249:1 11/11 None
GENEFINDER00000029190 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:6326344:6327249:1 11/11 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
T10E10.2.1 ENSEMBL cdna:known chromosome:CEL140:X:6323253:6324473:1 gene:T10E10.2 11/11 A 
T10E10.1 ENSEMBL cdna:known chromosome:CEL140:X:6326147:6327331:1 gene:T10E10.1 11/11 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_063961 1/11 Cross Hyb Matching Probes A 
NM_069466 1/11 Cross Hyb Matching Probes A 
NM_067504 1/11 Cross Hyb Matching Probes A 
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_059385 1/11 Cross Hyb Matching Probes A 
NM_072975 1/11 Cross Hyb Matching Probes A 
NM_001029722 6/11 Cross Hyb Matching Probes None
NM_001029723 6/11 Cross Hyb Matching Probes None
NM_182455 8/11 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
SNAP00000020589 1/11 Cross Hyb Matching Probes None
GENEFINDER00000020590 1/11 Cross Hyb Matching Probes None
SNAP00000034500 1/11 Cross Hyb Matching Probes None
GENEFINDER00000034516 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
SNAP00000023008 1/11 Cross Hyb Matching Probes None
SNAP00000023010 1/11 Cross Hyb Matching Probes None
GENEFINDER00000023016 1/11 Cross Hyb Matching Probes None
SNAP00000025313 1/11 Cross Hyb Matching Probes None
GENEFINDER00000025319 1/11 Cross Hyb Matching Probes None
SNAP00000029185 8/11 Cross Hyb Matching Probes None
GENEFINDER00000029188 8/11 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
SNAP00000003213 6/11 Cross Hyb Matching Probes None
GENEFINDER00000003228 6/11 Cross Hyb Matching Probes None
SNAP00000008288 1/11 Cross Hyb Matching Probes None
GENEFINDER00000008299 1/11 Cross Hyb Matching Probes None
SNAP00000031753 1/11 Cross Hyb Matching Probes None
GENEFINDER00000031755 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 
F38A3.2 1/11 Cross Hyb Matching Probes A 
F09G8.6 1/11 Cross Hyb Matching Probes A 
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
B0222.8 1/11 Cross Hyb Matching Probes A 
T07H6.3a 6/11 Cross Hyb Matching Probes A 
T07H6.3b.3 6/11 Cross Hyb Matching Probes None
T07H6.3b.2 6/11 Cross Hyb Matching Probes A 
T10E10.5 8/11 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:6326343-6327249(+) 95.7 100.0
chrX:6323443-6324349(+) 94.04 98.34
chrX:6331664-6332567(+) 92.6 96.91
chrX:6279972-6280878(+) 92.49 96.8
chrX:6329124-6330018(+) 91.5 95.81
Public Domain and Genome References
Gene Title collagen
collagen
collagen
Gene Symbol col-168
col-167
col-170
Ensembl T10E10.2
T10E10.1
T10E10.6
Entrez Gene 180907 Entrez gene
180908 Entrez gene
353462 Entrez gene
SwissProt Q22380 EMBL-EBI
Q22379 EMBL-EBI
Q86NE3 EMBL-EBI
WormBase CE23970 Wormbase
CE23969 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 AAO44907 Collagen protein 170 [Caenorhabditis elegans] ref|NP_872267.1| T10E10.6 [Caenorhabditis elegans] 4.0E-49
blast AAA80357 Collagen protein 168 [Caenorhabditis elegans] ref|NP_509060.1| T10E10.1 [Caenorhabditis elegans] 4.0E-47
blast CAE61240 Hypothetical protein CBG05040 [Caenorhabditis briggsae] 3.0E-46
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 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 IPR008160 EMBL-EBI Collagen triple helix repeat 1.7E-12
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 8.6E-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
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_872267.1 1 17-39
NP_509059.1 1 20-42
NP_509060.1 1 17-39
T10E10.2.1 1 20-42
T10E10.1 1 17-39
T10E10.6 1 17-39
SNAP00000029183 1 20-42
GENEFINDER00000029193 1 20-42
SNAP00000029184 1 17-39
GENEFINDER00000029190 1 17-39
SNAP00000029186 1 17-39
GENEFINDER00000029192 1 17-39
Sequence
Target Sequence 
>C. ELEGANS:172735_X_AT
tgaaggatcttccgttggacaccaaggaggatgctgcggatgtggagtatctgctgctgg
accaccaggagccccaggacaagacggagaagatggagctgatggacaaccaggagcccc
aggaaacgacggaccagacggaccagccgccactccagccccagctcacgagttctgctt
tgactgcccagccggaccaccaggaccagccggaccagctggaccaaagggaccaaacgg
aaactcaggatccgacggacagccaggagccccaggaaacaacggaaacgccggaggacc
aggagccccaggacaagccggacaagacggacacccaggaaacgccggagctccaggagc
cccaggaaaggtcaacgaggttccaggcccagccggagccccaggagccccaggaccaga
cggaccagctggaccagccggatccccaggagccccaggaaacccaggatcccaaggacc
acaaggaccagccggagacaacggaggagctggatccccaggacagccaggagccaacgg
agacaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGAAGGATCTTCCGTTGGACACCAA 527 575 297 Antisense
GTGGAGTATCTGCTGCTGGACCACC 291 491 338 Antisense
GAGCTGATGGACAACCAGGAGCCCC 315 387 392 Antisense
CAGCTCACGAGTTCTGCTTTGACTG 418 203 458 Antisense
GCCGGACCAGCTGGACCAAAGGGAC 378 283 505 Antisense
GGAAACTCAGGATCCGACGGACAGC 126 527 535 Antisense
GACAAGACGGACACCCAGGAAACGC 256 359 617 Antisense
GCTCCAGGAGCCCCAGGAAAGGTCA 447 297 646 Antisense
AGGACCAGACGGACCAGCTGGACCA 31 57 708 Antisense
ACCACAAGGACCAGCCGGAGACAAC 362 85 774 Antisense
GACAGCCAGGAGCCAACGGAGACAA 466 367 818 Antisense
Sequence Source Affymetrix Proprietary Database