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[172902_x_at] cuticular collagen

Description F36A4.10 /REP_DB=WormBase Gene ID /WP=CE07185 /GEN=col-34 /TR=Q20087 /GB=AAA96155.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_highest_10_10 > 34      6grp_high1_10_10 > 42      4grp_highest_8_8 > 10      4grp_high_8_8 > 54      6grp_highest_nonorm > 16      6grp_total > 21      4grp_total > 57      6grp_highest_sub > 02_03      6grp_cgc > 73      6grp_high1_sub > 02_03      6grp_cgc_sub > 02_03      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 24286
1 2 3 4 range
A 3881.9
(-2.2)
P 		24717.7
(3)
P 		23307
(2.7)
P 		444.2
(-3)
P 		24274
B 4101.2
(-2)
P 		19750.9
(2.4)
P 		22080.9
(3)
P 		551.9
(-3)
P 		21529
C 3854.1
(-1.9)
P 		17859.3
(2.4)
P 		19819.7
(3)
P 		431.4
(-3)
P 		19388
avr 3945.7
(-2) 		20776
(2.7) 		21735.9
(3) 		475.8
(-3) 		21260

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 11612
1 2 3 4 5 6 range
A 4954.1
(-2.3)
P 		13640.5
(3)
P 		11247.5
(1.5)
P 		7066.9
(-1)
P 		7187.3
(-1)
P 		3867.9
(-3)
P 		9773
B 5108.1
(-2.2)
P 		11837
(1.5)
P 		14487.9
(3)
P 		5905
(-1.8)
P 		7134.9
(-1.1)
P 		3743.1
(-3)
P 		10745
C 5258.2
(-1.4)
P 		10845.3
(2.5)
P 		11568.3
(3)
P 		4842.8
(-1.6)
P 		6787.8
(-0.3)
P 		2875.6
(-3)
P 		8693
avr 5106.8
(-1.9) 		12107.6
(2.8) 		12434.6
(3) 		5938.2
(-1.4) 		7036.7
(-0.6) 		3495.5
(-3) 		8939
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 6843
1 2 3 4 range
A 1413.4
(-1.7)
P 		5365.5
(2.3)
P 		6092.9
(3)
P 		65
(-3)
P 		6028
B 1307.8
(-1.6)
P 		4878
(2.7)
P 		5116.6
(3)
P 		117.6
(-3)
P 		4999
C 1275.8
(-1.9)
P 		5134.7
(1.4)
P 		6907.8
(3)
P 		72.7
(-3)
P 		6835
avr 1332.3
(-1.7) 		5126.1
(2.1) 		6039.1
(3) 		85.1
(-3) 		5954

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3938
1 2 3 4 5 6 range
A 913.2
(-3)
P 		4851.2
(3)
P 		2449.5
(-0.7)
P 		1792.3
(-1.7)
P 		2168.8
(-1.1)
P 		941.7
(-3)
P 		3938
B 1777.4
(-2.1)
P 		3940
(3)
P 		3518.1
(2)
P 		1564
(-2.6)
P 		2898.8
(0.5)
P 		1395.8
(-3)
P 		2544
C 1949
(-0.5)
P 		3309.2
(3)
P 		2944.3
(2.1)
P 		973.9
(-3)
P 		2196.4
(0.2)
P 		962.6
(-3)
P 		2347
avr 1546.5
(-2.1) 		4033.5
(3) 		2970.6
(0.8) 		1443.4
(-2.3) 		2421.3
(-0.3) 		1100
(-3) 		2934
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172902_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11183
Sequence Type Exemplar sequence
Representative Public ID F36A4.10 NCBI
Target Description F36A4.10 /REP_DB=WormBase Gene ID /WP=CE07185 /GEN=col-34 /TR=Q20087 /GB=AAA96155.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cuticular 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_068119(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068119 NCBI Caenorhabditis elegans COLlagen family member (col-34) (col-34) mRNA, complete cds. 11/11 None
SNAP00000033255 ENSEMBL cdna:SNAP chromosome:CEL140:IV:4243579:4244580:-1 11/11 None
GENEFINDER00000033279 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:4243579:4244580:-1 11/11 None
F36A4.10 ENSEMBL cdna:known chromosome:CEL140:IV:4243541:4244603:-1 gene:F36A4.10 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_062965 1/11 Cross Hyb Matching Probes A 
NM_182248 1/11 Cross Hyb Matching Probes A 
NM_001027491 1/11 Cross Hyb Matching Probes None
NM_067468 1/11 Cross Hyb Matching Probes A 
SNAP00000000073 1/11 Cross Hyb Matching Probes None
GENEFINDER00000000088 1/11 Cross Hyb Matching Probes None
SNAP00000032557 1/11 Cross Hyb Matching Probes None
GENEFINDER00000032568 1/11 Cross Hyb Matching Probes None
GENEFINDER00000028017 1/11 Cross Hyb Matching Probes None
T14B4.7a.2 1/11 Cross Hyb Matching Probes A 
T14B4.7b.1 1/11 Cross Hyb Matching Probes None
T14B4.7b.2 1/11 Cross Hyb Matching Probes None
K04H4.1a 1/11 Cross Hyb Matching Probes A 
F29C4.8 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:4243584-4244586(-) 95.0 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-34
Ensembl F36A4.10
Entrez Gene 177188 Entrez gene
SwissProt P34687 EMBL-EBI
WormBase CE07185 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 CAE61462 Hypothetical protein CBG05354 [Caenorhabditis briggsae] 2.0E-41
blast AAA27985 alpha-collagen 2.0E-41
blast AAA96155 Collagen protein 34 [Caenorhabditis elegans] ref|NP_500520.1| COLlagen family member (col-34) [Caenorhabditis elegans] gb|AAL76233.1| cuticular collagen RAM-4 [Caenorhabditis elegans] sp|P34687|COL34_CAEEL Cuticle collagen 34 (Abnormal ray morphology protein 4) 2.0E-41
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.6E-14
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.9E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.6E-14
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_500520.1 1 12-34
F36A4.10 1 12-34
SNAP00000033255 1 12-34
GENEFINDER00000033279 1 12-34
Sequence
Target Sequence 
>C. ELEGANS:172902_X_AT
tccaggaccaccaggtccagctggaacgcctggaaagcctggacgcccaggtaagcctgg
agcaccgggacttcctggaaacccgggacgcccaccacagcagccatgcgagccgattac
cccaccaccatgcaagccgtgcccacaaggaccaccaggaccaccaggaccacctgggcc
accaggagattctggagagccaggatcaccaggacttccgggacaagacgctgcaccagg
agagccgggaccaaagggaccaccaggaccacctggagctccaggagcacctggaacacc
aggagagccaggagtgcccgcacaaagcgaaccactcatcccaggagagccaggaccacc
aggagaggccggaccgcaaggaccaccaggatccccaggacaaccaggagccgacggatc
accaggacaacccggaccaaagggaccaaatggaccagatggtcagccaggagccgat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCCAGGACCACCAGGTCCAGCTGGA 457 587 315 Antisense
CAGCTGGAACGCCTGGAAAGCCTGG 266 203 332 Antisense
GAAAGCCTGGACGCCCAGGTAAGCC 257 359 347 Antisense
GCCCAGGTAAGCCTGGAGCACCGGG 400 285 359 Antisense
GACCACCTGGGCCACCAGGAGATTC 89 385 482 Antisense
GGAGAGCCAGGATCACCAGGACTTC 484 519 508 Antisense
CAGGACTTCCGGGACAAGACGCTGC 86 209 524 Antisense
ACAAGACGCTGCACCAGGAGAGCCG 180 113 537 Antisense
CACTCATCCCAGGAGAGCCAGGACC 448 195 647 Antisense
AACCAGGAGCCGACGGATCACCAGG 1 149 716 Antisense
ACCAGATGGTCAGCCAGGAGCCGAT 195 85 768 Antisense
Sequence Source Affymetrix Proprietary Database