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[194252_x_at] collagen

Description C69078 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F38A3.2 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C69078 /WB_GENE_ID=F38A3.2 /WP=CE02214 /CHR=2 /FEA=Genomic Cluster /DEF=collagen; C.elegans cDNA clone yk310f1 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 34      6grp_high1_10_10 > 43      4grp_highest_8_8 > 09      4grp_high_8_8 > 53      6grp_highest_nonorm > 07      6grp_total > 20      4grp_total > 58      6grp_highest_sub > 02_03      6grp_cgc > 62      6grp_high1_sub > 02      6grp_cgc_sub > 02      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 31974
1 2 3 4 range
A 9695.6
(-1.3)
P 		32649.8
(3)
P 		27089.5
(2)
P 		811.9
(-3)
P 		31838
B 9367.4
(-1.2)
P 		25706.8
(2.3)
P 		28890
(3)
P 		675.4
(-3)
P 		28215
C 8643
(-1.1)
P 		25164.1
(3)
P 		22440
(2.3)
P 		750.5
(-3)
P 		24414
avr 9235.3
(-1.1) 		27840.2
(3) 		26139.8
(2.6) 		745.9
(-3) 		27094

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 15934
1 2 3 4 5 6 range
A 8748.9
(-2.8)
P 		20572
(3)
P 		14319.6
(-0.1)
P 		13198.6
(-0.6)
P 		8370
(-3)
P 		8777.4
(-2.8)
P 		12202
B 8740.1
(-1.9)
P 		17186.8
(3)
P 		15365.2
(1.9)
P 		10363.9
(-0.9)
P 		8336
(-2.1)
P 		6807.7
(-3)
P 		10379
C 10933.9
(0.1)
P 		16229.7
(2.7)
P 		16768.5
(3)
P 		10530.9
(-0.1)
P 		11819.9
(0.6)
P 		4638.5
(-3)
P 		12130
avr 9474.3
(-1.5) 		17996.2
(3) 		15484.4
(1.7) 		11364.5
(-0.5) 		9508.6
(-1.5) 		6741.2
(-3) 		11255
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 7702
1 2 3 4 range
A 3530.2
(-0.1)
P 		7087.4
(3)
P 		7081.7
(3)
P 		118.8
(-3)
P 		6969
B 2987.2
(-0.4)
P 		6349
(2.7)
P 		6694.5
(3)
P 		143.9
(-3)
P 		6551
C 2861.1
(-0.9)
P 		7234.8
(2.5)
P 		7821
(3)
P 		126.6
(-3)
P 		7694
avr 3126.2
(-0.5) 		6890.4
(2.7) 		7199.1
(3) 		129.8
(-3) 		7069

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5764
1 2 3 4 5 6 range
A 1612.8
(-3)
P 		7316.4
(3)
P 		3118.5
(-1.4)
P 		3347.5
(-1.2)
P 		2525.7
(-2)
P 		2137
(-2.4)
P 		5704
B 3041.1
(-2.1)
P 		5720.7
(3)
P 		3731.1
(-0.8)
P 		2745
(-2.6)
P 		3386.8
(-1.4)
P 		2538.6
(-3)
P 		3182
C 4052.7
(1.4)
P 		4952.2
(3)
P 		4267.9
(1.8)
P 		2117.8
(-2)
P 		3824.7
(1)
P 		1552.8
(-3)
P 		3399
avr 2902.2
(-1.7) 		5996.4
(3) 		3705.8
(-0.5) 		2736.8
(-2) 		3245.7
(-1.2) 		2076.1
(-3) 		3920
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 194252_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.23187
Sequence Type Exemplar sequence
Representative Public ID C69078 NCBI
Target Description C69078 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F38A3.2 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C69078 /WB_GENE_ID=F38A3.2 /WP=CE02214 /CHR=2 /FEA=Genomic Cluster /DEF=collagen; C.elegans cDNA clone yk310f1 : 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_063961(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063961 NCBI Caenorhabditis elegans F38A3.2 (collagen) mRNA, complete cds. 11/11 A 
SNAP00000020589 ENSEMBL cdna:SNAP chromosome:CEL140:II:11015604:11016736:-1 10/11 None
GENEFINDER00000020590 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:11015604:11016736:-1 10/11 None
F38A3.2 ENSEMBL cdna:known chromosome:CEL140:II:11015500:11016754:-1 gene:F38A3.2 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_069125 1/11 Cross Hyb Matching Probes A 
NM_069126 1/11 Cross Hyb Matching Probes A 
NM_069971 1/11 Cross Hyb Matching Probes A 
NM_058793 1/11 Cross Hyb Matching Probes A 
NM_063358 1/11 Cross Hyb Matching Probes A 
NM_069706 2/11 Cross Hyb Matching Probes A 
NM_077559 1/11 Cross Hyb Matching Probes A 
NM_078121 1/11 Cross Hyb Matching Probes None
SNAP00000038906 1/11 Cross Hyb Matching Probes None
GENEFINDER00000038915 1/11 Cross Hyb Matching Probes None
SNAP00000004358 1/11 Cross Hyb Matching Probes None
GENEFINDER00000004367 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
SNAP00000037122 2/11 Cross Hyb Matching Probes None
GENEFINDER00000037126 2/11 Cross Hyb Matching Probes None
SNAP00000043808 1/11 Cross Hyb Matching Probes None
GENEFINDER00000043818 1/11 Cross Hyb Matching Probes None
SNAP00000037973 1/11 Cross Hyb Matching Probes None
GENEFINDER00000037983 1/11 Cross Hyb Matching Probes None
T28F2.6 1/11 Cross Hyb Matching Probes A 
M195.1 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 
C29F4.1.2 2/11 Cross Hyb Matching Probes None
C29F4.1.1 2/11 Cross Hyb Matching Probes None
F08G5.4 1/11 Cross Hyb Matching Probes A 
C44C10.1 1/11 Cross Hyb Matching Probes A 
T10B10.1 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:11015516-11016734(-) 94.93 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol ram-2
Ensembl F38A3.2
Entrez Gene 174687 Entrez gene
SwissProt Q20136 EMBL-EBI
WormBase CE02214 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
42329 structural constituent of cuticle (sensu Nematoda) inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA90188 Hypothetical protein F38A3.2 [Caenorhabditis elegans] ref|NP_496362.1| F38A3.2 [Caenorhabditis elegans] 1.0E-67
blast CAE59586 Hypothetical protein CBG02987 [Caenorhabditis briggsae] 2.0E-65
blast CAA91290 Hypothetical protein M195.1 [Caenorhabditis elegans] ref|NP_495759.1| COLlagen family member (col-77) [Caenorhabditis elegans] 1.0E-39
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.5E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.4E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.3E-13
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.8E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_496362.1 1 21-43
F38A3.2 1 21-43
SNAP00000020589 1 21-43
GENEFINDER00000020590 1 21-43
Sequence
Target Sequence 
>C. ELEGANS:194252_X_AT
gctgatgctgatccagaagccaccccatccgaggccgatttctgcttcgactgcccagcc
ggaccaccaggaccagccggaaacccaggaccaaagggaccatcaggaaacgctggagcc
gacggacaaccaggagccccaggaaacgccggagccgctggagccccaggagccccagga
ccagctggaccagacggacagccaggatctaccggacaagacggagccccaggagtcgtc
gaggaggtcgctgttccagccggaccagccggagccccaggaccagccggagccccagga
gccgatggagccgccggagccccaggacagccaggacaagacggaccacaaggaccagct
ggagatgctggaagcgatggagccgccggacaaccaggagccgctggagagcaaggacca
gctggagagccaggagcaggaggaggctgcgatcactgcccaccaccaagaaccgctcca
ggatattagaatgttgttatcttctgacttcatttatgtatattttctgtgttctttctt
gt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCTGATGCTGATCCAGAAGCCACCC 540 295 446 Antisense
GAAACGCTGGAGCCGACGGACAACC 416 357 552 Antisense
GGACCAGCTGGACCAGACGGACAGC 315 523 623 Antisense
GACGGACAGCCAGGATCTACCGGAC 125 375 638 Antisense
CAAGACGGAGCCCCAGGAGTCGTCG 276 183 662 Antisense
AGGAGTCGTCGAGGAGGTCGCTGTT 607 55 676 Antisense
GGACAGCCAGGACAAGACGGACCAC 610 525 770 Antisense
AGACGGACCACAAGGACCAGCTGGA 299 71 784 Antisense
TGCTGGAAGCGATGGAGCCGCCGGA 61 583 811 Antisense
GCAGGAGGAGGCTGCGATCACTGCC 584 311 881 Antisense
GTATATTTTCTGTGTTCTTTCTTGT 282 453 963 Antisense
Sequence Source Affymetrix Proprietary Database