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[188311_s_at] collagen

Description F38A3.2 /REP_DB=WormBase Gene ID /WP=CE02214 /TR=Q20136 /GB=CAA90188.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 34      6grp_high1_10_10 > 33      4grp_highest_8_8 > 01      4grp_high_8_8 > 45      6grp_highest_nonorm > 06      6grp_total > 20      4grp_total > 50      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 24544
1 2 3 4 range
A 5987.5
(-1.7)
P 		25052.9
(3)
P 		19132.1
(1.5)
P 		643
(-3)
P 		24410
B 6304.5
(-1.3)
P 		20624.8
(3)
P 		18720.5
(2.4)
P 		531.2
(-3)
P 		20094
C 5940.3
(-1.5)
P 		21928.9
(3)
P 		18032.3
(1.9)
P 		508.7
(-3)
P 		21420
avr 6077.4
(-1.5) 		22535.5
(3) 		18628.3
(1.9) 		561
(-3) 		21975

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 14069
1 2 3 4 5 6 range
A 5393.4
(-2.8)
P 		16614.5
(3)
P 		9041.6
(-0.9)
P 		10663.7
(-0.1)
P 		5048.7
(-3)
P 		6320.5
(-2.3)
P 		11566
B 5401.2
(-1.7)
P 		11923.5
(3)
P 		9686.5
(1.4)
P 		6969.1
(-0.6)
P 		5497.1
(-1.7)
P 		3650.7
(-3)
P 		8273
C 9085.7
(0.7)
P 		10576.7
(1.6)
P 		13107.8
(3)
P 		5927.8
(-1.1)
P 		9734.3
(1.1)
P 		2546
(-3)
P 		10562
avr 6626.8
(-1.3) 		13038.2
(3) 		10612
(1.4) 		7853.5
(-0.5) 		6760
(-1.2) 		4172.4
(-3) 		8866
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 6219
1 2 3 4 range
A 2180.1
(-0.7)
P 		5438.3
(3)
P 		5001.5
(2.5)
P 		94.1
(-3)
P 		5344
B 2010.4
(-0.7)
P 		5093.8
(3)
P 		4338
(2.1)
P 		113.2
(-3)
P 		4981
C 1966.4
(-1.2)
P 		6304.7
(3)
P 		6284.8
(3)
P 		85.8
(-3)
P 		6219
avr 2052.3
(-0.9) 		5612.3
(3) 		5208.1
(2.6) 		97.7
(-3) 		5515

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5057
1 2 3 4 5 6 range
A 994.2
(-3)
P 		5908.9
(3)
P 		1969.1
(-1.8)
P 		2704.6
(-0.9)
P 		1523.5
(-2.4)
P 		1538.8
(-2.3)
P 		4915
B 1879.3
(-1.8)
P 		3968.8
(3)
P 		2352.2
(-0.7)
P 		1845.9
(-1.9)
P 		2233.4
(-1)
P 		1361.3
(-3)
P 		2608
C 3367.7
(3)
P 		3227.3
(2.7)
P 		3336.2
(2.9)
P 		1192.1
(-2.2)
P 		3149.9
(2.5)
P 		852.3
(-3)
P 		2515
avr 2080.4
(-1.4) 		4368.3
(3) 		2552.5
(-0.5) 		1914.2
(-1.7) 		2302.3
(-1) 		1250.8
(-3) 		3118
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188311_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2699
Sequence Type Exemplar sequence
Representative Public ID F38A3.2 NCBI
Target Description F38A3.2 /REP_DB=WormBase Gene ID /WP=CE02214 /TR=Q20136 /GB=CAA90188.1 /SUBMIT=HINXTON /CHR=2 /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_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 11/11 None
GENEFINDER00000020590 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:11015604:11016736:-1 11/11 None
F38A3.2 ENSEMBL cdna:known chromosome:CEL140:II:11015500:11016754:-1 gene:F38A3.2 11/11 A 
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:11015600-11016733(-) 94.46 100.0
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:188311_S_AT
tcaagccaccactcaatcatctggaggaagctgctgctcttgcaaggccggagcatctgg
accaccaggaccaccaggaactgacggatccgacggaaaggatggactttctggaccaga
cggacaaccaggagctgatgctgatccagaagccaccccatccgaggccgatttctgctt
cgactgcccagccggaccaccaggaccagccggaaacccaggaccaaagggaccatcagg
aaacgctggagccgacggacaaccaggagccccaggaaacgccggagccgctggagcccc
aggagccccaggaccagctggaccagacggacagccaggatctaccggacaagacggagc
cccaggagtcgtcgaggaggtcgctgtt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCAAGCCACCACTCAATCATCTGGA 700 631 312 Antisense
GCCACCACTCAATCATCTGGAGGAA 132 281 316 Antisense
TCTGGAGGAAGCTGCTGCTCTTGCA 697 607 331 Antisense
CTGCTGCTCTTGCAAGGCCGGAGCA 512 237 342 Antisense
TTGCAAGGCCGGAGCATCTGGACCA 700 701 351 Antisense
CACCAGGAACTGACGGATCCGACGG 490 199 383 Antisense
AAGGATGGACTTTCTGGACCAGACG 708 157 409 Antisense
AAGGGACCATCAGGAAACGCTGGAG 298 71 538 Antisense
CGGACAGCCAGGATCTACCGGACAA 253 243 639 Antisense
GCCAGGATCTACCGGACAAGACGGA 281 281 645 Antisense
AGGAGTCGTCGAGGAGGTCGCTGTT 606 55 675 Antisense
Sequence Source Affymetrix Proprietary Database