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[188354_s_at]

Description C01G8.2 /REP_DB=WormBase Gene ID /WP=CE07802 /GEN=cln-3.2 /TR=P91012 /GB=AAB37639.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 58      6grp_high1_10_10 > 84      4grp_highest_8_8 > 43      4grp_high_8_8 > 24      6grp_highest_nonorm > 74      6grp_total > 75      4grp_total > 39      6grp_cgc > 67      6grp_cgc_sub > In      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 491
1 2 3 4 range
A 875.9
(3)
P 		384.5
(-3)
P 		576
(-0.7)
P 		630.2
(0)
P 		491
B 593.6
(3)
P 		494.8
(-3)
P 		515.9
(-1.7)
P 		550.3
(0.4)
P 		99
C 809
(3)
P 		550.8
(-2.7)
P 		586.5
(-1.9)
P 		536.5
(-3)
P 		273
avr 759.5
(3) 		476.7
(-3) 		559.5
(-1.2) 		572.3
(-1) 		283

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 236
1 2 3 4 5 6 range
A 601.9
(-0)
P 		555.7
(-3)
P 		640.8
(2.5)
P 		603
(0)
P 		649.2
(3)
P 		598.2
(-0.3)
P 		94
B 778.2
(3)
P 		617.4
(-3)
P 		691.5
(-0.2)
P 		712.9
(0.6)
P 		776.9
(3)
P 		726.2
(1.1)
P 		161
C 572.2
(-3)
P 		664
(-0.5)
P 		680.2
(-0.1)
P 		750.7
(1.9)
P 		584.1
(-2.7)
P 		791.9
(3)
P 		220
avr 650.8
(-0.5) 		612.4
(-3) 		670.8
(0.8) 		688.9
(1.9) 		670.1
(0.7) 		705.4
(3) 		93
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 235
1 2 3 4 range
A 318.9
(3)
P 		83.5
(-3)
P 		150.6
(-1.3)
P 		92.3
(-2.8)
P 		235
B 189.3
(3)
P 		122.2
(-2.6)
P 		119.5
(-2.8)
P 		117.3
(-3)
P 		72
C 267.8
(3)
P 		158.4
(-0.7)
P 		204.4
(0.9)
P 		90.5
(-3)
P 		177
avr 258.7
(3) 		121.4
(-2.2) 		158.2
(-0.8) 		100
(-3) 		159

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 205
1 2 3 4 5 6 range
A 111
(-3)
P 		197.6
(3)
P 		139.5
(-1)
P 		152.9
(-0.1)
P 		195.9
(2.9)
P 		145.6
(-0.6)
P 		87
B 270.8
(1.2)
P 		205.5
(-1.5)
P 		167.9
(-3)
P 		188.8
(-2.2)
P 		315.6
(3)
P 		270.8
(1.2)
P 		148
C 212.1
(0.2)
P 		202.6
(-0.3)
P 		173.1
(-1.8)
P 		151
(-3)
P 		189
(-1)
P 		265.1
(3)
P 		114
avr 198
(0.1) 		201.9
(0.4) 		160.2
(-3) 		164.2
(-2.7) 		233.5
(3) 		227.2
(2.5) 		73
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188354_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1580
Sequence Type Exemplar sequence
Representative Public ID C01G8.2 NCBI
Target Description C01G8.2 /REP_DB=WormBase Gene ID /WP=CE07802 /GEN=cln-3.2 /TR=P91012 /GB=AAB37639.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=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_059155(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059155 NCBI Caenorhabditis elegans human CLN (neuronal ceroid lipofuscinosis) related family member (cln-3.2) (cln-3.2) mRNA, complete cds. 11/11 None
GENEFINDER00000016702 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:5274663:5278701:-1 11/11 None
C01G8.2.1 ENSEMBL cdna:known chromosome:CEL140:I:5274699:5278710:-1 gene:C01G8.2 11/11 None
C01G8.2.2 ENSEMBL cdna:known chromosome:CEL140:I:5274773:5278711:-1 gene:C01G8.2 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000016690 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:5274772-5278701(-) 99.92 100.0
Public Domain and Genome References
Gene Title
Gene Symbol cln-3.2
Ensembl C01G8.2
Entrez Gene 172171 Entrez gene
SwissProt P91012 EMBL-EBI
WormBase CE07802 Wormbase
Functional Annotations
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
5765 lysosomal membrane inferred from sequence similarity QuickGO AmiGO
139 Golgi membrane inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB37639 Human cln (neuronal ceroid lipofuscinosis) related protein 3.2 [Caenorhabditis elegans] ref|NP_491556.1| human CLN (neuronal ceroid lipofuscinosis) related family member (cln-3.2) [Caenorhabditis elegans] gb|AAK38267.1| CLN-3.2 [Caenorhabditis elegans] 0.0
blast CAE67381 Hypothetical protein CBG12864 [Caenorhabditis briggsae] 0.0
blast CAB01140 Hypothetical protein F07B10.1 [Caenorhabditis elegans] ref|NP_505859.1| human CLN (neuronal ceroid lipofuscinosis) related family member (cln-3.1) [Caenorhabditis elegans] gb|AAK38269.1| CLN-3.1 [Caenorhabditis elegans] 2.0E-99
Protein Domains
Database ID Description E-Value
Pfam IPR003492 EMBL-EBI Battens disease protein Cln3 1.0E-126
Pfam IPR003492 EMBL-EBI Battens disease protein Cln3 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491556.1 8 15-37,66-88,119-141,148-170,185-202,344-363,367-389,402-424
C01G8.2.1 8 15-37,66-88,119-141,148-170,185-202,344-363,367-389,402-424
C01G8.2.2 8 15-37,66-88,119-141,148-170,185-202,344-363,367-389,402-424
GENEFINDER00000016702 8 15-37,66-88,117-139,146-168,183-200,342-361,365-387,400-422
Sequence
Target Sequence 
>C. ELEGANS:188354_S_AT
acattggaacgagtgctcccgttgctcaaatttatgattccattgatatcagtttatcta
gcagagtactatattaatcagggattgttggaattgctggaattcgactgtagccatggt
ttttcaatgagctcagagagccaatatagatggtttcaagttacctatcaacttggagta
tttatatctagatcttcatcaaactacgtcacaattccaacacaatatcttaaaagtcta
gctgttcttcagattttcaatgctggattcttcactataactgcaatctactcatttctt
cctcatattttgatcgcatttcttgtaattctttttgaaggattacttggaggagccagt
tatgttaacacgttccgtgctgttcataaagagattcccgccgattcccgagaattttcg
atgggcgttgtctcgatttcaga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACATTGGAACGAGTGCTCCCGTTGC 482 95 805 Antisense
GGAATTCGACTGTAGCCATGGTTTT 586 533 903 Antisense
GATCTTCATCAAACTACGTCACAAT 397 419 995 Antisense
AAGTCTAGCTGTTCTTCAGATTTTC 506 155 1038 Antisense
GCTGGATTCTTCACTATAACTGCAA 266 295 1066 Antisense
TAACTGCAATCTACTCATTTCTTCC 448 639 1082 Antisense
ATTTCTTCCTCATATTTTGATCGCA 174 17 1098 Antisense
CACGTTCCGTGCTGTTCATAAAGAG 686 197 1173 Antisense
TCATAAAGAGATTCCCGCCGATTCC 141 619 1188 Antisense
CCGCCGATTCCCGAGAATTTTCGAT 264 263 1202 Antisense
CGATGGGCGTTGTCTCGATTTCAGA 689 249 1223 Antisense
Sequence Source Affymetrix Proprietary Database