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[193098_at] intergral membrane protein

Description ZC190.1 /REP_DB=WormBase Gene ID /WP=CE27645 /GEN=cln-3.3 /TR=O76703 /GB=AAC26960.2 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=intergral membrane protein
Cluster 6grp_highest_10_10 > 32      6grp_high1_10_10 > 13      4grp_highest_8_8 > 51      4grp_high_8_8 > 32      6grp_highest_nonorm > 60      6grp_total > 24      4grp_total > 47      6grp_highest_sub > De      6grp_cgc > 33      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S2      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 480
1 2 3 4 range
A 711.5
(3)
P 		375.8
(-2.9)
P 		367.6
(-3)
P 		369.6
(-3)
P 		344
B 783.8
(3)
P 		373
(-2.1)
P 		303.7
(-3)
P 		365.1
(-2.2)
P 		480
C 733.6
(3)
P 		347.9
(-2.4)
P 		345
(-2.4)
P 		303.4
(-3)
P 		430
avr 743
(3) 		365.6
(-2.6) 		338.8
(-3) 		346
(-2.9) 		404

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 455
1 2 3 4 5 6 range
A 514.2
(3)
P 		502
(2.8)
P 		421.4
(1.4)
P 		268.1
(-1.1)
P 		191.5
(-2.4)
P 		156.1
(-3)
P 		358
B 523.6
(3)
P 		522.4
(3)
P 		321.8
(-0.1)
P 		222.7
(-1.7)
P 		138.7
(-3)
P 		161.8
(-2.6)
P 		385
C 435.6
(0.8)
P 		594
(3)
P 		395
(0.2)
P 		259
(-1.6)
P 		160.5
(-3)
P 		172
(-2.8)
P 		434
avr 491.1
(2.2) 		539.5
(3) 		379.4
(0.4) 		249.9
(-1.6) 		163.6
(-3) 		163.3
(-3) 		376
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 208
1 2 3 4 range
A 259.1
(3)
P 		81.6
(-2.2)
P 		96.1
(-1.8)
P 		54.1
(-3)
P 		205
B 250
(3)
P 		92.1
(-2.3)
P 		70.4
(-3)
P 		77.8
(-2.8)
P 		180
C 242.8
(3)
P 		100
(-1.5)
P 		120.2
(-0.8)
P 		51.2
(-3)
P 		192
avr 250.6
(3) 		91.2
(-2) 		95.6
(-1.9) 		61
(-3) 		190

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 144
1 2 3 4 5 6 range
A 94.8
(-0.6)
P 		178.5
(3)
P 		91.8
(-0.7)
P 		68
(-1.7)
P 		57.8
(-2.2)
P 		38
(-3)
P 		141
B 182.2
(3)
P 		173.9
(2.6)
P 		78.1
(-2)
P 		59
(-2.9)
P 		56.3
(-3)
P 		60.3
(-2.8)
P 		126
C 161.5
(2.1)
P 		181.3
(3)
P 		100.5
(-0.7)
P 		52.1
(-3)
P 		51.9
(-3)
P 		57.6
(-2.7)
P 		129
avr 146.2
(1.5) 		177.9
(3) 		90.1
(-1.2) 		59.7
(-2.6) 		55.3
(-2.8) 		52
(-3) 		126
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193098_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11317
Sequence Type Exemplar sequence
Representative Public ID ZC190.1 NCBI
Target Description ZC190.1 /REP_DB=WormBase Gene ID /WP=CE27645 /GEN=cln-3.3 /TR=O76703 /GB=AAC26960.2 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=intergral membrane protein
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_072836(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072836 NCBI Caenorhabditis elegans human CLN (neuronal ceroid lipofuscinosis) related family member (cln-3.3) (cln-3.3) mRNA, complete cds. 11/11 None
SNAP00000000634 ENSEMBL cdna:SNAP chromosome:CEL140:V:8687634:8688644:1 11/11 None
GENEFINDER00000000639 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:8685656:8688644:1 11/11 None
ZC190.1 ENSEMBL cdna:known chromosome:CEL140:V:8685640:8688644:1 gene:ZC190.1 11/11 None
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
chrV:8685984-8688645(+) 95.39 100.0
Public Domain and Genome References
Gene Title intergral membrane protein
Gene Symbol cln-3.3
Ensembl ZC190.1
Entrez Gene 179249 Entrez gene
SwissProt Q9BJW5 EMBL-EBI
WormBase CE27645 Wormbase
Functional Annotations
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3824 catalytic activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAC26960 Human cln (neuronal ceroid lipofuscinosis) related protein 3.3 [Caenorhabditis elegans] ref|NP_505237.1| human CLN (neuronal ceroid lipofuscinosis) related family member (cln-3.3) [Caenorhabditis elegans] gb|AAK38268.1| CLN-3.3 [Caenorhabditis elegans] 0.0
blast CAE58399 Hypothetical protein CBG01528 [Caenorhabditis briggsae] 0.0
blast AAC26960 Human cln (neuronal ceroid lipofuscinosis) related protein 3.3 [Caenorhabditis elegans] ref|NP_505237.1| human CLN (neuronal ceroid lipofuscinosis) related family member (cln-3.3) [Caenorhabditis elegans] gb|AAK38268.1| CLN-3.3 [Caenorhabditis elegans] 1.0E-140
blast CAE58399 Hypothetical protein CBG01528 [Caenorhabditis briggsae] 1.0E-127
blast CAE75206 Hypothetical protein CBG23153 [Caenorhabditis briggsae] 1.0E-122
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_505237.1 8 12-34,93-115,122-144,149-171,184-203,248-270,321-343,347-369
ZC190.1 8 12-34,93-115,122-144,149-171,184-203,248-270,321-343,347-369
SNAP00000000634 3 26-45,163-185,189-211
GENEFINDER00000000639 8 12-34,93-115,122-144,149-171,184-203,248-270,321-343,347-369
Sequence
Target Sequence 
>C. ELEGANS:193098_AT
tattctcctactcttgatccaaaatcatggattgttccgaaaggatatgatgattttatt
gtcagcgaacacagagtcccacagagagaactcggtccttcggatagattaaaactaatc
cttcctatgcttcatctaatgattcctctggcaatcgtttacgtaggagaatatatgatt
aatcaaggaatgactcaacaaattgttttcgattgtgctcatggtttcaatctatcactt
catagtcaatatcgatggtatcaagttttataccagttcggagtttttgtatcgagatct
tcaattagactagttgagctcccaatgtggatgctttatctgttaccctttcttcagtta
acaaatatgttattctttttcttcgatgcattatattggtttgtacctcaaattgccata
atcttcgcgttgatcattttcgaaggattgtttggaggttcttcgtatgtcaacacattc
cataaaattcataataaggttgaacccgatgttcgagaatactgtctttccgctgcttca
atgggtgacagtatcggagtaaacttcgcagcaggagtatcaatcccacttcat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TATTCTCCTACTCTTGATCCAAAAT 273 665 514 Antisense
TGTCAGCGAACACAGAGTCCCACAG 701 557 573 Antisense
GAGAACTCGGTCCTTCGGATAGATT 93 391 599 Antisense
TAAAACTAATCCTTCCTATGCTTCA 629 639 623 Antisense
GATTCCTCTGGCAATCGTTTACGTA 545 433 654 Antisense
GCTCATGGTTTCAATCTATCACTTC 450 301 730 Antisense
TTATCTGTTACCCTTTCTTCAGTTA 686 679 849 Antisense
GGAGGTTCTTCGTATGTCAACACAT 246 517 967 Antisense
GTTCGAGAATACTGTCTTTCCGCTG 251 443 1024 Antisense
TCTTTCCGCTGCTTCAATGGGTGAC 647 615 1038 Antisense
AGCAGGAGTATCAATCCCACTTCAT 105 79 1083 Antisense
Sequence Source Affymetrix Proprietary Database