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[173464_at] liprin-alpha

Description g5713195 /REP_DB=GenBank Identifier /5_PRIME_EXT_ID=F59F5.6 /5_PRIME_EXT_DB=WormBase Gene ID /WB_GENE_ID=F59F5.6 /WP=CE03447 /CHR=X /FEA=Genomic Cluster /GEN=syd-2 /DEF=liprin-alpha homolog SYD-2
Cluster 6grp_highest_10_10 > 43      6grp_high1_10_10 > 23      4grp_highest_8_8 > 41      4grp_high_8_8 > 49      6grp_highest_nonorm > 61      6grp_total > 12      4grp_total > 54      6grp_highest_sub > 02      6grp_cgc > 43      6grp_high1_sub > 02      6grp_cgc_sub > 02      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 377
1 2 3 4 range
A 537.7
(3)
P 		221.5
(-2.4)
P 		316.8
(-0.8)
P 		185.7
(-3)
P 		352
B 344.1
(2.3)
P 		352.1
(3)
P 		328.4
(1.1)
P 		278.6
(-3)
P 		74
C 509.1
(3)
P 		391.9
(1)
P 		303.7
(-0.5)
P 		160.6
(-3)
P 		349
avr 463.6
(3) 		321.8
(-0.3) 		316.3
(-0.5) 		208.3
(-3) 		255

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 456
1 2 3 4 5 6 range
A 339.1
(-0.8)
P 		532.4
(3)
P 		416.5
(0.7)
P 		228.3
(-3)
P 		403.7
(0.5)
P 		268
(-2.2)
P 		304
B 526.5
(0.8)
P 		684.5
(3)
P 		484.3
(0.2)
P 		523.4
(0.7)
P 		256.5
(-3)
P 		358.5
(-1.6)
P 		428
C 533.8
(1.6)
P 		617.7
(3)
P 		398.1
(-0.6)
P 		403.9
(-0.5)
P 		289.3
(-2.4)
P 		252
(-3)
P 		366
avr 466.5
(0.3) 		611.5
(3) 		433
(-0.4) 		385.2
(-1.3) 		316.5
(-2.6) 		292.8
(-3) 		319
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 169
1 2 3 4 range
A 195.8
(3)
P 		48.1
(-2.3)
P 		82.8
(-1)
P 		27.2
(-3)
P 		169
B 109.7
(3)
P 		87
(0.3)
P 		76.1
(-1)
P 		59.4
(-3)
P 		50
C 168.5
(3)
P 		112.7
(0.6)
P 		105.8
(0.3)
P 		27.1
(-3)
P 		141
avr 158
(3) 		82.6
(-0.8) 		88.2
(-0.5) 		37.9
(-3) 		120

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 170
1 2 3 4 5 6 range
A 62.5
(-2.8)
P 		189.3
(3)
P 		90.7
(-1.5)
P 		57.9
(-3)
P 		121.8
(-0.1)
P 		65.3
(-2.7)
P 		131
B 183.2
(0.8)
P 		227.8
(3)
P 		117.6
(-2.3)
P 		138.6
(-1.3)
P 		104.2
(-3)
P 		133.7
(-1.6)
P 		124
C 197.9
(3)
P 		188.5
(2.5)
P 		101.3
(-2)
P 		81.2
(-3)
P 		93.6
(-2.4)
P 		84.4
(-2.8)
P 		117
avr 147.9
(0) 		201.9
(3) 		103.2
(-2.4) 		92.6
(-3) 		106.5
(-2.2) 		94.5
(-2.9) 		109
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173464_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.25988
Sequence Type Exemplar sequence
Representative Public ID 5713195 NCBI
Target Description g5713195 /REP_DB=GenBank Identifier /5_PRIME_EXT_ID=F59F5.6 /5_PRIME_EXT_DB=WormBase Gene ID /WB_GENE_ID=F59F5.6 /WP=CE03447 /CHR=X /FEA=Genomic Cluster /GEN=syd-2 /DEF=liprin-alpha homolog SYD-2
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_077367(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077367 NCBI Caenorhabditis elegans F59F5.6 (liprin-alpha) mRNA, complete cds. 11/11 A 
F59F5.6 ENSEMBL cdna:known chromosome:CEL140:X:10549049:10554862:-1 gene:F59F5.6 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
chrX:10549059-10554863(-) 98.89 100.0
Public Domain and Genome References
Gene Title liprin-alpha
Gene Symbol syd-2
Ensembl F59F5.6
Entrez Gene 181255 Entrez gene
SwissProt Q21049 EMBL-EBI
WormBase CE03447 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1603007_AT similar to Liprin-alpha 1 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha 1) (PTPRF-interacting protein alpha 1) (LAR-interacting protein 1) (LIP.1) cfa
CANINE_2:CFAAFFX.16545.1.S1_S_AT similar to Liprin-alpha 1 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha 1) (PTPRF-interacting protein alpha 1) (LAR-interacting protein 1) (LIP.1) cfa
CANINE_2:CFAAFFX.16630.1.S1_S_AT similar to Liprin-alpha 1 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha 1) (PTPRF-interacting protein alpha 1) (LAR-interacting protein 1) (LIP.1) cfa
DROSOPHILA_2:1632099_S_AT dm
DROSGENOME1:154634_AT dm
CHICKEN:GGA.12241.1.S1_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 gga
CHICKEN:GGA.12241.1.S1_S_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 gga
CHICKEN:GGA.13097.1.S1_S_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 gga
CHICKEN:GGAAFFX.26244.4.S1_S_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 gga
HG-U95AV2:41782_G_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U133_PLUS_2:210236_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U133A:210236_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U133A_2:210236_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U95AV2:944_S_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HC-G110:944_S_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U133_PLUS_2:210235_S_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U133A:210235_S_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U133A_2:210235_S_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HU35KSUBB:RC_H97922_S_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HUGENEFL:U22815_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HUGENEFL:U22816_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HUGENEFL:D49354_S_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
U133_X3P:G930340_3P_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
U133_X3P:G930340_3P_A_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
U133_X3P:HS.183648.0.S3_3P_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
U133_X3P:HS.183648.0.S1_3P_A_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U133A_2:202065_S_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U133_PLUS_2:202065_S_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U133A:202065_S_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U133A_2:202066_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-FOCUS:202066_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U133_PLUS_2:202066_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U133A:202066_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U95AV2:41780_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U95AV2:41781_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U95B:44989_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U95B:45470_G_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U133_PLUS_2:242990_AT Protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U133B:242990_AT Protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U95C:51638_AT Protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U95D:67092_AT Protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U95D:77349_AT Protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
HG-U95D:89283_AT Protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 hs
MG-U74BV2:110020_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein, alpha 1 mm
MG-U74BV2:106650_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein, alpha 1 mm
MOE430B:1455478_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein, alpha 1 mm
MOUSE430_2:1455478_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein, alpha 1 mm
MOE430B:1435861_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein, alpha 1 mm
MOUSE430_2:1435861_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein, alpha 1 mm
MU19KSUBA:TC17068_AT PREDICTED: similar to Liprin-alpha 1 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha 1) (PTPRF-interacting protein alpha 1) (LAR-interacting protein 1) (LIP.1) [Mus musculus], mRNA sequence mm
MU19KSUBB:TC31494_AT PREDICTED: similar to Liprin-alpha 1 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha 1) (PTPRF-interacting protein alpha 1) (LAR-interacting protein 1) (LIP.1) [Mus musculus], mRNA sequence mm
MU19KSUBC:TC38950_AT PREDICTED: similar to Liprin-alpha 1 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha 1) (PTPRF-interacting protein alpha 1) (LAR-interacting protein 1) (LIP.1) [Mus musculus], mRNA sequence mm
MU19KSUBC:TC41568_AT PREDICTED: similar to Liprin-alpha 1 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha 1) (PTPRF-interacting protein alpha 1) (LAR-interacting protein 1) (LIP.1) [Mus musculus], mRNA sequence mm
MU19KSUBC:TC41568_G_AT PREDICTED: similar to Liprin-alpha 1 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha 1) (PTPRF-interacting protein alpha 1) (LAR-interacting protein 1) (LIP.1) [Mus musculus], mRNA sequence mm
RAE230B:1384832_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein, alpha 1 (predicted) rn
RAT230_2:1384832_AT protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein, alpha 1 (predicted) rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
7274 neuromuscular synaptic transmission inferred from direct assay QuickGO AmiGO
43113 receptor clustering inferred from sequence similarity QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
30424 axon inferred from direct assay QuickGO AmiGO
45202 synapse inferred from direct assay QuickGO AmiGO
5737 cytoplasm inferred from direct assay QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
19903 protein phosphatase binding inferred from physical interaction QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA90660 Hypothetical protein F59F5.6 [Caenorhabditis elegans] ref|NP_509768.1| F59F5.6 [Caenorhabditis elegans] gb|AAD47840.1| liprin-alpha homolog SYD-2 [Caenorhabditis elegans] sp|Q21049|LIPA_CAEEL Liprin alpha (LAR-interacting protein alpha) (Synapse defective protein 2) 0.0
blast CAE60801 Hypothetical protein CBG04493 [Caenorhabditis briggsae] 0.0
blast XP_238162 PREDICTED: similar to Liprin-alpha 1 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha 1) (PTPRF-interacting protein alpha 1) (LAR-interacting protein 1) (LIP.1) [Rattus norvegicus] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001660 EMBL-EBI Sterile alpha motif SAM 4.3E-8
Sequence
Target Sequence 
>C. ELEGANS:173464_AT
tttcctgtcattcgtgctagtctaaacgaccttataccgcctgcttctgtaattttttat
tgacgatttcagtttttcggtattttaagttttaattattctcattatcatatccatatt
ttttccattctcaagtttttccctaaatatctttttagcacgtttttcttctggtaaaaa
tcaaaaagatagaaagaaagtgcgctaatattcaatttttctacaaaaccaaatactttt
aacttatttccttgattattaattatagtttttatccaatctcatcatt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTTCCTGTCATTCGTGCTAGTCTAA 502 669 3484 Antisense
TAGTCTAAACGACCTTATACCGCCT 80 623 3501 Antisense
ACCGCCTGCTTCTGTAATTTTTTAT 9 1 3519 Antisense
TGACGATTTCAGTTTTTCGGTATTT 170 571 3544 Antisense
AATTATTCTCATTATCATATCCATA 632 175 3577 Antisense
ATCCATATTTTTTCCATTCTCAAGT 453 39 3595 Antisense
CATTCTCAAGTTTTTCCCTAAATAT 594 215 3609 Antisense
ATCTTTTTAGCACGTTTTTCTTCTG 339 31 3632 Antisense
GAAAGTGCGCTAATATTCAATTTTT 116 361 3679 Antisense
TAACTTATTTCCTTGATTATTAATT 342 637 3723 Antisense
ATAGTTTTTATCCAATCTCATCATT 180 23 3748 Antisense
Sequence Source GenBank