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[188309_s_at] SH3 domain

Description M28.7 /REP_DB=WormBase Gene ID /WP=CE16278 /TR=O17972 /GB=CAA90133.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=SH3 domain
Cluster 6grp_total > 08      4grp_total > 47      6grp_cgc > 10      6grp_total_sub > Decrease      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 136
1 2 3 4 range
A 92
(3)
A 		10.9
(-2.8)
A 		10.8
(-2.8)
A 		7.7
(-3)
A 		84
B 89.7
(3)
A 		57
(0.5)
A 		10.9
(-3)
A 		69.7
(1.5)
A 		79
C 143.9
(3)
A 		44.3
(-1.5)
A 		52
(-1.1)
A 		10.7
(-3)
A 		133
avr 108.5
(3) 		37.4
(-2.1) 		24.6
(-3) 		29.4
(-2.7) 		84

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 136
1 2 3 4 5 6 range
A 127.5
(3)
A 		64.3
(-0.3)
A 		11.5
(-3)
A 		94.7
(1.3)
A 		13.5
(-2.9)
A 		16.3
(-2.8)
A 		116
B 145.2
(3)
A 		80.9
(0.2)
A 		78.5
(0.1)
A 		59.4
(-0.8)
A 		9.4
(-3)
A 		22
(-2.4)
A 		136
C 128.2
(3)
P 		55.1
(-0.7)
A 		56.7
(-0.6)
A 		112.5
(2.2)
A 		9.7
(-3)
A 		35.9
(-1.7)
A 		119
avr 133.6
(3) 		66.8
(-0.3) 		48.9
(-1.1) 		88.9
(0.8) 		10.9
(-3) 		24.7
(-2.3) 		123
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 47
1 2 3 4 range
A 33.5
(3)
A 		2.4
(-2.8)
A 		2.8
(-2.7)
A 		1.1
(-3)
A 		32
B 28.6
(3)
A 		14.1
(-0.3)
A 		2.5
(-3)
A 		14.9
(-0.1)
A 		26
C 47.6
(3)
A 		12.7
(-1.6)
A 		18.1
(-0.9)
A 		1.8
(-3)
A 		46
avr 36.6
(3) 		9.7
(-2.3) 		7.8
(-2.6) 		5.9
(-3) 		31

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 48
1 2 3 4 5 6 range
A 23.5
(2.9)
A 		22.9
(2.7)
A 		2.5
(-3)
A 		24
(3)
A 		4.1
(-2.6)
A 		4
(-2.6)
A 		22
B 50.5
(3)
A 		26.9
(-0)
A 		19.1
(-1)
A 		15.7
(-1.5)
A 		3.8
(-3)
A 		8.2
(-2.4)
A 		47
C 47.5
(3)
P 		16.8
(-1.1)
A 		14.4
(-1.5)
A 		22.6
(-0.4)
A 		3.1
(-3)
A 		12
(-1.8)
A 		44
avr 40.5
(3) 		22.2
(0) 		12
(-1.6) 		20.8
(-0.2) 		3.7
(-3) 		8.1
(-2.3) 		37
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188309_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2628
Sequence Type Exemplar sequence
Representative Public ID M28.7 NCBI
Target Description M28.7 /REP_DB=WormBase Gene ID /WP=CE16278 /TR=O17972 /GB=CAA90133.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=SH3 domain
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_063897(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063897 NCBI Caenorhabditis elegans NePHronophthisis (human kidney disease) homolog family member (nph-1) (nph-1) mRNA, complete cds. 11/11 None
SNAP00000007405 ENSEMBL cdna:SNAP chromosome:CEL140:II:10648849:10652140:-1 11/11 None
GENEFINDER00000007412 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:10648849:10657781:-1 11/11 None
M28.7 ENSEMBL cdna:known chromosome:CEL140:II:10648849:10652140:-1 gene:M28.7 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
chrII:10648845-10652137(-) 100.0 100.0
Public Domain and Genome References
Gene Title SH3 domain
Gene Symbol nph-1
Ensembl M28.7
Entrez Gene 174643 Entrez gene
SwissProt O17972 EMBL-EBI
WormBase CE16278 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1582748_AT nephronophthisis 1 (juvenile) cfa
CANINE_2:CFA.3644.1.S1_AT nephronophthisis 1 (juvenile) cfa
CANINE_2:CFAAFFX.11462.1.S1_S_AT nephronophthisis 1 (juvenile) cfa
CHICKEN:GGA.18268.1.S1_AT nephronophthisis 1 (juvenile) gga
CHICKEN:GGA.6327.1.S1_AT nephronophthisis 1 (juvenile) gga
HG-U133_PLUS_2:206285_AT nephronophthisis 1 (juvenile) hs
HG-U133A:206285_AT nephronophthisis 1 (juvenile) hs
HG-FOCUS:206285_AT nephronophthisis 1 (juvenile) hs
HG-U133A_2:206285_AT nephronophthisis 1 (juvenile) hs
HU35KSUBC:RC_T25861_F_AT nephronophthisis 1 (juvenile) hs
HU35KSUBD:RC_W44768_AT nephronophthisis 1 (juvenile) hs
U133_X3P:G4557804_3P_X_AT nephronophthisis 1 (juvenile) hs
U133_X3P:G4557804_3P_AT nephronophthisis 1 (juvenile) hs
U133_X3P:HS.211782.0.A1_3P_S_AT nephronophthisis 1 (juvenile) hs
U133_X3P:HS.211782.0.A1_3P_AT nephronophthisis 1 (juvenile) hs
U133_X3P:206285_3P_AT nephronophthisis 1 (juvenile) hs
HG-U133_PLUS_2:238843_AT nephronophthisis 1 (juvenile) hs
HG-U133B:238843_AT nephronophthisis 1 (juvenile) hs
HG-U133_PLUS_2:238844_S_AT nephronophthisis 1 (juvenile) hs
HG-U133B:238844_S_AT nephronophthisis 1 (juvenile) hs
HG-U95AV2:40384_AT nephronophthisis 1 (juvenile) hs
HG-U95E:71118_AT nephronophthisis 1 (juvenile) hs
MOUSE430_2:1453686_X_AT nephronophthisis 1 (juvenile) homolog (human) mm
MOE430A:1453686_X_AT nephronophthisis 1 (juvenile) homolog (human) mm
MOUSE430A_2:1453686_X_AT nephronophthisis 1 (juvenile) homolog (human) mm
MOUSE430_2:1416919_A_AT nephronophthisis 1 (juvenile) homolog (human) mm
MOE430A:1416919_A_AT nephronophthisis 1 (juvenile) homolog (human) mm
MOUSE430A_2:1416919_A_AT nephronophthisis 1 (juvenile) homolog (human) mm
MG-U74AV2:98614_AT nephronophthisis 1 (juvenile) homolog (human) mm
MOE430A:1448523_AT nephronophthisis 1 (juvenile) homolog (human) mm
MOUSE430A_2:1448523_AT nephronophthisis 1 (juvenile) homolog (human) mm
MOUSE430_2:1448523_AT nephronophthisis 1 (juvenile) homolog (human) mm
MU19KSUBB:TC31803_AT Nephronophthisis 1 (juvenile) homolog (human) (Nphp1), mRNA mm
RG-U34C:RC_AI176028_AT nephronophthisis 1 (juvenile) (predicted) rn
RAE230A:1374508_AT nephronophthisis 1 (juvenile) (predicted) rn
RAT230_2:1374508_AT nephronophthisis 1 (juvenile) (predicted) rn
RAE230A:1372172_AT nephronophthisis 1 (juvenile) (predicted) rn
RAT230_2:1372172_AT nephronophthisis 1 (juvenile) (predicted) rn
RAE230B:1395458_AT nephronophthisis 1 (juvenile) (predicted) rn
RAT230_2:1395458_AT nephronophthisis 1 (juvenile) (predicted) rn
Protein Similarities
Method ID Description E-Value
blast CAA90133 Hypothetical protein M28.7 [Caenorhabditis elegans] ref|NP_496298.1| NePHronophthisis (human kidney disease) homolog family member (nph-1) [Caenorhabditis elegans] sp|O17972|NPHP1_CAEEL Nephrocystin-1-like protein 0.0
blast CAE59630 Hypothetical protein CBG03043 [Caenorhabditis briggsae] 0.0
blast CAA90128 Hypothetical protein M28.6 [Caenorhabditis elegans] ref|NP_496299.1| M28.6 [Caenorhabditis elegans] 0.0
blast AAH62574 NPHP1 protein [Homo sapiens] 1.0E-30
Protein Domains
Database ID Description E-Value
Pfam IPR001452 EMBL-EBI SH3 7.9E-7
Pfam IPR001452 EMBL-EBI SH3 7.9E-7
Pfam IPR001466 EMBL-EBI Beta-lactamase 5.3E-69
Sequence
Target Sequence 
>C. ELEGANS:188309_S_AT
cctccccgatgtcatagtattcaatgctctttatttaccattcttccacttttaccgccg
acgagctggaaccattttaattcgggacaatcggaatccattgagtgctgaatttatatc
tgacccacttctctctgtattcccatttgtttgtgaccagcatgacattatggatataat
gctgaaaatttggaaaaccaaaaagaaagtgctcgccaagaaaaacgaagctgaacaaac
tgccgagttcttccaaacttttctacacaccgcgttttttattcatgggattcgaatgat
ttcgtatgatgtcaaagatgatcttactctttcgattaggcaacagactatgcaacgatt
tgtggatgcattgaataagggacttttcaagcagttcatcgca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCTCCCCGATGTCATAGTATTCAAT 681 265 1587 Antisense
ATGCTCTTTATTTACCATTCTTCCA 10 43 1610 Antisense
GAACCATTTTAATTCGGGACAATCG 14 347 1655 Antisense
AATCGGAATCCATTGAGTGCTGAAT 443 169 1675 Antisense
GAATTTATATCTGACCCACTTCTCT 585 325 1696 Antisense
TCTCTCTGTATTCCCATTTGTTTGT 172 613 1716 Antisense
CCCATTTGTTTGTGACCAGCATGAC 638 257 1728 Antisense
ACAAACTGCCGAGTTCTTCCAAACT 394 111 1821 Antisense
GAGTTCTTCCAAACTTTTCTACACA 628 397 1831 Antisense
GATGATCTTACTCTTTCGATTAGGC 515 409 1903 Antisense
GGGACTTTTCAAGCAGTTCATCGCA 152 495 1965 Antisense
Sequence Source Affymetrix Proprietary Database