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[191730_s_at] membrane protein

Description T19B4.7 /REP_DB=WormBase Gene ID /WP=CE25115 /GEN=unc-40 /TR=P91456 /GB=AAB37635.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=membrane protein
Cluster 6grp_highest_10_10 > 52      6grp_high1_10_10 > 25      4grp_highest_8_8 > 57      4grp_high_8_8 > 34      6grp_highest_nonorm > 41      6grp_total > 26      4grp_total > 45      6grp_highest_sub > 01_02      6grp_cgc > 14      6grp_high1_sub > 01_02      6grp_cgc_sub > Cu      6grp_total_sub > Cup      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 685
1 2 3 4 range
A 1050.9
(3)
P 		737.1
(0.3)
P 		547.7
(-1.4)
P 		365.5
(-3)
P 		685
B 1026.1
(3)
P 		664.8
(-0.6)
P 		446.9
(-2.7)
P 		418
(-3)
P 		608
C 938.6
(3)
P 		648.3
(-0.4)
P 		523.5
(-1.9)
P 		430.1
(-3)
P 		509
avr 1005.2
(3) 		683.4
(-0.2) 		506
(-2) 		404.5
(-3) 		601

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 506
1 2 3 4 5 6 range
A 1023.5
(3)
P 		955.3
(2.2)
P 		517.8
(-3)
P 		575.9
(-2.3)
P 		622.5
(-1.8)
P 		704.9
(-0.8)
P 		506
B 908.1
(2.7)
P 		925.2
(3)
P 		586.8
(-2.3)
P 		616
(-1.9)
P 		544.7
(-3)
P 		647.8
(-1.4)
P 		381
C 916
(3)
P 		866.9
(2.2)
P 		717
(-0.1)
P 		627.4
(-1.4)
P 		525.1
(-3)
P 		549.3
(-2.6)
P 		391
avr 949.2
(3) 		915.8
(2.5) 		607.2
(-2.3) 		606.4
(-2.3) 		564.1
(-3) 		634
(-1.9) 		385
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 329
1 2 3 4 range
A 382.6
(3)
P 		160
(-1.1)
P 		143.2
(-1.4)
P 		53.5
(-3)
P 		329
B 327.2
(3)
P 		164.2
(-1.1)
P 		103.6
(-2.6)
P 		89.1
(-3)
P 		238
C 310.7
(3)
P 		186.4
(-0.1)
P 		182.5
(-0.2)
P 		72.5
(-3)
P 		238
avr 340.2
(3) 		170.2
(-0.8) 		143.1
(-1.4) 		71.7
(-3) 		269

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 227
1 2 3 4 5 6 range
A 188.7
(-1)
P 		339.8
(3)
P 		112.8
(-3)
P 		146.1
(-2.1)
P 		187.8
(-1)
P 		171.6
(-1.4)
P 		227
B 316
(3)
P 		308
(2.7)
P 		142.5
(-3)
P 		163.2
(-2.3)
P 		221.3
(-0.3)
P 		241.6
(0.4)
P 		174
C 339.5
(3)
P 		264.5
(0.9)
P 		182.5
(-1.4)
P 		126.2
(-3)
P 		169.9
(-1.8)
P 		183.9
(-1.4)
P 		213
avr 281.4
(2.1) 		304.1
(3) 		145.9
(-3) 		145.2
(-3) 		193
(-1.2) 		199
(-1) 		159
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 191730_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1303
Sequence Type Exemplar sequence
Representative Public ID T19B4.7 NCBI
Target Description T19B4.7 /REP_DB=WormBase Gene ID /WP=CE25115 /GEN=unc-40 /TR=P91456 /GB=AAB37635.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=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_059263(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059263 NCBI Caenorhabditis elegans UNCoordinated family member (unc-40) (unc-40) mRNA, complete cds. 11/11 A 
SNAP00000019538 ENSEMBL cdna:SNAP chromosome:CEL140:I:5680369:5687344:-1 11/11 None
GENEFINDER00000019547 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:5680369:5691857:-1 11/11 None
T19B4.7 ENSEMBL cdna:known chromosome:CEL140:I:5679847:5691490:-1 gene:T19B4.7 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
chrI:5680368-5691443(-) 100.0 100.0
Public Domain and Genome References
Gene Title membrane protein
Gene Symbol unc-40
Ensembl T19B4.7
Entrez Gene 172233 Entrez gene
SwissProt Q94155 EMBL-EBI
WormBase CE25115 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.1208.1.S1_S_AT similar to Netrin receptor DCC precursor (Tumor suppressor protein DCC) (Colorectal cancer suppressor) cfa
HG-U133_PLUS_2:206939_AT deleted in colorectal carcinoma hs
HG-U133A:206939_AT deleted in colorectal carcinoma hs
HG-FOCUS:206939_AT deleted in colorectal carcinoma hs
HG-U133A_2:206939_AT deleted in colorectal carcinoma hs
HUGENEFL:X76132_AT deleted in colorectal carcinoma hs
U133_X3P:G4885174_3P_AT deleted in colorectal carcinoma hs
HG-U95AV2:32890_AT deleted in colorectal carcinoma hs
HG-U95E:80344_AT deleted in colorectal carcinoma hs
HG-U95E:84675_S_AT deleted in colorectal carcinoma hs
HG-U95D:85111_AT deleted in colorectal carcinoma hs
HG-U95AV2:1349_AT Deleted in colorectal carcinoma hs
HC-G110:1349_AT Deleted in colorectal carcinoma hs
HUGENEFL:S81294_AT Deleted in colorectal carcinoma hs
MOE430A:1422162_AT deleted in colorectal carcinoma mm
MOUSE430A_2:1422162_AT deleted in colorectal carcinoma mm
MOUSE430_2:1422162_AT deleted in colorectal carcinoma mm
MU11KSUBB:MSA.3100.0_AT deleted in colorectal carcinoma mm
MG-U74AV2:102566_AT deleted in colorectal carcinoma mm
MG-U74CV2:136568_AT deleted in colorectal carcinoma mm
MOE430B:1440487_AT Deleted in colorectal carcinoma (Dcc), mRNA mm
MOUSE430_2:1440487_AT Deleted in colorectal carcinoma (Dcc), mRNA mm
RG-U34A:U68725_AT deleted in colorectal carcinoma rn
RAE230A:1369339_AT deleted in colorectal carcinoma rn
RAT230_2:1369339_AT deleted in colorectal carcinoma rn
RAE230B:1379855_AT Deleted in colorectal carcinoma rn
RAT230_2:1379855_AT Deleted in colorectal carcinoma rn
RAE230B:1380096_AT Deleted in colorectal carcinoma rn
RAT230_2:1380096_AT Deleted in colorectal carcinoma rn
RAE230A:1381907_AT Deleted in colorectal carcinoma rn
RAT230_2:1381907_AT Deleted in colorectal carcinoma rn
Protein Similarities
Method ID Description E-Value
blast AAB37634 Uncoordinated protein 40 [Caenorhabditis elegans] ref|NP_491664.1| UNCoordinated family member (unc-40) [Caenorhabditis elegans] gb|AAB17088.1| unc-40 [Caenorhabditis elegans] 0.0
blast CAE68937 Hypothetical protein CBG14917 [Caenorhabditis briggsae] 0.0
blast T25893 hypothetical protein T19B4.7 - Caenorhabditis elegans 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR003961 EMBL-EBI Fibronectin, type III 7.9E-19
Pfam IPR003961 EMBL-EBI Fibronectin, type III 1.9E-12
Pfam IPR003961 EMBL-EBI Fibronectin, type III 6.0E-23
Pfam IPR003961 EMBL-EBI Fibronectin, type III 1.4E-6
Pfam IPR003961 EMBL-EBI Fibronectin, type III 3.3E-14
Pfam IPR003961 EMBL-EBI Fibronectin, type III 2.1E-16
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 0.11
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 4.5E-6
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 2.0E-7
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 2.4E-4
Pfam IPR003961 EMBL-EBI Fibronectin, type III 7.9E-19
Pfam IPR003961 EMBL-EBI Fibronectin, type III 1.9E-12
Pfam IPR003961 EMBL-EBI Fibronectin, type III 6.0E-23
Pfam IPR003961 EMBL-EBI Fibronectin, type III 1.4E-6
Pfam IPR003961 EMBL-EBI Fibronectin, type III 3.3E-14
Pfam IPR003961 EMBL-EBI Fibronectin, type III 2.1E-16
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 0.97
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 4.5E-6
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 2.0E-7
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 2.4E-4
Pfam IPR003961 EMBL-EBI Fibronectin, type III 7.9E-19
Pfam IPR003961 EMBL-EBI Fibronectin, type III 1.9E-12
Pfam IPR003961 EMBL-EBI Fibronectin, type III 6.0E-23
Pfam IPR003961 EMBL-EBI Fibronectin, type III 1.4E-6
Pfam IPR003961 EMBL-EBI Fibronectin, type III 3.3E-14
Pfam IPR003961 EMBL-EBI Fibronectin, type III 2.1E-16
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 0.11
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 4.5E-6
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 2.0E-7
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 2.4E-4
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491664.1 1 1085-1107
T19B4.7 1 1085-1107
SNAP00000019538 1 988-1010
GENEFINDER00000019547 1 1139-1161
Sequence
Target Sequence 
>C. ELEGANS:191730_S_AT
aagtccttatggttcatcatctgcaattggatccgcctcgactccgcctctcccaatgca
agctccaccttctggtccacctacagtaatcgatggataccgtactctacgtggaacacc
tccaaattcatcagctgcaaatgctcttcggtcattcactcaattggcaggagcaacacc
acctccaccacactctgcggcatcatcatcttctcgaccgactattattgcagccggtgg
acggcaagttccagttggaagagcaactgctcaaccacgtgtcaatgttgcaaatatcta
cagtccatttgcatcatgctctgcatcttctgatg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAGTCCTTATGGTTCATCATCTGCA 49 159 3699 Antisense
CCTTCTGGTCCACCTACAGTAATCG 113 269 3766 Antisense
AATCGATGGATACCGTACTCTACGT 146 169 3786 Antisense
GAACACCTCCAAATTCATCAGCTGC 94 353 3812 Antisense
GCTGCAAATGCTCTTCGGTCATTCA 174 297 3832 Antisense
TCGGTCATTCACTCAATTGGCAGGA 421 605 3846 Antisense
TCATCATCTTCTCGACCGACTATTA 131 621 3901 Antisense
GCCGGTGGACGGCAAGTTCCAGTTG 555 281 3931 Antisense
AACTGCTCAACCACGTGTCAATGTT 385 141 3963 Antisense
TCTACAGTCCATTTGCATCATGCTC 354 613 3995 Antisense
GCATCATGCTCTGCATCTTCTGATG 344 309 4009 Antisense
Sequence Source Affymetrix Proprietary Database