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[176096_at]

Description Y41D4A.F /REP_DB=WormBase Gene ID /WP=CE21847 /CHR=4 /FEA=Sanger Annotation /DEF=(ST.LOUIS)
Cluster 6grp_highest_10_10 > 73      6grp_high1_10_10 > 37      4grp_highest_8_8 > 63      4grp_high_8_8 > 28      6grp_highest_nonorm > 90      6grp_total > 37      4grp_total > 36      6grp_highest_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 157
1 2 3 4 range
A 216.4
(-2)
P 		256.5
(0)
P 		196
(-3)
P 		315.1
(3)
P 		119
B 221.8
(0.5)
P 		254.6
(3)
P 		174.5
(-3)
P 		210.9
(-0.3)
P 		80
C 255.8
(3)
P 		255.6
(3)
P 		191.6
(-1)
P 		158.6
(-3)
P 		97
avr 231.3
(0.9) 		255.6
(3) 		187.4
(-3) 		228.2
(0.6) 		68

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 167
1 2 3 4 5 6 range
A 243.8
(3)
P 		204.9
(1.1)
P 		180.9
(-0.1)
P 		185.8
(0.1)
P 		123.7
(-3)
P 		193.4
(0.5)
P 		120
B 195.4
(2.7)
P 		198.3
(2.9)
P 		159.1
(1)
P 		143.1
(0.2)
P 		76.7
(-3)
P 		200.6
(3)
P 		124
C 241.3
(3)
P 		167.7
(-2.5)
P 		230.9
(2.2)
P 		161.6
(-3)
P 		222.9
(1.6)
P 		212
(0.8)
P 		80
avr 226.8
(3) 		190.3
(0.4) 		190.3
(0.4) 		163.5
(-1.4) 		141.1
(-3) 		202
(1.3) 		86
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 58
1 2 3 4 range
A 78.8
(3)
P 		55.7
(-1.2)
P 		51.2
(-2.1)
P 		46.1
(-3)
P 		33
B 70.7
(3)
P 		62.9
(1.5)
P 		40.4
(-3)
P 		44.9
(-2.1)
P 		30
C 84.7
(3)
P 		73.5
(1.8)
P 		66.8
(1.1)
P 		26.7
(-3)
P 		58
avr 78.1
(3) 		64
(0.8) 		52.8
(-0.9) 		39.2
(-3) 		39

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 58
1 2 3 4 5 6 range
A 44.9
(-1.7)
P 		72.9
(3)
P 		39.4
(-2.6)
P 		47.1
(-1.3)
P 		37.3
(-3)
P 		47.1
(-1.3)
P 		36
B 68
(2.1)
P 		66
(1.8)
P 		38.6
(-2)
P 		37.9
(-2.1)
P 		31.2
(-3)
P 		74.8
(3)
P 		44
C 89.4
(3)
P 		51.2
(-1)
P 		58.8
(-0.2)
P 		32.5
(-3)
P 		72.1
(1.2)
P 		71
(1.1)
P 		57
avr 67.4
(3) 		63.4
(2.1) 		45.6
(-1.6) 		39.2
(-3) 		46.9
(-1.4) 		64.3
(2.3) 		28
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 176096_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.19382
Sequence Type Exemplar sequence
Representative Public ID Y41D4A.F NCBI
Target Description Y41D4A.F /REP_DB=WormBase Gene ID /WP=CE21847 /CHR=4 /FEA=Sanger Annotation /DEF=(ST.LOUIS)
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_067729(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067729 NCBI Caenorhabditis elegans Y41D4A.4 (Y41D4A.4) mRNA, complete cds. 11/11 None
SNAP00000028255 ENSEMBL cdna:SNAP chromosome:CEL140:IV:1746001:1751315:1 11/11 None
GENEFINDER00000028268 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:1746001:1751315:1 11/11 None
Y41D4A.4.1 ENSEMBL cdna:known chromosome:CEL140:IV:1745952:1751699:1 gene:Y41D4A.4 11/11 None
Y41D4A.4.2 ENSEMBL cdna:known chromosome:CEL140:IV:1745999:1751699:1 gene:Y41D4A.4 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
chrIV:1746006-1751321(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl Y41D4A.4
Entrez Gene 176983 Entrez gene
SwissProt Q95Y24 EMBL-EBI
WormBase CE21847 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:260482_AT endomembrane protein 70, putative at
ATGENOME1:18639_AT endomembrane protein 70, putative at
CANINE_2:CFAAFFX.13912.1.S1_S_AT similar to Transmembrane 9 superfamily protein member 3 precursor cfa
CANINE_2:CFAAFFX.13989.1.S1_S_AT similar to Transmembrane 9 superfamily protein member 3 precursor cfa
CANINE_2:CFAAFFX.13999.1.S1_S_AT similar to Transmembrane 9 superfamily protein member 3 precursor cfa
CANINE_2:CFAAFFX.14006.1.S1_S_AT similar to Transmembrane 9 superfamily protein member 3 precursor cfa
DROSOPHILA_2:1624176_AT dm
DROSGENOME1:148229_AT dm
CHICKEN:GGA.4101.1.S1_S_AT transmembrane protein TM9SF3 gga
CHICKEN:GGAAFFX.26526.1.S1_S_AT transmembrane protein TM9SF3 gga
CHICKEN:GGA.4101.1.S1_AT Transmembrane protein TM9SF3 gga
HG-U133_PLUS_2:217758_S_AT SM-11044 binding protein hs
HG-U133A:217758_S_AT SM-11044 binding protein hs
HG-FOCUS:217758_S_AT SM-11044 binding protein hs
HG-U133A_2:217758_S_AT SM-11044 binding protein hs
HU35KSUBA:AA226865_AT SM-11044 binding protein hs
HU35KSUBA:AA437015_AT SM-11044 binding protein hs
HU35KSUBD:RC_AA457529_AT SM-11044 binding protein hs
U133_X3P:G10047129_3P_A_AT SM-11044 binding protein hs
U133_X3P:HS.8203.0.S1_3P_A_AT SM-11044 binding protein hs
HG-U133_PLUS_2:222399_S_AT SM-11044 binding protein hs
HG-U133B:222399_S_AT SM-11044 binding protein hs
HG-U95B:56452_AT SM-11044 binding protein hs
HG-U95E:71771_R_AT SM-11044 binding protein hs
HG-U133_PLUS_2:224755_AT SM-11044 binding protein hs
HG-U133B:224755_AT SM-11044 binding protein hs
HG-U133_PLUS_2:228610_AT SM-11044 binding protein hs
HG-U133B:228610_AT SM-11044 binding protein hs
HG-U133_PLUS_2:239626_X_AT SM-11044 binding protein hs
HG-U133B:239626_X_AT SM-11044 binding protein hs
HG-U95B:46307_AT SM-11044 binding protein hs
HG-U95C:59430_AT SM-11044 binding protein hs
HG-U95E:78652_AT SM-11044 binding protein hs
HU35KSUBA:RC_AA135850_AT SM-11044 binding protein hs
HU35KSUBC:RC_AA027853_AT SM-11044 binding protein hs
U133_X3P:HS.251237.0.A1_3P_AT SM-11044 binding protein hs
U133_X3P:HS.8203.1.S1_3P_AT SM-11044 binding protein hs
U133_X3P:HS.8203.2.S1_3P_AT SM-11044 binding protein hs
MU11KSUBA:AA408219_RC_S_AT SM-11044 binding protein mm
MG-U74AV2:96275_F_AT SM-11044 binding protein mm
MG-U74AV2:96276_R_AT SM-11044 binding protein mm
MG-U74BV2:106564_AT SM-11044 binding protein mm
MOE430A:1416509_AT SM-11044 binding protein mm
MOUSE430A_2:1416509_AT SM-11044 binding protein mm
MOUSE430_2:1416509_AT SM-11044 binding protein mm
MOE430A:1448375_AT SM-11044 binding protein mm
MOUSE430A_2:1448375_AT SM-11044 binding protein mm
MOUSE430_2:1448375_AT SM-11044 binding protein mm
MOE430A:1460186_AT SM-11044 binding protein mm
MOUSE430A_2:1460186_AT SM-11044 binding protein mm
MOUSE430_2:1460186_AT SM-11044 binding protein mm
MOE430B:1428412_AT SM-11044 binding protein mm
MOUSE430_2:1428412_AT SM-11044 binding protein mm
MOUSE430_2:1442821_AT SM-11044 binding protein (Smbp), transcript variant 1, mRNA mm
MOE430B:1442821_AT SM-11044 binding protein (Smbp), transcript variant 1, mRNA mm
MOE430B:1458681_AT SM-11044 binding protein (Smbp), transcript variant 1, mRNA mm
MOUSE430_2:1458681_AT SM-11044 binding protein (Smbp), transcript variant 1, mRNA mm
MU19KSUBB:TC34231_AT SM-11044 binding protein (Smbp), transcript variant 1, mRNA mm
MU19KSUBC:TC36593_AT SM-11044 binding protein (Smbp), transcript variant 1, mRNA mm
MU19KSUBC:TC37506_AT SM-11044 binding protein (Smbp), transcript variant 1, mRNA mm
RAE230A:1398973_AT similar to transmembrane protein TM9SF3 rn
RAT230_2:1398973_AT similar to transmembrane protein TM9SF3 rn
RG-U34B:RC_AA963367_AT similar to transmembrane protein TM9SF3 rn
RG-U34C:RC_AI232112_AT similar to transmembrane protein TM9SF3 rn
RAE230A:1371647_AT similar to transmembrane protein TM9SF3 rn
RAT230_2:1371647_AT similar to transmembrane protein TM9SF3 rn
RAE230B:1395343_AT similar to transmembrane protein TM9SF3 rn
RAT230_2:1395343_AT similar to transmembrane protein TM9SF3 rn
RAE230B:1380053_AT similar to transmembrane protein TM9SF3 rn
RAT230_2:1380053_AT similar to transmembrane protein TM9SF3 rn
RAE230B:1379627_AT similar to transmembrane protein TM9SF3 rn
RAT230_2:1379627_AT similar to transmembrane protein TM9SF3 rn
RG-U34B:RC_AI070173_AT Similar to transmembrane protein TM9SF3 rn
RG-U34C:RC_AI172333_AT Similar to transmembrane protein TM9SF3 rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6810 transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
16021 integral to membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5215 transporter activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAK68454 Hypothetical protein Y41D4A.4 [Caenorhabditis elegans] ref|NP_500130.1| Y41D4A.4 [Caenorhabditis elegans] 0.0
blast CAE63840 Hypothetical protein CBG08396 [Caenorhabditis briggsae] 0.0
blast XP_683858 PREDICTED: similar to Transmembrane 9 superfamily protein member 3 precursor (SM-11044 binding protein) (EP70-P-iso) [Danio rerio] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR004240 EMBL-EBI Nonaspanin (TM9SF) 1.0E-126
Pfam IPR004240 EMBL-EBI Nonaspanin (TM9SF) 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_500130.1 9 214-236,280-302,317-339,352-374,384-406,439-461,476-498,505-527,542-564
Y41D4A.4.1 9 214-236,280-302,317-339,352-374,384-406,439-461,476-498,505-527,542-564
Y41D4A.4.2 9 214-236,280-302,317-339,352-374,384-406,439-461,476-498,505-527,542-564
SNAP00000028255 9 214-236,280-302,317-339,352-374,384-406,439-461,476-498,505-527,542-564
GENEFINDER00000028268 9 214-236,288-310,330-352,365-387,397-419,453-475,490-512,519-541,556-578
Sequence
Target Sequence 
>C. ELEGANS:176096_AT
tccattcacaattatgctcgccgtctcggcgatctgcctctttgtgatccttccgctgac
tcttgtcggaactgtgatcggaagaaatatggctggaagtgcagactatccgtgtagagt
gaatgccgtgccgagacccattcctgataagaaatggttcgtccaaccgtggctcatcac
ccttgccggaggtgttctcccattcggatccatcttcatcgaaatgtactttatcttcac
ctcattctgggcgtacaaaatctattatgtgtacggattcatgcttttggtcacaataat
cctgtcaattgtcaccgtatgcgtcacaattgtctgctcctacttcctactcaacgccga
ggattatagatggagatggacgagcttcgcgtgtggagcatctactgcattctatgtgta
catgtattccatgtattatttcttcttcaagacaaaaatgtacggacttttccaaacggt
cttctactttggatacatgggaatcttcgccgccgctctcggactcatgaccggcaccat
cggatacgtcggaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCCATTCACAATTATGCTCGCCGTC 567 591 1155 Antisense
CCTTCCGCTGACTCTTGTCGGAACT 217 269 1203 Antisense
GTAGAGTGAATGCCGTGCCGAGACC 420 419 1268 Antisense
CCCATTCGGATCCATCTTCATCGAA 325 259 1353 Antisense
GAAATGTACTTTATCTTCACCTCAT 647 361 1375 Antisense
TTCACCTCATTCTGGGCGTACAAAA 327 681 1390 Antisense
TCCTGTCAATTGTCACCGTATGCGT 710 593 1454 Antisense
CGTATGCGTCACAATTGTCTGCTCC 491 247 1470 Antisense
CTTCGCGTGTGGAGCATCTACTGCA 197 219 1539 Antisense
TGGATACATGGGAATCTTCGCCGCC 126 551 1644 Antisense
ACCGGCACCATCGGATACGTCGGAA 289 87 1684 Antisense
Sequence Source Affymetrix Proprietary Database