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[190884_at] Putative membrane protein

Description C29F4.2 /REP_DB=WormBase Gene ID /WP=CE03039 /TR=Q18303 /GB=CAA92730.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Putative membrane protein
Cluster 6grp_high1_10_10 > 21      6grp_total > 32      4grp_total > 54      6grp_high1_sub > 03      6grp_total_sub > Hat      6grp_rule_based > S3      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 362
1 2 3 4 range
A 372.9
(3)
P 		170.7
(-1)
P 		167.8
(-1)
A 		66.4
(-3)
A 		307
B 354.3
(3)
P 		178.8
(-0.6)
P 		192.1
(-0.3)
P 		58.7
(-3)
A 		296
C 421.1
(3)
P 		176.3
(-1.8)
P 		192.7
(-1.5)
P 		113.6
(-3)
A 		308
avr 382.8
(3) 		175.3
(-1.1) 		184.2
(-0.9) 		79.6
(-3) 		303

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 233
1 2 3 4 5 6 range
A 235.6
(1.2)
P 		300.7
(3)
P 		255
(1.8)
P 		241.2
(1.4)
P 		147.9
(-1.2)
P 		81
(-3)
A 		220
B 181.8
(-0.1)
P 		257.8
(1.9)
P 		301.7
(3)
P 		163.8
(-0.6)
A 		143
(-1.2)
P 		72.4
(-3)
P 		229
C 274.5
(2.1)
P 		251.4
(1.5)
P 		305
(3)
P 		221.6
(0.6)
P 		184.5
(-0.5)
P 		96.2
(-3)
P 		209
avr 230.6
(1.3) 		270
(2.5) 		287.2
(3) 		208.9
(0.7) 		158.5
(-0.8) 		83.2
(-3) 		204
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 130
1 2 3 4 range
A 135.8
(3)
P 		37.1
(-1.7)
P 		43.9
(-1.4)
A 		9.7
(-3)
A 		126
B 113
(3)
P 		44.1
(-1.1)
P 		44.5
(-1.1)
P 		12.5
(-3)
A 		101
C 139.4
(3)
P 		50.7
(-1.4)
P 		67.2
(-0.6)
P 		19.2
(-3)
A 		120
avr 129.4
(3) 		44
(-1.4) 		51.9
(-1) 		13.8
(-3) 		116

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 87
1 2 3 4 5 6 range
A 43.4
(-1.4)
P 		106.9
(3)
P 		55.5
(-0.5)
P 		61.2
(-0.1)
P 		44.6
(-1.3)
P 		19.7
(-3)
A 		87
B 63.3
(0.7)
P 		85.8
(3)
P 		73.3
(1.7)
P 		43.4
(-1.3)
A 		58.1
(0.2)
P 		27
(-3)
P 		59
C 101.7
(3)
P 		76.7
(0.8)
P 		77.6
(0.9)
P 		44.6
(-1.9)
P 		59.7
(-0.6)
P 		32.2
(-3)
P 		70
avr 69.5
(1.1) 		89.8
(3) 		68.8
(1) 		49.7
(-0.8) 		54.1
(-0.4) 		26.3
(-3) 		64
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190884_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8973
Sequence Type Exemplar sequence
Representative Public ID C29F4.2 NCBI
Target Description C29F4.2 /REP_DB=WormBase Gene ID /WP=CE03039 /TR=Q18303 /GB=CAA92730.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Putative 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_069707(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069707 NCBI Caenorhabditis elegans C29F4.2 (C29F4.2) mRNA, complete cds. 11/11 None
SNAP00000037123 ENSEMBL cdna:SNAP chromosome:CEL140:IV:11226682:11228854:-1 11/11 None
GENEFINDER00000037125 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:11226682:11228870:-1 11/11 None
C29F4.2 ENSEMBL cdna:known chromosome:CEL140:IV:11226682:11230419:-1 gene:C29F4.2 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:11226687-11230425(-) 100.0 100.0
Public Domain and Genome References
Gene Title Putative membrane protein
Ensembl C29F4.2
Entrez Gene 178030 Entrez gene
SwissProt Q18303 EMBL-EBI
WormBase CE03039 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.1611.1.S1_AT similar to vitelliform macular dystrophy 2-like 3 cfa
CANINE_2:CFAAFFX.1612.1.S1_S_AT similar to vitelliform macular dystrophy 2-like 3 cfa
DROSOPHILA_2:1638972_AT Bestrophin 3 dm
DROSGENOME1:148799_AT Bestrophin 3 dm
CHICKEN:GGA.14572.1.S1_AT vitelliform macular dystrophy 2-like 3 gga
CHICKEN:GGAAFFX.6302.1.S1_AT vitelliform macular dystrophy 2-like 3 gga
U133_X3P:HS2.122128.2.S1_3P_AT vitelliform macular dystrophy 2-like 3 hs
U133_X3P:HS.125296.0.A1_3P_AT vitelliform macular dystrophy 2-like 3 hs
HG-U133_PLUS_2:1555492_A_AT vitelliform macular dystrophy 2-like 3 hs
HG-U133_PLUS_2:237003_AT vitelliform macular dystrophy 2-like 3 hs
HG-U133B:237003_AT vitelliform macular dystrophy 2-like 3 hs
HG-U95D:76431_AT vitelliform macular dystrophy 2-like 3 hs
HG-U95E:81849_AT vitelliform macular dystrophy 2-like 3 hs
U133_X3P:HS2.378547.1.S1_3P_AT Vitelliform macular dystrophy 2-like 3 hs
HG-U133_PLUS_2:1564632_AT Vitelliform macular dystrophy 2-like 3 hs
HG-U133_PLUS_2:240178_AT Vitelliform macular dystrophy 2-like 3 hs
HG-U133B:240178_AT Vitelliform macular dystrophy 2-like 3 hs
HG-U95B:56718_AT Vitelliform macular dystrophy 2-like 3 hs
U133_X3P:HS.9451.0.A1_3P_AT Vitelliform macular dystrophy 2-like 3 hs
HU35KSUBB:RC_H94266_S_AT Vitelliform macular dystrophy 2-like 3 hs
Protein Similarities
Method ID Description E-Value
blast CAA92730 Hypothetical protein C29F4.2 [Caenorhabditis elegans] ref|NP_502108.1| C29F4.2 [Caenorhabditis elegans] 0.0
blast CAE56138 Hypothetical protein CBG23750 [Caenorhabditis briggsae] 0.0
blast CAE62025 Hypothetical protein CBG06036 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000615 EMBL-EBI Bestrophin 1.0E-126
Pfam IPR000615 EMBL-EBI Bestrophin 1.0E-126
Pfam IPR000615 EMBL-EBI Bestrophin 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_502108.1 4 76-98,119-138,273-295,315-332
C29F4.2 4 76-98,119-138,273-295,315-332
SNAP00000037123 1 13-30
GENEFINDER00000037125 3 13-35,170-192,212-229
Sequence
Target Sequence 
>C. ELEGANS:190884_AT
aatgatacagtatcccctctttattcaagtgctgctgcacaaagaaatgtcaatttctac
tttggaagtgcaaccaatgcagatgcccaaataccggatgacgttcgtcaaatcacaatg
attcctcatccattaaatgaaaaactagatcaaatgtacggaaaacgaacaaaccgaccg
cctgtacaaagtgtggttgaattaaaaagagatcagaggttttccactggaaataatcga
aaacagacattggaagcaaagttttcaaataaacttggagctatgttccagaagagacac
tctaaatctctaacatttacacctgaatccagcacaaaagctcgtgcttcaacagacatc
gaaactgtttctacatttgaaaatacacagaaaccatgttacagtaatccagattgtatc
gtggaagttgatgaagaatctcaagatattccaaaagtaacagaagagccaaaacaggaa
ccgccta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AATGATACAGTATCCCCTCTTTATT 676 161 1159 Antisense
TCCCCTCTTTATTCAAGTGCTGCTG 327 597 1171 Antisense
GAAGTGCAACCAATGCAGATGCCCA 625 335 1223 Antisense
GATGCCCAAATACCGGATGACGTTC 590 403 1240 Antisense
AAATCACAATGATTCCTCATCCATT 483 117 1268 Antisense
AACCGACCGCCTGTACAAAGTGTGG 675 95 1330 Antisense
GAGATCAGAGGTTTTCCACTGGAAA 320 397 1367 Antisense
ATCTCTAACATTTACACCTGAATCC 78 33 1464 Antisense
ACCTGAATCCAGCACAAAAGCTCGT 589 87 1479 Antisense
AAAGCTCGTGCTTCAACAGACATCG 663 123 1495 Antisense
GAAGAGCCAAAACAGGAACCGCCTA 381 335 1621 Antisense
Sequence Source Affymetrix Proprietary Database