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[190985_at] 7TM chemoreceptor, srj family

Description F31F4.8 /REP_DB=WormBase Gene ID /WP=CE26679 /GEN=srj-6 /TR=O17125 /GB=AAG24098.2 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=chemoreceptor
Cluster 6grp_total > 10      4grp_total > 03      6grp_cgc > 54      6grp_total_sub > Hat      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 182
1 2 3 4 range
A 72.8
(-1)
A 		21.9
(-3)
A 		34.9
(-2.5)
A 		174.9
(3)
A 		153
B 55.6
(-1.8)
A 		53.6
(-1.9)
A 		34.4
(-3)
A 		141.5
(3)
A 		107
C 49.7
(-2.5)
A 		43.1
(-2.7)
A 		35
(-3)
A 		203.8
(3)
A 		169
avr 59.4
(-1.9) 		39.5
(-2.8) 		34.8
(-3) 		173.4
(3) 		139

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 74
1 2 3 4 5 6 range
A 17.9
(-2.4)
A 		33.9
(-0.9)
A 		77.1
(3)
A 		20.9
(-2.1)
A 		44
(0)
A 		10.9
(-3)
A 		66
B 35.7
(0)
A 		67.9
(3)
A 		18.6
(-1.6)
A 		3.4
(-3)
A 		57.2
(2)
A 		43.4
(0.7)
A 		65
C 39.7
(-2)
A 		52.5
(0.8)
A 		62.3
(3)
A 		44.5
(-0.9)
A 		58.8
(2.2)
A 		35.1
(-3)
A 		27
avr 31.1
(-1.4) 		51.4
(2.6) 		52.7
(2.9) 		22.9
(-3) 		53.3
(3) 		29.8
(-1.6) 		30
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 30
1 2 3 4 range
A 26.5
(3)
A 		4.8
(-3)
A 		9.1
(-1.8)
A 		25.6
(2.8)
A 		22
B 17.7
(-0.4)
A 		13.2
(-1.6)
A 		8
(-3)
A 		30.2
(3)
A 		22
C 16.4
(-1.9)
A 		12.4
(-2.9)
A 		12.2
(-3)
A 		34.4
(3)
A 		22
avr 20.2
(0.1) 		10.1
(-2.9) 		9.8
(-3) 		30.1
(3) 		20

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 22
1 2 3 4 5 6 range
A 3.3
(-2.7)
A 		12
(1)
A 		16.8
(3)
A 		5.3
(-1.9)
A 		13.3
(1.5)
A 		2.7
(-3)
A 		14
B 12.4
(0.1)
A 		22.6
(2.8)
A 		4.5
(-2)
A 		0.9
(-3)
A 		23.2
(3)
A 		16.2
(1.1)
A 		22
C 14.7
(0.4)
A 		16
(1.2)
A 		15.9
(1.2)
A 		8.9
(-3)
A 		19
(3)
A 		11.7
(-1.3)
A 		10
avr 10.1
(-0.7) 		16.9
(2.3) 		12.4
(0.3) 		5
(-3) 		18.5
(3) 		10.2
(-0.7) 		14
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190985_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.15459
Sequence Type Exemplar sequence
Representative Public ID F31F4.8 NCBI
Target Description F31F4.8 /REP_DB=WormBase Gene ID /WP=CE26679 /GEN=srj-6 /TR=O17125 /GB=AAG24098.2 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=chemoreceptor
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_070879(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070879 NCBI Caenorhabditis elegans Serpentine Receptor, class J family member (srj-6) (srj-6) mRNA, complete cds. 11/11 None
SNAP00000012361 ENSEMBL cdna:SNAP chromosome:CEL140:V:653132:654155:-1 11/11 None
GENEFINDER00000012378 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:650100:655615:-1 9/11 None
F31F4.8 ENSEMBL cdna:known chromosome:CEL140:V:653132:654332:-1 gene:F31F4.8 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
chrV:653131-654332(-) 100.0 100.0
Public Domain and Genome References
Gene Title 7TM chemoreceptor, srj family
Gene Symbol srj-6
Ensembl F31F4.8
Entrez Gene 191933 Entrez gene
SwissProt O17125 EMBL-EBI
WormBase CE09828 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast NP_503280 Serpentine Receptor, class J family member (srj-6) [Caenorhabditis elegans] gb|AAG24098.3| Serpentine receptor, class j protein 6 [Caenorhabditis elegans] pir||T32305 hypothetical protein F31F4.8 - Caenorhabditis elegans 0.0
blast NP_503279 Serpentine Receptor, class J family member (srj-5) [Caenorhabditis elegans] gb|AAG24099.1| Serpentine receptor, class j protein 5 [Caenorhabditis elegans] 1.0E-172
blast NP_503279 Serpentine Receptor, class J family member (srj-5) [Caenorhabditis elegans] gb|AAG24099.1| Serpentine receptor, class j protein 5 [Caenorhabditis elegans] 1.0E-169
blast NP_503280 Serpentine Receptor, class J family member (srj-6) [Caenorhabditis elegans] gb|AAG24098.3| Serpentine receptor, class j protein 6 [Caenorhabditis elegans] pir||T32305 hypothetical protein F31F4.8 - Caenorhabditis elegans 1.0E-152
blast CAE71085 Hypothetical protein CBG17935 [Caenorhabditis briggsae] 1.0E-145
blast CAE71085 Hypothetical protein CBG17935 [Caenorhabditis briggsae] 1.0E-142
blast NP_503279 Serpentine Receptor, class J family member (srj-5) [Caenorhabditis elegans] gb|AAG24099.1| Serpentine receptor, class j protein 5 [Caenorhabditis elegans] 1.0E-135
blast NP_503279 Serpentine Receptor, class J family member (srj-5) [Caenorhabditis elegans] gb|AAG24099.1| Serpentine receptor, class j protein 5 [Caenorhabditis elegans] 1.0E-122
blast NP_503280 Serpentine Receptor, class J family member (srj-6) [Caenorhabditis elegans] gb|AAG24098.3| Serpentine receptor, class j protein 6 [Caenorhabditis elegans] pir||T32305 hypothetical protein F31F4.8 - Caenorhabditis elegans 1.0E-118
Protein Domains
Database ID Description E-Value
Pfam IPR003003 EMBL-EBI 7TM chemoreceptor, subfamily 2 1.2E-51
Pfam IPR003003 EMBL-EBI 7TM chemoreceptor, subfamily 2 1.2E-4
Pfam IPR003003 EMBL-EBI 7TM chemoreceptor, subfamily 2 1.2E-5
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_503280.2 7 10-32,45-67,96-115,128-147,196-218,244-266,276-298
F31F4.8 7 10-32,45-67,96-115,128-147,196-218,241-263,278-300
SNAP00000012361 6 5-24,29-51,63-82,131-153,179-201,211-233
GENEFINDER00000012378 12 20-42,46-68,89-108,147-169,190-212,292-314,340-362,382-401,449-471,498-520,532-554,574-596
Sequence
Target Sequence 
>C. ELEGANS:190985_AT
gatgcttcaacctcttggagtttttgctatgattgctctcacagctgcccacggagcatc
gtggacttggctctgcgactggtgtttggcaccaaatgaagagatcagggatatcgtccg
gcctgcattcaaggaggtacaccatgtcaactcggataatatatccctgctcactgggca
atataggaatgccagcaattttgttgtctacaaaagttggttcggtatcttatcactcac
cctattttcatgctactgcatgagtgtatatctagttcttggatataagattatgaagaa
aatgaatcaaaataccaacatgagcacaattagtgcaacactaaaccggcaacttttcaa
ggcgctggttgcccaaacatgtatcccaatgttcgccagttttctaccaactgtcattgc
ctggtatgcgccgatgtttttgattaatgttacgtggtggaacaactatatctgcaatgt
tgctttatctgcttttccgttgatcgaccccgtggtggtgatcta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATGCTTCAACCTCTTGGAGTTTTT 226 411 381 Antisense
AGAGATCAGGGATATCGTCCGGCCT 580 67 480 Antisense
GTCCGGCCTGCATTCAAGGAGGTAC 384 475 496 Antisense
GGAGGTACACCATGTCAACTCGGAT 600 515 513 Antisense
ATATATCCCTGCTCACTGGGCAATA 21 19 539 Antisense
GTTGGTTCGGTATCTTATCACTCAC 210 437 596 Antisense
GCTGGTTGCCCAAACATGTATCCCA 398 293 744 Antisense
ATGTTCGCCAGTTTTCTACCAACTG 49 47 769 Antisense
CCAACTGTCATTGCCTGGTATGCGC 30 277 787 Antisense
AATGTTGCTTTATCTGCTTTTCCGT 276 163 856 Antisense
TGATCGACCCCGTGGTGGTGATCTA 485 473 881 Antisense
Sequence Source Affymetrix Proprietary Database