[Home] | [Total List]

[173193_s_at]

Description AV177163_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AV177163 /DEF=Caenorhabditis elegans cDNA clone:yk525c11 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 30      6grp_high1_10_10 > 05      4grp_highest_8_8 > 26      4grp_high_8_8 > 59      6grp_highest_nonorm > 56      6grp_total > 05      4grp_total > 60      6grp_highest_sub > De      6grp_cgc > 22      6grp_high1_sub > De      6grp_cgc_sub > De      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2180
1 2 3 4 range
A 3592.8
(2.2)
P 		2284.3
(-1.6)
P 		3876.8
(3)
P 		1808.2
(-3)
P 		2069
B 3286
(-1.3)
P 		3468.2
(-0.2)
P 		3988.2
(3)
P 		3009.3
(-3)
P 		979
C 3358
(2.8)
P 		3370.2
(3)
P 		3316
(2.3)
P 		2935.1
(-3)
P 		435
avr 3412.3
(1.3) 		3040.9
(-0.6) 		3727
(3) 		2584.2
(-3) 		1143

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1258
1 2 3 4 5 6 range
A 1921.8
(-1.8)
P 		2517.8
(3)
P 		2148.2
(-0)
P 		1780.2
(-3)
P 		2428.3
(2.3)
P 		2057.5
(-0.7)
P 		738
B 2844.2
(3)
P 		2123.2
(-0.4)
P 		1953.2
(-1.3)
P 		2576.3
(1.7)
P 		1910.2
(-1.5)
P 		1586.5
(-3)
P 		1258
C 2608.7
(3)
P 		2355.6
(1.5)
P 		2277.8
(1)
P 		1608
(-3)
P 		2175.6
(0.4)
P 		2208
(0.6)
P 		1001
avr 2458.2
(3) 		2332.2
(1.5) 		2126.4
(-0.9) 		1988.2
(-2.6) 		2171.4
(-0.4) 		1950.7
(-3) 		508
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1043
1 2 3 4 range
A 1308.1
(3)
P 		495.9
(-1.7)
P 		1013.5
(1.3)
P 		264.7
(-3)
P 		1043
B 1047.9
(3)
P 		856.6
(0.2)
P 		924.2
(1.2)
P 		641.3
(-3)
P 		407
C 1111.6
(2.6)
P 		969
(1.3)
P 		1155.7
(3)
P 		494.9
(-3)
P 		661
avr 1155.9
(3) 		773.8
(-0.3) 		1031.1
(1.9) 		467
(-3) 		689

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 666
1 2 3 4 5 6 range
A 354.3
(-3)
P 		895.4
(3)
P 		467.8
(-1.7)
P 		451.5
(-1.9)
P 		732.7
(1.2)
P 		500.9
(-1.4)
P 		541
B 989.6
(3)
P 		706.7
(-0.3)
P 		474.3
(-3)
P 		682.4
(-0.6)
P 		776.1
(0.5)
P 		591.6
(-1.6)
P 		515
C 966.9
(3)
P 		718.8
(0.7)
P 		579.7
(-0.6)
P 		323.4
(-3)
P 		704
(0.5)
P 		739.1
(0.9)
P 		644
avr 770.3
(2.9) 		773.6
(3) 		507.3
(-2.6) 		485.8
(-3) 		737.6
(2.2) 		610.5
(-0.4) 		288
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173193_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27055
Sequence Type Exemplar sequence
Representative Public ID AV177163 NCBI
Target Description AV177163_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AV177163 /DEF=Caenorhabditis elegans cDNA clone:yk525c11 : 3prime end, single read.
Cluster Evidence This cluster is supported by a EST Transcript.
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_076671(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076671 NCBI Caenorhabditis elegans LAMP/CD68 related family member (lmp-1) (lmp-1) mRNA, complete cds. 11/11 A 
C03B1.12.1 ENSEMBL cdna:known chromosome:CEL140:X:6376393:6377639:-1 gene:C03B1.12 11/11 A 
C03B1.12.2 ENSEMBL cdna:known chromosome:CEL140:X:6376393:6377643:-1 gene:C03B1.12 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
chrX:6376503-6376776(-) 91.0 91.0
Public Domain and Genome References
Gene Title
Gene Symbol lmp-1
Ensembl C03B1.12
Entrez Gene 180912 Entrez gene
SwissProt Q11117 EMBL-EBI
WormBase CE03912 Wormbase
Functional Annotations
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAA81746 Lamp (lysosome-associated membrane protein) homolog protein 1 [Caenorhabditis elegans] ref|NP_509072.1| LAMP/CD68 related family member (lmp-1) [Caenorhabditis elegans] gb|AAD56712.1| LMP-1 protein [Caenorhabditis elegans] sp|Q11117|LMP1_CAEEL LAMP family protein lmp-1 precursor 1.0E-114
blast CAE61249 Hypothetical protein CBG05052 [Caenorhabditis briggsae] 6.0E-88
Protein Domains
Database ID Description E-Value
Pfam IPR002000 EMBL-EBI Lysosome-associated membrane glycoprotein (Lamp)/CD68 9.4E-7
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_509072.1 1 202-224
C03B1.12.1 1 202-224
C03B1.12.2 1 202-224
Sequence
Target Sequence 
>C. ELEGANS:173193_S_AT
tatgccagcgtctaaatctttgctattgttgtgaaactgttcttatcatcattcaatcaa
aatattatcaatagccttgttcatgctcagaatctgatgattctttgtttccatttcctc
tgttgcaatgttgtgcaatcatccaacatttcctcttttacttatctcagttctatttca
tttttctgatattctcttccatt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TATGCCAGCGTCTAAATCTTTGCTA 386 657 61 Antisense
GCGTCTAAATCTTTGCTATTGTTGT 533 291 68 Antisense
CTTTGCTATTGTTGTGAAACTGTTC 237 223 78 Antisense
TTCTTATCATCATTCAATCAAAATA 204 691 100 Antisense
TTCCATTTCCTCTGTTGCAATGTTG 353 699 169 Antisense
TCCTCTGTTGCAATGTTGTGCAATC 414 593 176 Antisense
TTGTGCAATCATCCAACATTTCCTC 384 709 191 Antisense
CATTTCCTCTTTTACTTATCTCAGT 408 215 207 Antisense
CCTCTTTTACTTATCTCAGTTCTAT 58 269 212 Antisense
CAGTTCTATTTCATTTTTCTGATAT 343 207 228 Antisense
CATTTTTCTGATATTCTCTTCCATT 619 215 239 Antisense
Sequence Source Affymetrix Proprietary Database