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[178608_s_at]

Description F25D7.1 /REP_DB=WormBase Gene ID /WP=CE09629 /TR=Q93561 /GB=CAB01696.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 29      6grp_high1_10_10 > 92      4grp_highest_8_8 > 20      4grp_high_8_8 > 31      6grp_highest_nonorm > 55      6grp_total > 94      4grp_total > 32      6grp_highest_sub > 04_05      6grp_cgc > 87      6grp_high1_sub > 04_05      6grp_cgc_sub > 05      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 746
1 2 3 4 range
A 872.2
(-3)
P 		1283.8
(1.6)
P 		1406.2
(3)
P 		1210.9
(0.8)
P 		534
B 822.3
(-3)
P 		1072.7
(-0.8)
P 		1519.4
(3)
P 		1476.8
(2.6)
P 		697
C 773.9
(-3)
P 		942.7
(-1.6)
P 		1513.9
(3)
P 		1406
(2.1)
P 		740
avr 822.8
(-3) 		1099.7
(-0.5) 		1479.8
(3) 		1364.6
(1.9) 		657

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 837
1 2 3 4 5 6 range
A 1084.3
(-3)
P 		1137.8
(-2.4)
P 		1239.4
(-1.2)
P 		1495.9
(1.7)
P 		1609.6
(3)
P 		1262.8
(-1)
P 		525
B 1123.7
(-3)
P 		1141.4
(-2.9)
P 		1271.6
(-1.9)
P 		1615.8
(0.7)
P 		1921.3
(3)
P 		1386.8
(-1)
P 		798
C 1148.5
(-3)
P 		1202.8
(-2.6)
P 		1262.8
(-2.1)
P 		1913.7
(3)
P 		1504.1
(-0.2)
P 		1415.8
(-0.9)
P 		765
avr 1118.8
(-3) 		1160.7
(-2.6) 		1257.9
(-1.5) 		1675.1
(3) 		1678.3
(3) 		1355.1
(-0.5) 		560
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 351
1 2 3 4 range
A 317.6
(1.4)
P 		278.7
(0.2)
P 		367.6
(3)
P 		177.2
(-3)
P 		190
B 262.2
(-3)
P 		264.9
(-2.8)
P 		352.1
(3)
P 		314.7
(0.5)
P 		90
C 256.2
(-2.6)
P 		271
(-2.3)
P 		527.7
(3)
P 		237.1
(-3)
P 		291
avr 278.7
(-1.8) 		271.5
(-2) 		415.8
(3) 		243
(-3) 		173

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 581
1 2 3 4 5 6 range
A 199.9
(-3)
P 		404.6
(1.3)
P 		269.9
(-1.5)
P 		379.4
(0.8)
P 		485.7
(3)
P 		307.5
(-0.7)
P 		286
B 391
(-2)
P 		379.9
(-2.1)
P 		308.8
(-3)
P 		428
(-1.5)
P 		780.6
(3)
P 		517.1
(-0.4)
P 		472
C 425.7
(0.8)
P 		367
(-1.3)
P 		321.4
(-3)
P 		384.8
(-0.7)
P 		486.7
(3)
P 		473.9
(2.5)
P 		165
avr 338.9
(-2.2) 		383.8
(-1.2) 		300
(-3) 		397.4
(-0.9) 		584.3
(3) 		432.8
(-0.2) 		284
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 178608_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1500
Sequence Type Exemplar sequence
Representative Public ID F25D7.1 NCBI
Target Description F25D7.1 /REP_DB=WormBase Gene ID /WP=CE09629 /TR=Q93561 /GB=CAB01696.1 /SUBMIT=HINXTON /CHR=1 /FEA=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_060320(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060320 NCBI Caenorhabditis elegans F25D7.1 (F25D7.1) mRNA, complete cds. 11/11 None
SNAP00000011697 ENSEMBL cdna:SNAP chromosome:CEL140:I:10407279:10408299:-1 11/11 None
GENEFINDER00000011707 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:10407279:10408299:-1 11/11 None
F25D7.1 ENSEMBL cdna:known chromosome:CEL140:I:10407122:10408299:-1 gene:F25D7.1 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
chrI:10407209-10408230(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol cup-2
Ensembl F25D7.1
Entrez Gene 172915 Entrez gene
SwissProt Q93561 EMBL-EBI
WormBase CE09629 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1584938_AT similar to Der1-like domain family, member 1 cfa
CANINE_2:CFA.11324.1.A1_AT similar to Der1-like domain family, member 1 cfa
CANINE_2:CFAAFFX.2365.1.S1_AT similar to Der1-like domain family, member 1 cfa
CANINE_2:CFAAFFX.2368.1.S1_AT similar to Der1-like domain family, member 1 cfa
CANINE_2:CFAAFFX.2368.1.S1_S_AT similar to Der1-like domain family, member 1 cfa
DROSOPHILA_2:1624372_AT dm
DROSGENOME1:152197_AT dm
CHICKEN:GGAAFFX.11528.1.S1_AT Der1-like domain family, member 1 gga
HG-U133_PLUS_2:225488_AT Der1-like domain family, member 1 hs
HG-U133B:225488_AT Der1-like domain family, member 1 hs
HU35KSUBC:RC_F13780_AT Der1-like domain family, member 1 hs
HU35KSUBD:RC_AA279171_AT Der1-like domain family, member 1 hs
HU35KSUBD:RC_AA461503_AT Der1-like domain family, member 1 hs
HG-U133A:219402_S_AT Der1-like domain family, member 1 hs
HG-U133_PLUS_2:219402_S_AT Der1-like domain family, member 1 hs
HG-U133A_2:219402_S_AT Der1-like domain family, member 1 hs
HG-U133A:218172_S_AT Der1-like domain family, member 1 hs
HG-U133_PLUS_2:218172_S_AT Der1-like domain family, member 1 hs
HG-U133A_2:218172_S_AT Der1-like domain family, member 1 hs
U133_X3P:G8924181_3P_A_AT Der1-like domain family, member 1 hs
U133_X3P:HS.323114.1.S1_3P_A_AT Der1-like domain family, member 1 hs
U133_X3P:HS.241576.0.S2_3P_AT Der1-like domain family, member 1 hs
HG-U133_PLUS_2:222543_AT Der1-like domain family, member 1 hs
HG-U133B:222543_AT Der1-like domain family, member 1 hs
HG-U95B:45326_AT Der1-like domain family, member 1 hs
HG-U95E:91552_AT Der1-like domain family, member 1 hs
MG-U74AV2:93982_AT Der1-like domain family, member 1 mm
MG-U74AV2:93983_AT Der1-like domain family, member 1 mm
MOE430A:1423082_AT Der1-like domain family, member 1 mm
MOUSE430A_2:1423082_AT Der1-like domain family, member 1 mm
MOUSE430_2:1423082_AT Der1-like domain family, member 1 mm
MOE430A:1433563_S_AT Der1-like domain family, member 1 mm
MOUSE430A_2:1433563_S_AT Der1-like domain family, member 1 mm
MOUSE430_2:1433563_S_AT Der1-like domain family, member 1 mm
MOE430A:1415693_AT Der1-like domain family, member 1 mm
MOE430B:1415693_AT Der1-like domain family, member 1 mm
MOUSE430A_2:1415693_AT Der1-like domain family, member 1 mm
MOUSE430_2:1415693_AT Der1-like domain family, member 1 mm
MOE430A:1437723_S_AT Der1-like domain family, member 1 mm
MOUSE430A_2:1437723_S_AT Der1-like domain family, member 1 mm
MOUSE430_2:1437723_S_AT Der1-like domain family, member 1 mm
MU19KSUBA:TC19474_AT Der1-like domain family, member 1, mRNA (cDNA clone MGC:6901 IMAGE:2655640) mm
MU19KSUBA:TC23317_AT Der1-like domain family, member 1, mRNA (cDNA clone MGC:6901 IMAGE:2655640) mm
MU19KSUBB:TC31163_AT Der1-like domain family, member 1, mRNA (cDNA clone MGC:6901 IMAGE:2655640) mm
RG-U34C:RC_AA818203_AT similar to Der1-like domain family, member 1 rn
RG-U34C:RC_AI146034_AT similar to Der1-like domain family, member 1 rn
RAE230A:1367529_AT similar to Der1-like domain family, member 1 rn
RAE230B:1367529_AT similar to Der1-like domain family, member 1 rn
RAT230_2:1367529_AT similar to Der1-like domain family, member 1 rn
RAE230A:1389615_AT similar to Der1-like domain family, member 1 rn
RAT230_2:1389615_AT similar to Der1-like domain family, member 1 rn
RAE230A:1374581_AT similar to Der1-like domain family, member 1 rn
RAT230_2:1374581_AT similar to Der1-like domain family, member 1 rn
Protein Similarities
Method ID Description E-Value
blast CAB01696 Hypothetical protein F25D7.1 [Caenorhabditis elegans] ref|NP_492721.1| F25D7.1 [Caenorhabditis elegans] sp|Q93561|DERL1_CAEEL Derlin-1 (DER1-like protein 1) (cDerlin-1) 1.0E-149
blast CAE58932 Hypothetical protein CBG02198 [Caenorhabditis briggsae] 1.0E-145
blast XP_797383 PREDICTED: similar to Der1-like domain family, member 1 [Strongylocentrotus purpuratus] 4.0E-69
Protein Domains
Database ID Description E-Value
Pfam IPR007599 EMBL-EBI Der1-like domain 4.3E-105
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_492721.1 3 16-38,58-80,101-120
F25D7.1 3 16-38,58-80,101-120
SNAP00000011697 3 16-38,58-80,101-120
GENEFINDER00000011707 3 16-38,58-80,101-120
Sequence
Target Sequence 
>C. ELEGANS:178608_S_AT
ttctggaggcctctgacagcgttaatatattatccagtcacaccgcagacgggattccat
tggctgatgatgtgctattttctttacaactattcaaaagcattggaaagtgaaacatat
cgcggaagatcagcggattaccttttcatgctcattttcaactggttcttctgctcggga
ctttgcatggctctggatatctacttccttctcgaaccgatggtgatctcagtactttac
gtctggtgccaagtcaacaaggacacaattgtatcgttctggtttggaatgcgattccca
gctcgctaccttccatgggtgctctggggcttcaatgccgttctccgtggtggtggaacc
aacgaacttgtcggaattctggttggacatgcctatttctttgtggctcttaaatatcca
gacgaatacggcgttgatttgatctccactcctgaatttttgca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCTGGAGGCCTCTGACAGCGTTAA 473 693 163 Antisense
ATATATTATCCAGTCACACCGCAGA 40 21 187 Antisense
ACCGCAGACGGGATTCCATTGGCTG 125 89 204 Antisense
AGATCAGCGGATTACCTTTTCATGC 467 65 289 Antisense
CATGCTCATTTTCAACTGGTTCTTC 244 211 309 Antisense
TTCTTCTGCTCGGGACTTTGCATGG 533 689 328 Antisense
GCATGGCTCTGGATATCTACTTCCT 398 311 347 Antisense
TACTTCCTTCTCGAACCGATGGTGA 340 643 364 Antisense
ATCTCAGTACTTTACGTCTGGTGCC 383 29 388 Antisense
GACATGCCTATTTCTTTGTGGCTCT 441 369 548 Antisense
TGATCTCCACTCCTGAATTTTTGCA 572 565 602 Antisense
Sequence Source Affymetrix Proprietary Database