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[172888_x_at] possible trans-splice site at 5004

Description C40D2.2 /REP_DB=WormBase Gene ID /WP=CE19374 /TR=O76558 /GB=AAC26265.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=possible trans-splice site at 5004
Cluster 6grp_highest_10_10 > 27      6grp_high1_10_10 > 72      4grp_highest_8_8 > 21      4grp_high_8_8 > 23      6grp_highest_nonorm > 53      6grp_total > 72      4grp_total > 16      6grp_highest_sub > 03_04      6grp_high1_sub > 04      6grp_total_sub > Hat      6grp_rule_based > S4      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 574
1 2 3 4 range
A 494
(-3)
P 		628.7
(-0.1)
P 		659.8
(0.5)
P 		776
(3)
P 		282
B 510.9
(-3)
P 		606.4
(-2)
P 		687.5
(-1.1)
P 		1068.4
(3)
P 		558
C 547.7
(-3)
P 		551.4
(-3)
P 		767.7
(-0.4)
P 		1048
(3)
P 		500
avr 517.5
(-3) 		595.5
(-2) 		705
(-0.5) 		964.1
(3) 		447

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 753
1 2 3 4 5 6 range
A 396
(-3)
P 		753.3
(0.2)
P 		1066.7
(3)
P 		1003.8
(2.4)
P 		741.7
(0.1)
P 		531.4
(-1.8)
P 		671
B 396.4
(-3)
P 		852.9
(1.5)
P 		965.1
(2.6)
P 		1008.5
(3)
P 		765.1
(0.6)
P 		703.6
(0)
P 		612
C 437.3
(-3)
P 		791.2
(-0)
P 		779.3
(-0.1)
P 		1148.9
(3)
P 		660.8
(-1.1)
P 		759.5
(-0.3)
P 		712
avr 409.9
(-3) 		799.1
(0.6) 		937
(1.9) 		1053.7
(3) 		722.5
(-0.1) 		664.8
(-0.6) 		644
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 154
1 2 3 4 range
A 179.9
(3)
P 		136.5
(-0.9)
P 		172.5
(2.3)
P 		113.6
(-3)
P 		66
B 162.9
(-2)
P 		149.8
(-3)
P 		159.3
(-2.3)
P 		227.7
(3)
P 		78
C 181.3
(-1.7)
P 		158.5
(-3)
P 		267.6
(3)
P 		176.7
(-2)
P 		109
avr 174.7
(0.1) 		148.3
(-3) 		199.8
(3) 		172.7
(-0.2) 		52

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 238
1 2 3 4 5 6 range
A 73
(-3)
P 		267.9
(3)
P 		232.3
(1.9)
P 		254.6
(2.6)
P 		223.8
(1.6)
P 		129.4
(-1.3)
P 		195
B 137.9
(-3)
P 		283.9
(2.1)
P 		234.4
(0.3)
P 		267.1
(1.5)
P 		310.8
(3)
P 		262.4
(1.3)
P 		173
C 162.1
(-3)
P 		241.4
(2.2)
P 		198.3
(-0.6)
P 		231.1
(1.5)
P 		213.8
(0.4)
P 		254.2
(3)
P 		92
avr 124.3
(-3) 		264.4
(3) 		221.7
(1.2) 		250.9
(2.4) 		249.5
(2.4) 		215.3
(0.9) 		140
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172888_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4391
Sequence Type Exemplar sequence
Representative Public ID C40D2.2 NCBI
Target Description C40D2.2 /REP_DB=WormBase Gene ID /WP=CE19374 /TR=O76558 /GB=AAC26265.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=possible trans-splice site at 5004
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_061745(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_061745 NCBI Caenorhabditis elegans C40D2.2 (C40D2.2) mRNA, complete cds. 11/11 None
SNAP00000024877 ENSEMBL cdna:SNAP chromosome:CEL140:II:1996557:1998473:1 10/11 None
GENEFINDER00000024883 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:1996557:1998473:1 11/11 None
C40D2.2.2 ENSEMBL cdna:known chromosome:CEL140:II:1996531:1998473:1 gene:C40D2.2 11/11 None
C40D2.2.1 ENSEMBL cdna:known chromosome:CEL140:II:1996538:1998515:1 gene:C40D2.2 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_061749 1/11 Cross Hyb Matching Probes A 
NM_061738 4/11 Cross Hyb Matching Probes A 
SNAP00000002419 2/11 Cross Hyb Matching Probes None
GENEFINDER00000002444 2/11 Cross Hyb Matching Probes None
SNAP00000013031 3/11 Cross Hyb Matching Probes None
GENEFINDER00000013042 4/11 Cross Hyb Matching Probes None
ZK250.8 4/11 Cross Hyb Matching Probes A 
F59H6.4 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:1996555-1998472(+) 100.0 100.0
Public Domain and Genome References
Gene Title possible trans-splice site at 5004
Ensembl C40D2.2
Entrez Gene 173562 Entrez gene
SwissProt O76558 EMBL-EBI
WormBase CE19374 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAC26265 Hypothetical protein C40D2.2 [Caenorhabditis elegans] ref|NP_494146.1| C40D2.2 [Caenorhabditis elegans] 0.0
blast AAB71077 Hypothetical protein ZK250.8 [Caenorhabditis elegans] ref|NP_494139.1| ZK250.8 [Caenorhabditis elegans] 0.0
blast AAB70958 Hypothetical protein C46F9.3 [Caenorhabditis elegans] ref|NP_494116.1| C46F9.3 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR002083 EMBL-EBI MATH 2.1E-41
Pfam IPR002083 EMBL-EBI MATH 4.7E-34
Pfam IPR002083 EMBL-EBI MATH 2.7E-50
Pfam IPR002083 EMBL-EBI MATH 7.9E-17
Sequence
Target Sequence 
>C. ELEGANS:172888_X_AT
aaggctatatttggagcgtcgaataggggaatccctaattttattagttggaatgatatg
gaaaaagattatgtgaccaatggcagtatcgatgtggaagttcatgtcaaaataattcaa
attacagaattgtcatgccaagagaaatcatttgtactatcccatactgtcaagaacatg
tcaagtattgaagaaggaaggatcatcttttcggacacccaaactcgcttcaacattcta
tggaaattgaaaattcgaaagcaagacgggttttttgaattatttctcctatgtgacaaa
caactatgtaaatccagaaaatggtcaattgaaactgtatttcaattgaaaatagtgtct
tccaatgggagaagtttagtgttgttgaaaacaacacgtgtgtttaataaagcaaccggt
tacggatggcttaagctcataagatgggacagtttggaggaaaaatacatagtcgacgat
actctcacaattgaagctcacgtgaagattcttaatatgactggaattgaagatgaaacc
gctgttgagaaaccttctg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAGGCTATATTTGGAGCGTCGAATA 446 161 694 Antisense
GGAGCGTCGAATAGGGGAATCCCTA 490 521 706 Antisense
TGTGACCAATGGCAGTATCGATGTG 516 555 765 Antisense
TCATTTGTACTATCCCATACTGTCA 640 619 841 Antisense
AGGAAGGATCATCTTTTCGGACACC 412 55 888 Antisense
CCCAAACTCGCTTCAACATTCTATG 31 259 911 Antisense
GAATTATTTCTCCTATGTGACAAAC 109 325 970 Antisense
ACCGGTTACGGATGGCTTAAGCTCA 83 1 1108 Antisense
CATAGTCGACGATACTCTCACAATT 252 213 1161 Antisense
ATACTCTCACAATTGAAGCTCACGT 227 23 1172 Antisense
GAAACCGCTGTTGAGAAACCTTCTG 560 357 1228 Antisense
Sequence Source Affymetrix Proprietary Database