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[190890_s_at] calpain (TRA-3)

Description LLC1.1 /REP_DB=WormBase Gene ID /WP=CE16260 /GEN=tra-3 /TR=Q22036 /GB=CAB05248.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=calpain (TRA-3)
Cluster 6grp_highest_10_10 > 05      6grp_high1_10_10 > 41      4grp_highest_8_8 > 41      4grp_high_8_8 > 50      6grp_highest_nonorm > 62      6grp_total > 31      4grp_total > 53      6grp_highest_sub > 03_04      6grp_cgc > 71      6grp_high1_sub > 03      6grp_cgc_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.
4 296
1 2 3 4 range
A 453.4
(3)
P 		442.1
(2.6)
P 		384.5
(0.5)
P 		290.5
(-3)
P 		163
B 521.8
(3)
P 		389.1
(0)
P 		440.6
(1.2)
P 		255.2
(-3)
P 		267
C 551.3
(3)
P 		423.2
(-0.4)
P 		418.2
(-0.5)
P 		324.1
(-3)
P 		227
avr 508.8
(3) 		418.1
(0.5) 		414.4
(0.4) 		289.9
(-3) 		219

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 406
1 2 3 4 5 6 range
A 520.2
(0.8)
P 		444.7
(-0.6)
P 		649.9
(3)
P 		397.7
(-1.4)
P 		511.6
(0.6)
P 		303.3
(-3)
P 		347
B 495
(1)
P 		436.2
(-0.3)
P 		557
(2.3)
P 		589.9
(3)
P 		352.8
(-2.1)
P 		311
(-3)
P 		279
C 420.4
(-0.3)
P 		633
(3)
P 		553.3
(1.8)
P 		573.8
(2.1)
P 		366.4
(-1.1)
P 		244
(-3)
P 		389
avr 478.5
(0.8) 		504.6
(1.4) 		586.7
(3) 		520.5
(1.7) 		410.3
(-0.5) 		286.1
(-3) 		301
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 140
1 2 3 4 range
A 165.1
(3)
P 		96
(-0.4)
P 		100.5
(-0.2)
P 		42.5
(-3)
P 		123
B 166.4
(3)
P 		96.1
(-0.8)
P 		102.1
(-0.4)
P 		54.4
(-3)
P 		112
C 182.5
(3)
P 		121.7
(0.1)
P 		145.8
(1.3)
P 		54.7
(-3)
P 		128
avr 171.3
(3) 		104.6
(-0.3) 		116.1
(0.3) 		50.5
(-3) 		121

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 119
1 2 3 4 5 6 range
A 95.9
(-1.4)
P 		158.1
(3)
P 		141.5
(1.8)
P 		100.9
(-1.1)
P 		154.4
(2.7)
P 		73.8
(-3)
P 		84
B 172.2
(3)
P 		145.2
(0.1)
P 		135.3
(-0.9)
P 		156.2
(1.3)
P 		143.3
(-0.1)
P 		116
(-3)
P 		56
C 155.8
(1)
P 		193.2
(3)
P 		140.8
(0.2)
P 		115.4
(-1.2)
P 		118.6
(-1)
P 		81.7
(-3)
P 		112
avr 141.3
(1.1) 		165.5
(3) 		139.2
(0.9) 		124.2
(-0.3) 		138.8
(0.9) 		90.5
(-3) 		75
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 190890_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10171
Sequence Type Exemplar sequence
Representative Public ID LLC1.1 NCBI
Target Description LLC1.1 /REP_DB=WormBase Gene ID /WP=CE16260 /GEN=tra-3 /TR=Q22036 /GB=CAB05248.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=calpain (TRA-3)
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_070350(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070350 NCBI Caenorhabditis elegans TRAnsformer : XX animals transformed into males family member (tra-3) (tra-3) mRNA, complete cds. 11/11 None
SNAP00000039829 ENSEMBL cdna:SNAP chromosome:CEL140:IV:14436646:14442310:-1 11/11 None
GENEFINDER00000039834 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:14436646:14444116:-1 11/11 None
LLC1.1 ENSEMBL cdna:known chromosome:CEL140:IV:14436334:14444150:-1 gene:LLC1.1 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
chrIV:14436651-14444122(-) 100.0 100.0
Public Domain and Genome References
Gene Title calpain (TRA-3)
Gene Symbol tra-3
Ensembl LLC1.1
Entrez Gene 178385 Entrez gene
SwissProt Q22036 EMBL-EBI
WormBase CE16260 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.8728.1.S1_AT similar to Calpain-5 (nCL-3) cfa
CHICKEN:GGAAFFX.496.1.S1_AT similar to calpain-like protease gga
HG-U133_PLUS_2:205166_AT calpain 5 hs
HG-U133A:205166_AT calpain 5 hs
HG-FOCUS:205166_AT calpain 5 hs
HG-U133A_2:205166_AT calpain 5 hs
HU35KSUBB:RC_Z39842_AT calpain 5 hs
U133_X3P:G6552324_3P_AT calpain 5 hs
U133_X3P:HS.6133.1.S1_3P_AT calpain 5 hs
HG-U133_PLUS_2:226292_AT calpain 5 hs
HG-U133B:226292_AT calpain 5 hs
HG-U95AV2:38504_AT calpain 5 hs
HG-U95B:53942_AT calpain 5 hs
HG-U95E:78506_AT Calpain 5 hs
HU35KSUBC:RC_H81543_AT Calpain 5 hs
MU11KSUBB:Y10656_S_AT calpain 5 mm
MG-U74AV2:102316_AT calpain 5 mm
MG-U74BV2:109830_AT calpain 5 mm
MOE430A:1418671_AT calpain 5 mm
MOUSE430A_2:1418671_AT calpain 5 mm
MOUSE430_2:1418671_AT calpain 5 mm
MOE430A:1449165_AT calpain 5 mm
MOUSE430A_2:1449165_AT calpain 5 mm
MOUSE430_2:1449165_AT calpain 5 mm
MU19KSUBA:TC15986_AT Calpain 5, mRNA (cDNA clone MGC:25253 IMAGE:4458488) mm
MU19KSUBB:TC30215_AT Calpain 5, mRNA (cDNA clone MGC:25253 IMAGE:4458488) mm
MU19KSUBB:TC30215_G_AT Calpain 5, mRNA (cDNA clone MGC:25253 IMAGE:4458488) mm
RAE230A:1369441_AT calpain 5 rn
RAT230_2:1369441_AT calpain 5 rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6508 proteolysis inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5622 intracellular inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4197 cysteine-type endopeptidase activity inferred from electronic annotation QuickGO AmiGO
4198 calpain activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB60256 sex determination [Caenorhabditis elegans] emb|CAB05248.1| Hypothetical protein LLC1.1 [Caenorhabditis elegans] ref|NP_502751.1| TRAnsformer : XX animals transformed into males family member (tra-3) [Caenorhabditis elegans] sp|Q22036|CAN5_CAEEL Calpain-5 (Sex-determining transformer protein 3) 0.0
blast CAE73955 Hypothetical protein CBG21580 [Caenorhabditis briggsae] 0.0
blast AAT77812 calpain T [Gecarcinus lateralis] 1.0E-129
Protein Domains
Database ID Description E-Value
Pfam IPR001300 EMBL-EBI Peptidase C2, calpain 4.9E-112
Pfam IPR000008 EMBL-EBI C2 domain 2.4E-4
Pfam IPR001300 EMBL-EBI Peptidase C2, calpain 7.9E-78
Pfam IPR001300 EMBL-EBI Peptidase C2, calpain 3.7E-55
Pfam IPR000008 EMBL-EBI C2 domain 2.4E-4
Pfam IPR001300 EMBL-EBI Peptidase C2, calpain 7.9E-78
Sequence
Target Sequence 
>C. ELEGANS:190890_S_AT
gagtacatacagccatgcatccaattgcaatttcggattatgcgtcgggtcgatcggttt
atttgcatctgcagagtttgccacgtggcagatatttattgattccgacgacatttgcac
cgaaagaacagacgctttttatgttgagagtgtattccgatgaacatatccatttttcac
cgttgacaaagcacgctccaaaactcggtctcctgaaatgcaaatctgcacaaagtgtaa
ctcgtctgacaattcacggagtcgacttcaactcagcctcaacgggaactcacaatgtct
acgcaattctcaaagattccagaaaatcgttcagaacgaaaactttgagtggagtgaagt
cgattcaatgggatgagcaatttttatttcataaatcaaaaaatcgtcagcaatacaaaa
tcgaagtgtgggaagatcgtaaaatggctcgagaccaccttcttgctcaatccgttatca
ttgctctaatcgataacgagaatcgtgatacgacccttcagttgacagatc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGTACATACAGCCATGCATCCAAT 527 399 1361 Antisense
GCGTCGGGTCGATCGGTTTATTTGC 101 283 1402 Antisense
GCATCTGCAGAGTTTGCCACGTGGC 306 309 1425 Antisense
TTGATTCCGACGACATTTGCACCGA 186 705 1459 Antisense
ACATATCCATTTTTCACCGTTGACA 465 105 1524 Antisense
ACAAAGCACGCTCCAAAACTCGGTC 529 111 1546 Antisense
AACTCGGTCTCCTGAAATGCAAATC 413 141 1562 Antisense
TCAACTCAGCCTCAACGGGAACTCA 265 627 1628 Antisense
TAAAATGGCTCGAGACCACCTTCTT 668 637 1800 Antisense
AATCCGTTATCATTGCTCTAATCGA 635 167 1829 Antisense
GATACGACCCTTCAGTTGACAGATC 33 383 1867 Antisense
Sequence Source Affymetrix Proprietary Database