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[173915_at] calpain (TRA-3)

Description AV198163 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=LLC1.1 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV198163 /WB_GENE_ID=LLC1.1 /WP=CE16260 /CHR=4 /FEA=Genomic Cluster /GEN=tra-3 /DEF=calpain (TRA-3); Caenorhabditis elegans cDNA clone:yk675f9 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 03      6grp_high1_10_10 > 11      4grp_highest_8_8 > 17      4grp_high_8_8 > 60      6grp_highest_nonorm > 31      6grp_total > 23      4grp_total > 59      6grp_highest_sub > De      6grp_cgc > 70      6grp_high1_sub > De      6grp_total_sub > Decrease      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 776
1 2 3 4 range
A 721
(0.6)
P 		642.5
(-0)
P 		1034.3
(3)
P 		257.9
(-3)
P 		776
B 754.4
(0)
P 		960.4
(3)
P 		831.9
(1.1)
P 		545.1
(-3)
P 		415
C 666.2
(0.9)
P 		637.4
(0.3)
P 		786.1
(3)
P 		450.5
(-3)
P 		336
avr 713.9
(0.8) 		746.8
(1.2) 		884.1
(3) 		417.8
(-3) 		466

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1061
1 2 3 4 5 6 range
A 1447.9
(3)
P 		744
(-1)
P 		1235.5
(1.8)
P 		577
(-1.9)
P 		848.8
(-0.4)
P 		386.9
(-3)
P 		1061
B 1079.6
(1.9)
P 		1201.3
(3)
P 		993.7
(1.1)
P 		1185.5
(2.9)
P 		841.6
(-0.3)
P 		554.5
(-3)
P 		647
C 845.8
(0.8)
P 		1011.9
(3)
P 		745.1
(-0.5)
P 		783.2
(0)
P 		774.2
(-0.1)
P 		548.4
(-3)
P 		464
avr 1124.4
(3) 		985.7
(1.7) 		991.4
(1.7) 		848.6
(0.4) 		821.5
(0.1) 		496.6
(-3) 		628
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 236
1 2 3 4 range
A 262.5
(2.8)
P 		139.5
(-0.4)
P 		270.4
(3)
P 		37.7
(-3)
P 		233
B 240.6
(3)
P 		237.2
(2.8)
P 		192.8
(0.7)
P 		116.2
(-3)
P 		124
C 220.5
(1.4)
P 		183.2
(0.2)
P 		274
(3)
P 		76
(-3)
P 		198
avr 241.2
(2.8) 		186.6
(0.9) 		245.7
(3) 		76.6
(-3) 		169

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 306
1 2 3 4 5 6 range
A 266.9
(2.9)
P 		264.6
(2.8)
P 		269.1
(3)
P 		146.3
(-1.2)
P 		256.1
(2.6)
P 		94.2
(-3)
P 		175
B 375.6
(2.2)
P 		399.9
(3)
P 		241.3
(-1.9)
P 		314
(0.3)
P 		341.9
(1.2)
P 		206.8
(-3)
P 		193
C 313.5
(3)
P 		308.8
(2.8)
P 		189.6
(-1.8)
P 		157.5
(-3)
P 		250.5
(0.6)
P 		183.6
(-2)
P 		156
avr 318.7
(2.8) 		324.4
(3) 		233.3
(-0.4) 		205.9
(-1.4) 		282.8
(1.5) 		161.5
(-3) 		163
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173915_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24761
Sequence Type Exemplar sequence
Representative Public ID AV198163 NCBI
Target Description AV198163 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=LLC1.1 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV198163 /WB_GENE_ID=LLC1.1 /WP=CE16260 /CHR=4 /FEA=Genomic Cluster /GEN=tra-3 /DEF=calpain (TRA-3); Caenorhabditis elegans cDNA clone:yk675f9 : 5prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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
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:14436409-14444123(-) 98.9 100.0
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
Sequence
Target Sequence 
>C. ELEGANS:173915_AT
gaaactttccatgttatttcttattcaaactcccaccaaaaatcgccgccactaaaatca
gtattttcctcttatgttgtcttgttatacggttaatttcgtttctttttcttttttcaa
tttcaaaattttaaataatttttcaattttcccttgatagcattatatgtatatcaggtt
tatcattgttcctcgttcaaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAACTTTCCATGTTATTTCTTATT 191 357 1971 Antisense
TATTTCTTATTCAAACTCCCACCAA 265 663 1985 Antisense
TATTCAAACTCCCACCAAAAATCGC 600 659 1992 Antisense
CACCAAAAATCGCCGCCACTAAAAT 508 201 2004 Antisense
AAATCGCCGCCACTAAAATCAGTAT 577 117 2010 Antisense
ATCAGTATTTTCCTCTTATGTTGTC 603 29 2027 Antisense
ATTTTCCTCTTATGTTGTCTTGTTA 143 15 2033 Antisense
TTGTCTTGTTATACGGTTAATTTCG 401 705 2047 Antisense
CAATTTTCCCTTGATAGCATTATAT 296 181 2114 Antisense
ATCAGGTTTATCATTGTTCCTCGTT 614 29 2143 Antisense
GGTTTATCATTGTTCCTCGTTCAAA 485 505 2147 Antisense
Sequence Source Affymetrix Proprietary Database