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[189502_at] gamma-sarcoglycan

Description F07H5.2 /REP_DB=WormBase Gene ID /WP=CE05569 /TR=Q19185 /GB=CAA92663.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=gamma-sarcoglycan
Cluster 6grp_highest_10_10 > 33      6grp_high1_10_10 > 23      4grp_highest_8_8 > 24      4grp_high_8_8 > 52      6grp_highest_nonorm > 61      6grp_total > 12      4grp_total > 52      6grp_highest_sub > 02      6grp_cgc > 61      6grp_high1_sub > 02      6grp_cgc_sub > De      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 533
1 2 3 4 range
A 491.3
(1.7)
P 		572.6
(3)
P 		500.7
(1.9)
P 		183.8
(-3)
P 		389
B 528.9
(2)
P 		607.9
(3)
P 		485.2
(1.4)
P 		150.2
(-3)
P 		458
C 492.7
(0.6)
P 		683.6
(3)
P 		553.2
(1.4)
P 		202.4
(-3)
P 		481
avr 504.3
(1.4) 		621.4
(3) 		513
(1.5) 		178.8
(-3) 		443

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 445
1 2 3 4 5 6 range
A 641.2
(3)
P 		579.3
(2.2)
P 		572.9
(2.1)
P 		478.2
(0.8)
P 		373.3
(-0.6)
P 		196.6
(-3)
P 		445
B 483.6
(1.1)
P 		612
(3)
P 		391.3
(-0.2)
P 		431.8
(0.4)
P 		362.9
(-0.6)
P 		199.8
(-3)
P 		412
C 435.6
(-0)
P 		640.5
(3)
P 		479.2
(0.6)
P 		496
(0.9)
P 		299.9
(-2)
P 		233.2
(-3)
P 		407
avr 520.1
(1.6) 		610.6
(3) 		481.1
(1.1) 		468.7
(0.9) 		345.4
(-1) 		209.9
(-3) 		401
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 170
1 2 3 4 range
A 178.9
(3)
P 		124.3
(0.8)
P 		130.9
(1.1)
P 		26.9
(-3)
P 		152
B 168.7
(3)
P 		150.1
(2.2)
P 		112.4
(0.5)
P 		32
(-3)
P 		137
C 163.1
(1.8)
P 		196.5
(3)
P 		192.8
(2.9)
P 		34.1
(-3)
P 		162
avr 170.2
(3) 		157
(2.4) 		145.4
(1.9) 		31
(-3) 		139

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 158
1 2 3 4 5 6 range
A 118.2
(-0.3)
P 		206
(3)
P 		124.8
(-0.1)
P 		121.3
(-0.2)
P 		112.6
(-0.5)
P 		47.9
(-3)
P 		158
B 168.3
(1.4)
P 		203.7
(3)
P 		95
(-2)
P 		114.4
(-1.1)
P 		147.5
(0.4)
P 		74.5
(-3)
P 		129
C 161.5
(1.3)
P 		195.4
(3)
P 		122
(-0.8)
P 		99.7
(-1.9)
P 		97
(-2)
P 		78.1
(-3)
P 		117
avr 149.3
(0.7) 		201.7
(3) 		113.9
(-0.9) 		111.8
(-1) 		119
(-0.7) 		66.8
(-3) 		135
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189502_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3353
Sequence Type Exemplar sequence
Representative Public ID F07H5.2 NCBI
Target Description F07H5.2 /REP_DB=WormBase Gene ID /WP=CE05569 /TR=Q19185 /GB=CAA92663.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=gamma-sarcoglycan
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_063466(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063466 NCBI Caenorhabditis elegans F07H5.2 (gamma-sarcoglycan) mRNA, complete cds. 11/11 None
SNAP00000026204 ENSEMBL cdna:SNAP chromosome:CEL140:II:8781992:8783467:-1 11/11 None
GENEFINDER00000026220 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:8781992:8783443:-1 9/11 None
F07H5.2 ENSEMBL cdna:known chromosome:CEL140:II:8781992:8783557:-1 gene:F07H5.2 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
chrII:8781988-8783464(-) 100.0 100.0
Public Domain and Genome References
Gene Title gamma-sarcoglycan
Gene Symbol sgn-1
Ensembl F07H5.2
Entrez Gene 184162 Entrez gene
SwissProt Q19185 EMBL-EBI
WormBase CE05569 Wormbase
Functional Annotations
Ortholog
ID Title Organism
U133_X3P:HS2.348641.1.S1_3P_AT sarcoglycan zeta hs
HG-U133_PLUS_2:1552971_AT sarcoglycan zeta hs
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
7010 cytoskeleton organization and biogenesis inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
16012 sarcoglycan complex inferred from electronic annotation QuickGO AmiGO
16021 integral to membrane inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA92663 Hypothetical protein F07H5.2 [Caenorhabditis elegans] ref|NP_495867.1| F07H5.2 [Caenorhabditis elegans] 0.0
blast CAE59733 Hypothetical protein CBG03169 [Caenorhabditis briggsae] 0.0
blast CAA92663 Hypothetical protein F07H5.2 [Caenorhabditis elegans] ref|NP_495867.1| F07H5.2 [Caenorhabditis elegans] 1.0E-180
blast CAE59733 Hypothetical protein CBG03169 [Caenorhabditis briggsae] 1.0E-171
blast CAE59733 Hypothetical protein CBG03169 [Caenorhabditis briggsae] 1.0E-117
blast CAA92663 Hypothetical protein F07H5.2 [Caenorhabditis elegans] ref|NP_495867.1| F07H5.2 [Caenorhabditis elegans] 1.0E-112
blast AAP76378 zeta-sarcoglycan [Mus musculus] 3.0E-46
Protein Domains
Database ID Description E-Value
Pfam IPR006875 EMBL-EBI Sarcoglycan complex subunit protein 1.0E-126
Pfam IPR006875 EMBL-EBI Sarcoglycan complex subunit protein 1.0E-126
Pfam IPR006875 EMBL-EBI Sarcoglycan complex subunit protein 6.4E-55
Pfam IPR006875 EMBL-EBI Sarcoglycan complex subunit protein 1.4E-66
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_495867.1 1 82-104
F07H5.2 1 82-104
SNAP00000026204 1 82-104
GENEFINDER00000026220 1 74-96
Sequence
Target Sequence 
>C. ELEGANS:189502_AT
agagctcaattcgatagacctgtacatttctcacagctgagcacacttgatgaagaaacg
ctaacagttgactcattccgaggtgtcaatcttcaagctcgaaaaccaaatggcgatgtt
gcctcgaaattttcattaatgcctgaaggaaaagctcaaatgacttgtgatcggtttgag
gtgttcgatgaggatcagaagttgctcttctttgcagattcggacgaaattgggctgaag
ctcgaaaatttgagaattttggaagatggaggtagtgtgttcgaaggagctattcaaaca
tcatcagttcgtcctcaaccagattctccacttcgcttagaatctcccactcggagtgtt
tcagtagatgctgctcaagatattgaaatcctcgcagcagccggagaagtttcggtgaac
tcactactagatatttctatttcttcaaaacagggagaaattcgtctcgaatcatcctcg
atttatatggaaaaattagcccgatccgatggaagaggaagtccacaaactcaagtttgt
gtctgtcataatggacgactattccttgctgct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGAGCTCAATTCGATAGACCTGTAC 682 69 400 Antisense
AGACCTGTACATTTCTCACAGCTGA 355 71 415 Antisense
AACGCTAACAGTTGACTCATTCCGA 602 145 456 Antisense
CATTCCGAGGTGTCAATCTTCAAGC 382 217 473 Antisense
GGCGATGTTGCCTCGAAATTTTCAT 479 541 511 Antisense
TCAAACATCATCAGTTCGTCCTCAA 546 629 693 Antisense
ATTCTCCACTTCGCTTAGAATCTCC 133 11 722 Antisense
GAATCTCCCACTCGGAGTGTTTCAG 94 329 739 Antisense
AGATATTGAAATCCTCGCAGCAGCC 690 65 777 Antisense
AATTCGTCTCGAATCATCCTCGATT 139 177 858 Antisense
TAATGGACGACTATTCCTTGCTGCT 591 635 948 Antisense
Sequence Source Affymetrix Proprietary Database