[Home] | [Total List]

[192356_s_at] spectrin alpha chain

Description K10B3.10 /REP_DB=WormBase Gene ID /WP=CE07373 /GEN=spc-1 /TR=Q21408 /GB=AAB53876.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=spectrin alpha chain
Cluster 6grp_highest_10_10 > 51      6grp_high1_10_10 > 26      4grp_highest_8_8 > 48      4grp_high_8_8 > 42      6grp_highest_nonorm > 01      6grp_total > 26      4grp_total > 53      6grp_highest_sub > De      6grp_cgc > 14      6grp_high1_sub > De      6grp_cgc_sub > Cu      6grp_total_sub > Cup      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2128
1 2 3 4 range
A 2759.9
(3)
P 		2135
(1)
P 		1405.3
(-1.3)
P 		858.4
(-3)
P 		1902
B 2849.8
(3)
P 		1980.5
(0.4)
P 		1476.3
(-1.1)
P 		818.5
(-3)
P 		2031
C 2528.9
(3)
P 		1985.9
(1.2)
P 		1629.5
(0)
P 		721.8
(-3)
P 		1807
avr 2712.9
(3) 		2033.8
(0.9) 		1503.7
(-0.8) 		799.6
(-3) 		1913

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1942
1 2 3 4 5 6 range
A 2721.5
(2.8)
P 		2763.9
(3)
P 		1114
(-3)
P 		1323.1
(-2.2)
P 		1106
(-3)
P 		1635.3
(-1.1)
P 		1658
B 2646.6
(3)
P 		2222.6
(1.6)
P 		1171.3
(-1.9)
P 		1251.3
(-1.6)
P 		821.5
(-3)
P 		1165.1
(-1.9)
P 		1825
C 2743.7
(3)
P 		2156.9
(1)
P 		1761.1
(-0.4)
P 		1002.5
(-3)
P 		1403.2
(-1.6)
P 		1070.1
(-2.8)
P 		1741
avr 2703.9
(3) 		2381.1
(1.8) 		1348.8
(-2.1) 		1192.3
(-2.7) 		1110.2
(-3) 		1290.2
(-2.3) 		1594
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 883
1 2 3 4 range
A 1004.9
(3)
P 		463.4
(-0.7)
P 		367.4
(-1.4)
P 		125.7
(-3)
P 		879
B 908.8
(3)
P 		489.1
(-0.4)
P 		342.1
(-1.6)
P 		174.4
(-3)
P 		734
C 837.2
(3)
P 		571
(0.8)
P 		567.9
(0.7)
P 		121.7
(-3)
P 		716
avr 917
(3) 		507.8
(-0.2) 		425.8
(-0.8) 		140.6
(-3) 		776

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 815
1 2 3 4 5 6 range
A 501.7
(-0.9)
P 		983
(3)
P 		242.6
(-3)
P 		335.6
(-2.2)
P 		333.7
(-2.3)
P 		398.2
(-1.7)
P 		740
B 920.9
(3)
P 		739.8
(1.3)
P 		284.4
(-3)
P 		331.4
(-2.6)
P 		333.8
(-2.5)
P 		434.5
(-1.6)
P 		637
C 1017
(3)
P 		658.1
(0.4)
P 		448.2
(-1.2)
P 		201.6
(-3)
P 		454
(-1.1)
P 		358.2
(-1.8)
P 		815
avr 813.2
(3) 		793.6
(2.8) 		325.1
(-2.6) 		289.5
(-3) 		373.8
(-2) 		397
(-1.8) 		524
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192356_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.18444
Sequence Type Exemplar sequence
Representative Public ID K10B3.10 NCBI
Target Description K10B3.10 /REP_DB=WormBase Gene ID /WP=CE07373 /GEN=spc-1 /TR=Q21408 /GB=AAB53876.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=spectrin alpha chain
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_076136(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076136 NCBI Caenorhabditis elegans SPeCtrin family member (spc-1) (spc-1) mRNA, complete cds. 11/11 A 
SNAP00000032574 ENSEMBL cdna:SNAP chromosome:CEL140:X:3117935:3127052:-1 11/11 None
GENEFINDER00000032579 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:3117935:3127920:-1 11/11 None
K10B3.10 ENSEMBL cdna:known chromosome:CEL140:X:3117430:3127061:-1 gene:K10B3.10 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
chrX:3117934-3127052(-) 100.0 100.0
Public Domain and Genome References
Gene Title spectrin alpha chain
Gene Symbol spc-1
Ensembl K10B3.10
Entrez Gene 180603 Entrez gene
SwissProt Q21408 EMBL-EBI
WormBase CE07373 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1606042_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) cfa
CANINE:1583448_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) cfa
CANINE:1582820_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) cfa
CANINE_2:CFA.11603.1.A1_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) cfa
CANINE_2:CFA.18239.1.S1_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) cfa
CANINE_2:CFA.196.1.S1_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) cfa
CANINE_2:CFAAFFX.30684.1.S1_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) cfa
CANINE_2:CFAAFFX.30684.1.S1_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) cfa
DROSOPHILA_2:1626349_AT Spectrin dm
CHICKEN:GGA.11413.1.S1_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) gga
CHICKEN:GGA.4441.1.S1_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) gga
CHICKEN:GGAAFFX.21304.1.S1_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) gga
HG-U133_PLUS_2:208611_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133A:208611_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-FOCUS:208611_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133A_2:208611_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HUGENEFL:J05243_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133_PLUS_2:214925_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133A_2:214925_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133A:214925_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
U133_X3P:HS.77196.2.A1_3P_A_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
U133_X3P:HS.321666.0.S1_3P_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U95AV2:33833_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U95D:89935_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133_PLUS_2:214926_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133A_2:214926_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133A:214926_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133_PLUS_2:215235_AT Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133A_2:215235_AT Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133A:215235_AT Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HU35KSUBB:RC_H15913_AT Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
U133_X3P:HS.31396.0.A1_3P_AT Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133_PLUS_2:241150_AT Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133B:241150_AT Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U95C:64221_AT Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U95E:90760_AT Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
RG-U34A:AF084186_S_AT hypothetical gene supported by NM_171983 rn
RG-U34B:RC_AA849856_AT hypothetical gene supported by NM_171983 rn
RAE230A:1370838_S_AT hypothetical gene supported by NM_171983 rn
RAT230_2:1370838_S_AT hypothetical gene supported by NM_171983 rn
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
5509 calcium ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB53876 Spectrin protein 1 [Caenorhabditis elegans] ref|NP_508537.1| SPeCtrin family member (spc-1) [Caenorhabditis elegans] 0.0
blast CAE68383 Hypothetical protein CBG14139 [Caenorhabditis briggsae] 0.0
blast XP_623691 PREDICTED: similar to GA15168-PA [Apis mellifera] 0.0
Protein Domains
Database ID Description E-Value
scop a.2.7.Seryl-tRNA synthetase (SerRS) All alpha proteins; Long alpha-hairpin; tRNA-binding arm; Seryl-tRNA synthetase (SerRS) 5.80000019073486
scop a.2.7.Seryl-tRNA synthetase (SerRS) All alpha proteins; Long alpha-hairpin; tRNA-binding arm; Seryl-tRNA synthetase (SerRS) 4.19999980926514
Pfam IPR002048 EMBL-EBI Calcium-binding EF-hand 1.3E-5
Pfam IPR002048 EMBL-EBI Calcium-binding EF-hand 4.7E-6
Pfam IPR001452 EMBL-EBI SH3 4.1E-20
Pfam IPR002017 EMBL-EBI Spectrin repeat 0.43
Pfam IPR002017 EMBL-EBI Spectrin repeat 9.0E-30
Pfam IPR002017 EMBL-EBI Spectrin repeat 3.0E-27
Pfam IPR002017 EMBL-EBI Spectrin repeat 4.2E-30
Pfam IPR002017 EMBL-EBI Spectrin repeat 2.5E-24
Pfam IPR002017 EMBL-EBI Spectrin repeat 1.3E-33
Pfam IPR002017 EMBL-EBI Spectrin repeat 9.3E-31
Pfam IPR002017 EMBL-EBI Spectrin repeat 3.7E-31
Pfam IPR002017 EMBL-EBI Spectrin repeat 4.8E-28
Pfam IPR002017 EMBL-EBI Spectrin repeat 6.5E-21
Pfam IPR002017 EMBL-EBI Spectrin repeat 0.11
Pfam IPR002017 EMBL-EBI Spectrin repeat 1.0E-24
Pfam IPR002017 EMBL-EBI Spectrin repeat 3.1E-32
Pfam IPR002017 EMBL-EBI Spectrin repeat 1.3E-30
Pfam IPR002017 EMBL-EBI Spectrin repeat 1.3E-29
Pfam IPR002017 EMBL-EBI Spectrin repeat 3.9E-28
Pfam IPR002017 EMBL-EBI Spectrin repeat 5.2E-29
Pfam IPR002017 EMBL-EBI Spectrin repeat 1.1E-32
Pfam IPR002017 EMBL-EBI Spectrin repeat 4.3E-28
Pfam IPR002017 EMBL-EBI Spectrin repeat 1.6E-30
Pfam IPR002017 EMBL-EBI Spectrin repeat 7.3E-20
Pfam IPR002017 EMBL-EBI Spectrin repeat 8.7E-11
Pfam IPR002048 EMBL-EBI Calcium-binding EF-hand 1.3E-5
Pfam IPR002048 EMBL-EBI Calcium-binding EF-hand 4.7E-6
Pfam IPR001452 EMBL-EBI SH3 4.1E-20
Pfam IPR002017 EMBL-EBI Spectrin repeat 0.43
Pfam IPR002017 EMBL-EBI Spectrin repeat 9.0E-30
Pfam IPR002017 EMBL-EBI Spectrin repeat 3.0E-27
Pfam IPR002017 EMBL-EBI Spectrin repeat 4.2E-30
Pfam IPR002017 EMBL-EBI Spectrin repeat 2.5E-24
Pfam IPR002017 EMBL-EBI Spectrin repeat 1.3E-33
Pfam IPR002017 EMBL-EBI Spectrin repeat 9.3E-31
Pfam IPR002017 EMBL-EBI Spectrin repeat 3.7E-31
Pfam IPR002017 EMBL-EBI Spectrin repeat 4.8E-28
Pfam IPR002017 EMBL-EBI Spectrin repeat 6.5E-21
Pfam IPR002017 EMBL-EBI Spectrin repeat 0.11
Pfam IPR002017 EMBL-EBI Spectrin repeat 6.5E-20
Pfam IPR002017 EMBL-EBI Spectrin repeat 3.1E-32
Pfam IPR002017 EMBL-EBI Spectrin repeat 1.3E-30
Pfam IPR002017 EMBL-EBI Spectrin repeat 1.3E-29
Pfam IPR002017 EMBL-EBI Spectrin repeat 3.9E-28
Pfam IPR002017 EMBL-EBI Spectrin repeat 5.2E-29
Pfam IPR002017 EMBL-EBI Spectrin repeat 1.1E-32
Pfam IPR002017 EMBL-EBI Spectrin repeat 4.3E-28
Pfam IPR002017 EMBL-EBI Spectrin repeat 1.6E-30
Pfam IPR002017 EMBL-EBI Spectrin repeat 7.3E-20
Pfam IPR002017 EMBL-EBI Spectrin repeat 8.7E-11
Sequence
Target Sequence 
>C. ELEGANS:192356_S_AT
ggatcagctagccatgcgaatgcaacacaatttggaacaacagattcaagccagaaatca
atctggagtatcggaagaagcccttcgtgagttctcaatgatgttcaagcacttcgacaa
ggagaaaactggaagactcgaccaccagcagttcaagagttgtctgcgagctcttggata
cgatctgccgatggtggacgaaggccaaccagaacccgagttccagagaattttggatat
tgtcgacccgaacagagatggttacgtaactctgcaagagtacatggcgttcatgatcag
caaagaaaccgagaacatccagtcttcggaagaaatcgagatggcattcagagctctttc
gaaggaattccgaccatatgtcacggcagaggagctctacgcgaacctgacaccggagca
agccgaattctgcatacgaagaatgaagccatacatggacgccatttcaggtcgttccat
ccaaggtggtctcgac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGATCAGCTAGCCATGCGAATGCAA 66 481 6765 Antisense
GAAGAAGCCCTTCGTGAGTTCTCAA 425 339 6838 Antisense
TCGACCACCAGCAGTTCAAGAGTTG 72 603 6902 Antisense
GTTGTCTGCGAGCTCTTGGATACGA 312 435 6923 Antisense
GGATACGATCTGCCGATGGTGGACG 634 509 6940 Antisense
GAGATGGCATTCAGAGCTCTTTCGA 575 395 7102 Antisense
GAATTCCGACCATATGTCACGGCAG 460 323 7129 Antisense
GTCACGGCAGAGGAGCTCTACGCGA 631 465 7144 Antisense
GACACCGGAGCAAGCCGAATTCTGC 104 369 7173 Antisense
ATGGACGCCATTTCAGGTCGTTCCA 133 53 7219 Antisense
TCGTTCCATCCAAGGTGGTCTCGAC 518 603 7236 Antisense
Sequence Source Affymetrix Proprietary Database