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[173857_at] S1 RNA binding domain

Description CEK004A5F /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=T04A8.14 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D27809 /WB_GENE_ID=T04A8.14 /WP=CE13120 /CHR=3 /FEA=Genomic Cluster /GEN=emb-5 /DEF=S1 RNA binding domain; C.elegans cDNA clone yk4a5 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 64      6grp_high1_10_10 > 46      4grp_highest_8_8 > 41      4grp_high_8_8 > 49      6grp_highest_nonorm > 57      6grp_total > 47      4grp_total > 62      6grp_highest_sub > Cu      6grp_cgc > 26      6grp_high1_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1242
1 2 3 4 range
A 2688.6
(3)
P 		2254.3
(0.5)
P 		2203.3
(0.2)
P 		1637.3
(-3)
P 		1051
B 2878.9
(3)
P 		2155.4
(-0.6)
P 		1986.6
(-1.5)
P 		1685.1
(-3)
P 		1194
C 2645.3
(3)
P 		2028.8
(-1.1)
P 		2445.3
(1.7)
P 		1734.1
(-3)
P 		911
avr 2737.6
(3) 		2146.2
(-0.4) 		2211.7
(0) 		1685.5
(-3) 		1052

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1648
1 2 3 4 5 6 range
A 3037
(3)
P 		2454.1
(0.2)
P 		1958.4
(-2.2)
P 		1797.7
(-3)
P 		1976.3
(-2.1)
P 		2609.3
(0.9)
P 		1239
B 2579.1
(2.7)
P 		2263.1
(1.1)
P 		2061
(0)
P 		2316.6
(1.4)
P 		1482.6
(-3)
P 		2628.9
(3)
P 		1146
C 2082.1
(1.1)
P 		2195.5
(1.8)
P 		2158
(1.6)
P 		2308.9
(2.5)
P 		1388.9
(-3)
P 		2396.5
(3)
P 		1008
avr 2566.1
(3) 		2304.2
(1.3) 		2059.1
(-0.2) 		2141.1
(0.3) 		1615.9
(-3) 		2544.9
(2.9) 		950
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 739
1 2 3 4 range
A 978.9
(3)
P 		489.3
(-1)
P 		576
(-0.3)
P 		239.7
(-3)
P 		739
B 918
(3)
P 		532.3
(-1.1)
P 		460.3
(-1.9)
P 		359.1
(-3)
P 		559
C 875.7
(3)
P 		583.3
(-0)
P 		852.3
(2.8)
P 		292.4
(-3)
P 		583
avr 924.2
(3) 		535
(-0.7) 		629.5
(0.2) 		297.1
(-3) 		627

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 554
1 2 3 4 5 6 range
A 559.8
(-1.2)
P 		872.8
(3)
P 		426.5
(-3)
P 		456
(-2.6)
P 		596.4
(-0.7)
P 		635.3
(-0.2)
P 		446
B 897.4
(2)
P 		753.3
(0.2)
P 		500.5
(-3)
P 		613.6
(-1.6)
P 		602.3
(-1.7)
P 		980.3
(3)
P 		480
C 771.8
(2.5)
P 		669.9
(0.7)
P 		549.3
(-1.3)
P 		464.3
(-2.7)
P 		449.4
(-3)
P 		802.3
(3)
P 		353
avr 743
(1.8) 		765.3
(2.2) 		492.1
(-3) 		511.3
(-2.6) 		549.4
(-1.9) 		806
(3) 		314
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173857_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24295
Sequence Type Exemplar sequence
Representative Public ID CEK004A5F NCBI
Target Description CEK004A5F /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=T04A8.14 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D27809 /WB_GENE_ID=T04A8.14 /WP=CE13120 /CHR=3 /FEA=Genomic Cluster /GEN=emb-5 /DEF=S1 RNA binding domain; C.elegans cDNA clone yk4a5 : 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_065568(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065568 NCBI Caenorhabditis elegans abnormal EMBroygenesis family member (emb-5) (emb-5) mRNA, complete cds. 11/11 None
T04A8.14 ENSEMBL cdna:known chromosome:CEL140:III:4715255:4720627:-1 gene:T04A8.14 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
chrIII:4715277-4720628(-) 100.0 100.0
Public Domain and Genome References
Gene Title S1 RNA binding domain
Gene Symbol emb-5
Ensembl T04A8.14
Entrez Gene 175621 Entrez gene
SwissProt P34703 EMBL-EBI
WormBase CE13120 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:264155_AT glycine-rich protein at
ATGENOME1:14532_AT glycine-rich protein at
CANINE:1600222_AT similar to suppressor of Ty 6 homolog cfa
CANINE:1599755_AT similar to suppressor of Ty 6 homolog cfa
CANINE_2:CFA.12745.1.A1_AT similar to suppressor of Ty 6 homolog cfa
CANINE_2:CFA.12745.1.A1_S_AT similar to suppressor of Ty 6 homolog cfa
CANINE_2:CFAAFFX.28672.1.S1_S_AT similar to suppressor of Ty 6 homolog cfa
DROSOPHILA_2:1634924_AT dm
DROSGENOME1:141281_AT dm
CHICKEN:GGAAFFX.99.2.S1_S_AT similar to putative chromatin structure regulator gga
HG-U133_PLUS_2:208420_X_AT suppressor of Ty 6 homolog (S. cerevisiae) hs
HG-U133A:208420_X_AT suppressor of Ty 6 homolog (S. cerevisiae) hs
HG-U133A_2:208420_X_AT suppressor of Ty 6 homolog (S. cerevisiae) hs
HG-U133A:208831_X_AT suppressor of Ty 6 homolog (S. cerevisiae) hs
HG-U133_PLUS_2:208831_X_AT suppressor of Ty 6 homolog (S. cerevisiae) hs
HG-U133A_2:208831_X_AT suppressor of Ty 6 homolog (S. cerevisiae) hs
HU35KSUBD:RC_R38625_S_AT suppressor of Ty 6 homolog (S. cerevisiae) hs
HUGENEFL:D79984_S_AT suppressor of Ty 6 homolog (S. cerevisiae) hs
U133_X3P:G1136385_3P_A_AT suppressor of Ty 6 homolog (S. cerevisiae) hs
U133_X3P:HS.12303.1.S1_3P_S_AT suppressor of Ty 6 homolog (S. cerevisiae) hs
HG-U133_PLUS_2:1554311_A_AT suppressor of Ty 6 homolog (S. cerevisiae) hs
HG-U133A_2:208830_S_AT suppressor of Ty 6 homolog (S. cerevisiae) hs
HG-FOCUS:208830_S_AT suppressor of Ty 6 homolog (S. cerevisiae) hs
HG-U133_PLUS_2:208830_S_AT suppressor of Ty 6 homolog (S. cerevisiae) hs
HG-U133A:208830_S_AT suppressor of Ty 6 homolog (S. cerevisiae) hs
HG-U95AV2:41659_AT suppressor of Ty 6 homolog (S. cerevisiae) hs
MOUSE430_2:1430458_AT suppressor of Ty 6 homolog (S. cerevisiae) mm
MOE430B:1430458_AT suppressor of Ty 6 homolog (S. cerevisiae) mm
MU11KSUBA:U40375_S_AT suppressor of Ty 6 homolog (S. cerevisiae) mm
MG-U74AV2:103668_AT suppressor of Ty 6 homolog (S. cerevisiae) mm
MOE430A:1417628_AT suppressor of Ty 6 homolog (S. cerevisiae) mm
MOUSE430A_2:1417628_AT suppressor of Ty 6 homolog (S. cerevisiae) mm
MOUSE430_2:1417628_AT suppressor of Ty 6 homolog (S. cerevisiae) mm
MU19KSUBA:TC15981_AT Suppressor of Ty 6 homolog (S. cerevisiae) (Supt6h), mRNA mm
RG-U34B:RC_AA925105_AT suppressor of Ty 6 homolog (S. cerevisiae) (predicted) rn
RAE230A:1374398_AT suppressor of Ty 6 homolog (S. cerevisiae) (predicted) rn
RAT230_2:1374398_AT suppressor of Ty 6 homolog (S. cerevisiae) (predicted) rn
YEAST_2:1773275_AT Essential protein that interacts with histones and is involved in nucleosome disassembly and reassembly during transcription elongation Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism inferred from electronic annotation QuickGO AmiGO
7242 intracellular signaling cascade inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3723 RNA binding inferred from electronic annotation QuickGO AmiGO
16788 hydrolase activity, acting on ester bonds inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA84801 Hypothetical protein T04A8.14 [Caenorhabditis elegans] emb|CAA84737.1| Hypothetical protein T04A8.14 [Caenorhabditis elegans] ref|NP_497969.1| abnormal EMBroygenesis family member (emb-5) [Caenorhabditis elegans] dbj|BAA03484.1| EMB-5 [Caenorhabditis elegans] sp|P34703|EMB5_CAEEL Abnormal embryogenesis protein 0.0
blast CAE71146 Hypothetical protein CBG18001 [Caenorhabditis briggsae] 0.0
blast BAA13699.1 EMB-5 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR003029 EMBL-EBI RNA binding S1 6.5E-15
Sequence
Target Sequence 
>C. ELEGANS:173857_AT
gtcggctatcactgaaaaccctgatcttattctctttattacccacaccttatcagacac
attcaatcctgtttcctttgttccagtctatcaacgatgatctaattttaatttatagaa
tacaacatccatctgtcttaatcccacataatttgttttgatttcggtaatccgttcatc
ctcgatttttacttttcaaacatttttatatatctatcaaaatatttattcaagcagtca
tactgttcatgagctc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTCGGCTATCACTGAAAACCCTGAT 177 471 4565 Antisense
GAAAACCCTGATCTTATTCTCTTTA 338 355 4578 Antisense
TGATCTTATTCTCTTTATTACCCAC 603 563 4586 Antisense
TTATTACCCACACCTTATCAGACAC 86 679 4600 Antisense
CAGACACATTCAATCCTGTTTCCTT 286 205 4618 Antisense
CTGTTTCCTTTGTTCCAGTCTATCA 266 239 4633 Antisense
TAGAATACAACATCCATCTGTCTTA 106 653 4680 Antisense
ATCCATCTGTCTTAATCCCACATAA 696 39 4691 Antisense
TGATTTCGGTAATCCGTTCATCCTC 377 561 4723 Antisense
GTAATCCGTTCATCCTCGATTTTTA 583 461 4731 Antisense
AAGCAGTCATACTGTTCATGAGCTC 185 149 4796 Antisense
Sequence Source Affymetrix Proprietary Database