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[174082_at] RNA-binding protein

Description CEC8544 /REP_DB=TREMBL Accession /GB=C11854 /CHR=5 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk125h3 : 5prime end, single read.
Cluster 6grp_high1_10_10 > 88      6grp_total > 88      4grp_total > 24      6grp_cgc > 59      6grp_high1_sub > Da      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 194
1 2 3 4 range
A 63
(-3)
M 		122.6
(-1)
P 		176.7
(0.8)
P 		243.2
(3)
P 		180
B 63.8
(-3)
A 		127.4
(0.5)
P 		171.4
(3)
P 		162.9
(2.5)
P 		108
C 49.1
(-3)
A 		146.1
(0.3)
P 		169.7
(1.1)
P 		224.2
(3)
P 		175
avr 58.6
(-3) 		132
(-0.1) 		172.6
(1.5) 		210.1
(3) 		152

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3411
1 2 3 4 5 6 range
A 84.3
(-3)
P 		75.4
(-3)
A 		105
(-2.9)
P 		227
(-2.6)
P 		2004.1
(1.6)
P 		2566
(3)
P 		2491
B 99.1
(-3)
P 		78.1
(-3)
P 		78.3
(-3)
A 		320.8
(-2.6)
P 		1732.4
(-0.1)
P 		3474.4
(3)
P 		3396
C 63
(-3)
A 		113.3
(-2.9)
P 		118.2
(-2.9)
P 		212.1
(-2.7)
P 		1228.3
(-0.7)
P 		3077.7
(3)
P 		3015
avr 82.1
(-3) 		88.9
(-3) 		100.5
(-3) 		253.3
(-2.7) 		1654.9
(0.2) 		3039.4
(3) 		2957
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 43
1 2 3 4 range
A 22.9
(-3)
M 		26.6
(-2)
P 		46.2
(3)
P 		35.6
(0.3)
P 		23
B 20.3
(-3)
A 		31.5
(0.5)
P 		39.7
(3)
P 		34.7
(1.5)
P 		19
C 16.2
(-3)
A 		42
(0.6)
P 		59.2
(3)
P 		37.8
(0)
P 		43
avr 19.8
(-3) 		33.4
(-0.1) 		48.4
(3) 		36
(0.4) 		29

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1280
1 2 3 4 5 6 range
A 15.5
(-3)
P 		26.8
(-2.9)
A 		22.9
(-2.9)
P 		57.6
(-2.6)
P 		604.8
(2.8)
P 		624.8
(3)
P 		609
B 34.5
(-2.9)
P 		26
(-3)
P 		19
(-3)
A 		85
(-2.7)
P 		703.8
(0.2)
P 		1295.6
(3)
P 		1277
C 23.4
(-3)
A 		34.6
(-2.9)
P 		30.1
(-3)
P 		42.6
(-2.9)
P 		397.4
(-0.8)
P 		1030.3
(3)
P 		1007
avr 24.5
(-3) 		29.1
(-3) 		24
(-3) 		61.7
(-2.8) 		568.7
(0.4) 		983.6
(3) 		960
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174082_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21789
Sequence Type Exemplar sequence
Representative Public ID CEC8544 NCBI
Target Description CEC8544 /REP_DB=TREMBL Accession /GB=C11854 /CHR=5 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk125h3 : 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_072316(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072316 NCBI Caenorhabditis elegans SPiNdle orientation defective family member (spn-4) (spn-4) mRNA, complete cds. 11/11 None
ZC404.8 ENSEMBL cdna:known chromosome:CEL140:V:6785780:6787497:-1 gene:ZC404.8 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
chrV:6785803-6786138(-) 100.0 100.0
Public Domain and Genome References
Gene Title RNA-binding protein
Gene Symbol spn-4
Ensembl ZC404.8
Entrez Gene 179070 Entrez gene
SwissProt Q23287 EMBL-EBI
WormBase CE07598 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAA97963 Spindle orientation defective protein 4 [Caenorhabditis elegans] ref|NP_504717.1| SPiNdle orientation defective family member (spn-4) [Caenorhabditis elegans] dbj|BAC65239.1| PIP-1 [Caenorhabditis elegans] 0.0
blast CAE71949 Hypothetical protein CBG19017 [Caenorhabditis briggsae] 1.0E-135
blast CAI29625 hypothetical protein [Pongo pygmaeus] 2.0E-17
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 2.8E-16
Sequence
Target Sequence 
>C. ELEGANS:174082_AT
cgacactcgttgtccttgtcaaatgattcgttgctagtttttcttccctgtagcttctat
atcgacccccccggtgttattttgtaggaatgcgtttcagcatcttccctattttgccat
ctctcacatacactcaacattagcaatcggaaaacagatcttctatattgaaaatatact
accagtccgtttaacctacctcgcttgctaacattattgaatgtgcccacgtattgtatt
ttctgagcatctttctgttttttttgtattttatagacgctgtgttcgcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CGACACTCGTTGTCCTTGTCAAATG 88 253 28 Antisense
ACTCGTTGTCCTTGTCAAATGATTC 460 97 32 Antisense
GTCCTTGTCAAATGATTCGTTGCTA 494 477 39 Antisense
TGATTCGTTGCTAGTTTTTCTTCCC 129 565 51 Antisense
TTCTTCCCTGTAGCTTCTATATCGA 481 689 68 Antisense
TCTTCCCTGTAGCTTCTATATCGAC 431 617 69 Antisense
AATCGGAAAACAGATCTTCTATATT 431 169 172 Antisense
TGAAAATATACTACCAGTCCGTTTA 431 571 196 Antisense
TTTTCTGAGCATCTTTCTGTTTTTT 286 677 266 Antisense
TCTGAGCATCTTTCTGTTTTTTTTG 283 609 269 Antisense
GTATTTTATAGACGCTGTGTTCGCC 43 453 293 Antisense
Sequence Source Affymetrix Proprietary Database