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[173781_s_at]

Description AV193224 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y116A8C.35 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV193224 /WB_GENE_ID=Y116A8C.35 /WP=CE23341 /CHR=4 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk614g12 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 71      6grp_high1_10_10 > 28      4grp_highest_8_8 > 16      4grp_high_8_8 > 60      6grp_highest_nonorm > 50      6grp_total > 17      4grp_total > 59      6grp_highest_sub > De      6grp_cgc > 06      6grp_high1_sub > De      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 321
1 2 3 4 range
A 497.5
(-1.8)
P 		527.2
(-0.8)
P 		645.6
(3)
P 		460.3
(-3)
P 		185
B 545.5
(3)
P 		488.3
(1.3)
P 		446.4
(0.1)
P 		338.6
(-3)
P 		207
C 462
(0.2)
P 		582.2
(3)
P 		536.9
(1.9)
P 		324.8
(-3)
P 		257
avr 501.7
(1.5) 		532.6
(2.6) 		543
(3) 		374.6
(-3) 		168

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 630
1 2 3 4 5 6 range
A 699.2
(3)
P 		443.8
(-2.6)
P 		436.6
(-2.8)
P 		497.5
(-1.4)
P 		426.7
(-3)
P 		593.6
(0.7)
P 		273
B 945.6
(3)
P 		594.3
(-0.3)
P 		402.1
(-2.2)
P 		449
(-1.7)
P 		316
(-3)
P 		587.7
(-0.4)
P 		630
C 769.4
(3)
P 		515.6
(-0.4)
P 		489
(-0.8)
P 		321
(-3)
P 		501.4
(-0.6)
P 		373.5
(-2.3)
P 		448
avr 804.7
(3) 		517.9
(-1.4) 		442.6
(-2.6) 		422.5
(-2.9) 		414.7
(-3) 		518.3
(-1.4) 		390
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 132
1 2 3 4 range
A 181.1
(3)
P 		114.4
(-0.5)
P 		168.8
(2.4)
P 		67.4
(-3)
P 		114
B 173.9
(3)
P 		120.6
(-0.1)
P 		103.4
(-1.2)
P 		72.2
(-3)
P 		102
C 152.9
(1.4)
P 		167.4
(2.1)
P 		187.1
(3)
P 		54.8
(-3)
P 		132
avr 169.3
(3) 		134.1
(1) 		153.1
(2.1) 		64.8
(-3) 		105

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 264
1 2 3 4 5 6 range
A 128.9
(0.2)
P 		157.8
(3)
P 		95.1
(-3)
P 		126.2
(-0)
P 		128.8
(0.2)
P 		144.5
(1.7)
P 		63
B 329
(3)
P 		197.8
(-0.4)
P 		97.6
(-3)
P 		118.9
(-2.4)
P 		128.4
(-2.2)
P 		219.1
(0.2)
P 		231
C 285.2
(3)
P 		157.3
(-0.5)
P 		124.4
(-1.4)
P 		64.6
(-3)
P 		162.2
(-0.3)
P 		125
(-1.4)
P 		221
avr 247.7
(3) 		171
(-0.2) 		105.7
(-2.9) 		103.2
(-3) 		139.8
(-1.5) 		162.9
(-0.5) 		145
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173781_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24774
Sequence Type Exemplar sequence
Representative Public ID AV193224 NCBI
Target Description AV193224 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y116A8C.35 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV193224 /WB_GENE_ID=Y116A8C.35 /WP=CE23341 /CHR=4 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk614g12 : 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_070635(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070635 NCBI Caenorhabditis elegans U2AF splicing factor family member (uaf-2) (uaf-2) mRNA, complete cds. 11/11 None
SNAP00000004106 ENSEMBL cdna:SNAP chromosome:CEL140:IV:17116843:17118499:-1 11/11 None
GENEFINDER00000004185 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:17116843:17118499:-1 11/11 None
Y116A8C.35 ENSEMBL cdna:known chromosome:CEL140:IV:17116719:17118716:-1 gene:Y116A8C.35 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_182462 4/11 Cross Hyb Matching Probes None
SNAP00000014002 4/11 Cross Hyb Matching Probes None
Y108F1.2 4/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:17116799-17118506(-) 84.58 100.0
Public Domain and Genome References
Gene Title
Gene Symbol uaf-2
Ensembl Y116A8C.35
Entrez Gene 178489 Entrez gene
SwissProt Q9U2U0 EMBL-EBI
WormBase CE23341 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:249164_AT U2 snRNP auxiliary factor small subunit, putative at
CANINE:1584383_AT similar to Splicing factor U2AF 35 kDa subunit (U2 auxiliary factor 35 kDa subunit) (U2 snRNP auxiliary factor small subunit) cfa
CANINE_2:CFA.10736.1.A1_S_AT similar to Splicing factor U2AF 35 kDa subunit (U2 auxiliary factor 35 kDa subunit) (U2 snRNP auxiliary factor small subunit) cfa
DROSOPHILA_2:1625231_AT U2 small nuclear riboprotein auxiliary factor 38 dm
DROSGENOME1:154225_AT U2 small nuclear riboprotein auxiliary factor 38 dm
HG-U133_PLUS_2:231904_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HG-U133B:231904_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HG-U133_PLUS_2:232141_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HG-U133B:232141_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HG-U133_PLUS_2:202858_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HG-U133A:202858_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HG-FOCUS:202858_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HG-U133A_2:202858_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HU35KSUBA:HUM_ALU_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HU35KSUBB:HUM_ALU_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HU35KSUBC:HUM_ALU_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HU35KSUBD:HUM_ALU_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HUGENEFL:HUM_ALU_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HC-G110:HUM_ALU_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HU35KSUBC:RC_W74700_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HU35KSUBC:RC_AA099429_S_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HU35KSUBD:RC_AA448683_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HUGENEFL:M96982_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
U133_X3P:G5803206_3P_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
U133_X3P:HS.272188.0.S1_3P_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
U133_X3P:HS.271687.0.S1_3P_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
U133_X3P:HS.221554.0.S1_3P_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
U133_X3P:232141_3P_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HG-U133_PLUS_2:242499_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HG-U133B:242499_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HG-U95AV2:36517_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HG-U95B:44904_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HG-U95E:68830_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HG-U95E:78888_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
HG-U95C:63962_S_AT U2(RNU2) small nuclear RNA auxiliary factor 1 hs
MU11KSUBB:MSA.34473.0_S_AT U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 1 mm
MU11KSUBB:W20545_AT U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 1 mm
MG-U74AV2:97486_AT U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 1 mm
MOE430A:1422509_AT U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 1 mm
MOUSE430A_2:1422509_AT U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 1 mm
MOUSE430_2:1422509_AT U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 1 mm
MU11KSUBB:W20545_AT similar to Splicing factor U2AF 35 kDa subunit (U2 auxiliary factor 35 kDa subunit) (U2 snRNP auxiliary factor small subunit) mm
MG-U74AV2:97486_AT similar to Splicing factor U2AF 35 kDa subunit (U2 auxiliary factor 35 kDa subunit) (U2 snRNP auxiliary factor small subunit) mm
MU19KSUBC:TC40583_AT U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 1 (U2af1), mRNA mm
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3676 nucleic acid binding inferred from electronic annotation QuickGO AmiGO
3723 RNA binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB55137 Hypothetical protein Y116A8C.35 [Caenorhabditis elegans] ref|NP_503036.1| U2AF splicing factor family member (uaf-2) [Caenorhabditis elegans] 1.0E-113
blast CAE57455 Hypothetical protein CBG00419 [Caenorhabditis briggsae] 1.0E-113
blast CAF98200 unnamed protein product [Tetraodon nigroviridis] 3.0E-70
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 5.1E-11
Pfam IPR000571 EMBL-EBI Zn-finger, C-x8-C-x5-C-x3-H type 8.8E-9
Sequence
Target Sequence 
>C. ELEGANS:173781_S_AT
ttcaacggacaaccaatctacgcagagttgtgccctgtcaccgacttccgcgagtctaga
tgccgtcaacacgaagttacaacctgctcgaaaggaggattctgcaatttcatgcacttg
aaggcaatttccgccgaacttggagatcgtctgtatggtagacgtggacgacgagccgac
gcagctggacattatccatcacaacgtggaggttccggaggcggcggtggaggtggtggc
ggcggtggctatggaagcggtggaggatggggtggcggcggtggcggcagagatcgtgat
cgtggaggatggggtggaggcggcggaggtcgtggatatggaggtggcggtggcggtgga
ggctacggatatggaggtggaggcggtggaagacgccgcagtcgaagccgtgatcgaag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCAACGGACAACCAATCTACGCAG 161 681 443 Antisense
AATCTACGCAGAGTTGTGCCCTGTC 67 171 457 Antisense
GTCAACACGAAGTTACAACCTGCTC 177 465 507 Antisense
TGCACTTGAAGGCAATTTCCGCCGA 514 575 555 Antisense
TTCCGCCGAACTTGGAGATCGTCTG 560 697 571 Antisense
TGGTAGACGTGGACGACGAGCCGAC 657 551 598 Antisense
GACGCAGCTGGACATTATCCATCAC 681 379 620 Antisense
AAGCGGTGGAGGATGGGGTGGCGGC 495 149 697 Antisense
CGGTGGCGGCAGAGATCGTGATCGT 127 245 721 Antisense
GGAGGCGGTGGAAGACGCCGCAGTC 447 515 821 Antisense
GCCGCAGTCGAAGCCGTGATCGAAG 102 285 837 Antisense
Sequence Source Affymetrix Proprietary Database