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[188970_at] ARID DNA-binding protein

Description T23D8.8 /REP_DB=WormBase Gene ID /WP=CE25123 /GB=CAB03395.2 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Mouse bright protein like
Cluster 6grp_total > 93      4grp_total > 39      6grp_cgc > 99      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 52
1 2 3 4 range
A 37.3
(3)
A 		2.3
(-3)
A 		2.8
(-2.9)
A 		2.8
(-2.9)
A 		35
B 7.8
(-1.5)
A 		22.2
(3)
A 		3
(-3)
A 		16.9
(1.3)
A 		19
C 54.5
(3)
A 		3.3
(-3)
A 		15.3
(-1.6)
A 		15.1
(-1.6)
A 		51
avr 33.2
(3) 		9.3
(-2.5) 		7
(-3) 		11.6
(-1.9) 		26

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 32
1 2 3 4 5 6 range
A 7.7
(-2)
A 		2.8
(-3)
A 		33.4
(3)
A 		3.1
(-2.9)
A 		15.1
(-0.6)
A 		3
(-3)
A 		31
B 6.9
(3)
A 		4.8
(0.7)
A 		4.2
(0.1)
A 		3.4
(-0.8)
A 		4.4
(0.3)
A 		1.4
(-3)
A 		6
C 1.5
(-3)
A 		5
(-2.3)
A 		4.5
(-2.4)
A 		3.7
(-2.5)
A 		30.6
(3)
A 		23.2
(1.5)
A 		29
avr 5.4
(-2.1) 		4.2
(-2.6) 		14
(1.8) 		3.4
(-3) 		16.7
(3) 		9.2
(-0.4) 		13
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 18
1 2 3 4 range
A 13.6
(3)
A 		0.5
(-3)
A 		0.7
(-2.9)
A 		0.4
(-3)
A 		13
B 2.5
(-0.8)
A 		5.5
(3)
A 		0.7
(-3)
A 		3.6
(0.6)
A 		5
C 18.1
(3)
A 		1
(-3)
A 		5.3
(-1.5)
A 		2.5
(-2.5)
A 		17
avr 11.4
(3) 		2.3
(-2.9) 		2.2
(-3) 		2.2
(-3) 		9

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 9
1 2 3 4 5 6 range
A 1.4
(-2.4)
A 		1
(-2.7)
A 		7.3
(3)
A 		0.8
(-2.9)
A 		4.6
(0.5)
A 		0.7
(-3)
A 		7
B 2.4
(3)
A 		1.6
(0.5)
A 		1
(-1.4)
A 		0.9
(-1.7)
A 		1.8
(1.1)
A 		0.5
(-3)
A 		2
C 0.6
(-3)
A 		1.5
(-2.4)
A 		1.1
(-2.7)
A 		0.8
(-2.9)
A 		9.9
(3)
A 		7.8
(1.6)
A 		9
avr 1.5
(-2.1) 		1.4
(-2.2) 		3.1
(-0) 		0.8
(-3) 		5.4
(3) 		3
(-0.1) 		5
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188970_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1907
Sequence Type Exemplar sequence
Representative Public ID T23D8.8 NCBI
Target Description T23D8.8 /REP_DB=WormBase Gene ID /WP=CE25123 /GB=CAB03395.2 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Mouse bright protein like
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_060243(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060243 NCBI Caenorhabditis elegans CEM Fate Inhibitor family member (cfi-1) (cfi-1) mRNA, complete cds. 11/11 None
SNAP00000036754 ENSEMBL cdna:SNAP chromosome:CEL140:I:10002852:10003982:-1 10/11 None
GENEFINDER00000036757 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:10002852:10005214:-1 11/11 None
T23D8.8 ENSEMBL cdna:known chromosome:CEL140:I:10002852:10008049:-1 gene:T23D8.8 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
chrI:10002782-10004111(-) 100.0 100.0
Public Domain and Genome References
Gene Title ARID DNA-binding protein
Gene Symbol cfi-1
Ensembl T23D8.8
Entrez Gene 188793 Entrez gene
SwissProt O02326 EMBL-EBI
WormBase CE31068 Wormbase
Functional Annotations
Ortholog
ID Title Organism
HU35KSUBA:U88047_AT AT rich interactive domain 3A (BRIGHT- like) hs
HUGENEFL:U88047_AT AT rich interactive domain 3A (BRIGHT- like) hs
HG-U133A:205865_AT AT rich interactive domain 3A (BRIGHT- like) hs
HG-U133_PLUS_2:205865_AT AT rich interactive domain 3A (BRIGHT- like) hs
HG-FOCUS:205865_AT AT rich interactive domain 3A (BRIGHT- like) hs
HG-U133A_2:205865_AT AT rich interactive domain 3A (BRIGHT- like) hs
U133_X3P:G4885192_3P_AT AT rich interactive domain 3A (BRIGHT- like) hs
HG-U95AV2:35913_AT AT rich interactive domain 3A (BRIGHT- like) hs
HG-U133_PLUS_2:234909_AT AT rich interactive domain 3A (BRIGHT- like) hs
HG-U133B:234909_AT AT rich interactive domain 3A (BRIGHT- like) hs
HG-U133_PLUS_2:234911_AT AT rich interactive domain 3A (BRIGHT- like) hs
HG-U133B:234911_AT AT rich interactive domain 3A (BRIGHT- like) hs
MG-U74AV2:103496_AT AT rich interactive domain 3A (Bright like) mm
MOUSE430A_2:1419396_AT AT rich interactive domain 3A (Bright like) mm
MOE430A:1419396_AT AT rich interactive domain 3A (Bright like) mm
MOUSE430_2:1419396_AT AT rich interactive domain 3A (Bright like) mm
MU11KSUBA:U60335_S_AT AT rich interactive domain 3A (Bright like) mm
MU19KSUBC:TC39043_AT AT rich interactive domain 3A (Bright like) (Arid3a), mRNA mm
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
5622 intracellular inferred from electronic annotation QuickGO AmiGO
5634 nucleus inferred from direct assay QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
3677 DNA binding inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB03395 Hypothetical protein T23D8.8 [Caenorhabditis elegans] emb|CAD36479.1| Hypothetical protein T23D8.8 [Caenorhabditis elegans] emb|CAD36497.1| Hypothetical protein T23D8.8 [Caenorhabditis elegans] ref|NP_492644.2| CEM Fate Inhibitor family member (cfi-1) [Caenorhabditis elegans] gb|AAL93258.1| ARID DNA binding protein CFI-1 [Caenorhabditis elegans] 0.0
blast CAB03395 Hypothetical protein T23D8.8 [Caenorhabditis elegans] emb|CAD36479.1| Hypothetical protein T23D8.8 [Caenorhabditis elegans] emb|CAD36497.1| Hypothetical protein T23D8.8 [Caenorhabditis elegans] ref|NP_492644.2| CEM Fate Inhibitor family member (cfi-1) [Caenorhabditis elegans] gb|AAL93258.1| ARID DNA binding protein CFI-1 [Caenorhabditis elegans] 1.0E-148
blast CAE60214 Hypothetical protein CBG03778 [Caenorhabditis briggsae] 1.0E-116
blast CAB03395 Hypothetical protein T23D8.8 [Caenorhabditis elegans] emb|CAD36479.1| Hypothetical protein T23D8.8 [Caenorhabditis elegans] emb|CAD36497.1| Hypothetical protein T23D8.8 [Caenorhabditis elegans] ref|NP_492644.2| CEM Fate Inhibitor family member (cfi-1) [Caenorhabditis elegans] gb|AAL93258.1| ARID DNA binding protein CFI-1 [Caenorhabditis elegans] 1.0E-108
blast CAE60214 Hypothetical protein CBG03778 [Caenorhabditis briggsae] 2.0E-99
blast BAE06382.1 dead ringer homolog [Ciona intestinalis] 5.0E-58
Protein Domains
Database ID Description E-Value
scop a.4.3.ARID domain All alpha proteins; DNA/RNA-binding 3-helical bundle; ARID-like; ARID domain 0.0
scop a.4.3.ARID domain All alpha proteins; DNA/RNA-binding 3-helical bundle; ARID-like; ARID domain 4.99983292071095E-42
Pfam IPR001606 EMBL-EBI ARID (AT-rich interaction domain) protein 1.8E-43
Pfam IPR001606 EMBL-EBI ARID (AT-rich interaction domain) protein 1.0E-30
Pfam IPR001606 EMBL-EBI ARID (AT-rich interaction domain) protein 1.8E-43
Sequence
Target Sequence 
>C. ELEGANS:188970_AT
gtaatcgacgagaagcacctggaagacggacggctccatcatttccattaccttttcaac
ttccacatgctgcaagtgctgctgcaacaatgcttaataatcaattaaatggattaggaa
tgagaaatgacctccttgacgatgaaaatacattaagtctccaggcttctggcctctttg
gaacaagctatggagccgagcaaatggcaatacttgaagctcatcaaagaaatctagaaa
gagctcagagagctgttcaacagcaagtcgcgcgccaaagtctagggctcacagcatgtt
caaatggcaatggaggaaatattcataattctggaagagaatctacgtctagtaatgact
cagacattcctgcgaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTAATCGACGAGAAGCACCTGGAAG 379 463 290 Antisense
CACCTGGAAGACGGACGGCTCCATC 502 201 305 Antisense
ATCATTTCCATTACCTTTTCAACTT 439 29 327 Antisense
TTCCACATGCTGCAAGTGCTGCTGC 563 701 350 Antisense
GAAATGACCTCCTTGACGATGAAAA 213 361 413 Antisense
CATTAAGTCTCCAGGCTTCTGGCCT 120 215 440 Antisense
CTTCTGGCCTCTTTGGAACAAGCTA 385 219 455 Antisense
AGCTGTTCAACAGCAAGTCGCGCGC 588 81 540 Antisense
TCGCGCGCCAAAGTCTAGGGCTCAC 396 597 557 Antisense
AGGGCTCACAGCATGTTCAAATGGC 70 59 573 Antisense
GTAATGACTCAGACATTCCTGCGAA 254 463 641 Antisense
Sequence Source Affymetrix Proprietary Database