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[192735_s_at] Helix-loop-helix DNA-binding domain

Description Y47D3B.7 /REP_DB=WormBase Gene ID /WP=CE19180 /TR=Q9XX00 /GB=CAA21042.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Helix-loop-helix DNA-binding domain
Cluster 6grp_highest_10_10 > 17      6grp_high1_10_10 > 51      4grp_highest_8_8 > 50      4grp_high_8_8 > 33      6grp_highest_nonorm > 43      6grp_total > 51      4grp_total > 47      6grp_highest_sub > 04      6grp_cgc > 74      6grp_high1_sub > 03      6grp_cgc_sub > 02_03_04_05      6grp_total_sub > Hat      6grp_rule_based > S3      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 493
1 2 3 4 range
A 909.6
(3)
P 		632.3
(-1.7)
P 		557.2
(-3)
P 		578.1
(-2.6)
P 		352
B 1050.3
(3)
P 		711.5
(-1.7)
P 		663.8
(-2.3)
P 		615.6
(-3)
P 		435
C 981.8
(3)
P 		588.5
(-2.8)
P 		605.8
(-2.6)
P 		576.8
(-3)
P 		405
avr 980.6
(3) 		644.1
(-2.2) 		608.9
(-2.7) 		590.2
(-3) 		390

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 852
1 2 3 4 5 6 range
A 871.2
(-1.2)
P 		1284.2
(2.6)
P 		1063.2
(0.6)
P 		1322.9
(3)
P 		917.1
(-0.8)
P 		681.7
(-3)
P 		641
B 818.5
(-0.2)
P 		1075.2
(2.2)
P 		1163.2
(3)
P 		1073.2
(2.2)
P 		942.3
(0.9)
P 		518
(-3)
P 		645
C 840.9
(-0.7)
P 		957.1
(0.2)
P 		1361.4
(3)
P 		1100.6
(1.2)
P 		1232.9
(2.1)
P 		509.1
(-3)
P 		852
avr 843.5
(-0.4) 		1105.5
(2.1) 		1195.9
(3) 		1165.6
(2.7) 		1030.8
(1.4) 		569.6
(-3) 		626
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 250
1 2 3 4 range
A 331.2
(3)
P 		137.3
(-1.7)
P 		145.7
(-1.5)
P 		84.6
(-3)
P 		247
B 334.9
(3)
P 		175.7
(-1.7)
P 		153.8
(-2.3)
P 		131.2
(-3)
P 		204
C 325
(3)
P 		169.2
(-1.1)
P 		211.1
(-0)
P 		97.3
(-3)
P 		228
avr 330.4
(3) 		160.7
(-1.5) 		170.2
(-1.3) 		104.4
(-3) 		226

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 296
1 2 3 4 5 6 range
A 160.6
(-3)
P 		456.7
(3)
P 		231.5
(-1.6)
P 		335.5
(0.5)
P 		276.8
(-0.6)
P 		166
(-2.9)
P 		296
B 284.8
(-0.1)
P 		357.9
(2.2)
P 		282.5
(-0.2)
P 		284.3
(-0.1)
P 		382.9
(3)
P 		193.2
(-3)
P 		190
C 311.7
(0.7)
P 		292
(0.2)
P 		346.5
(1.6)
P 		221.3
(-1.7)
P 		399
(3)
P 		170.4
(-3)
P 		229
avr 252.4
(-0.6) 		368.9
(3) 		286.8
(0.4) 		280.4
(0.2) 		352.9
(2.5) 		176.5
(-3) 		192
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192735_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7817
Sequence Type Exemplar sequence
Representative Public ID Y47D3B.7 NCBI
Target Description Y47D3B.7 /REP_DB=WormBase Gene ID /WP=CE19180 /TR=Q9XX00 /GB=CAA21042.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Helix-loop-helix DNA-binding domain
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_067071(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067071 NCBI Caenorhabditis elegans Sterol regulatory element Binding Protein family member (sbp-1) (sbp-1) mRNA, complete cds. 11/11 None
GENEFINDER00000004522 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:11428294:11442441:-1 11/11 None
SNAP00000004516 ENSEMBL cdna:SNAP chromosome:CEL140:III:11428508:11442441:-1 9/11 None
Y47D3B.7 ENSEMBL cdna:known chromosome:CEL140:III:11428241:11442442:-1 gene:Y47D3B.7 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
chrIII:11428289-11442437(-) 100.0 100.0
Public Domain and Genome References
Gene Title Helix-loop-helix DNA-binding domain
Gene Symbol sbp-1
Ensembl Y47D3B.7
Entrez Gene 176574 Entrez gene
SwissProt Q9XX00 EMBL-EBI
WormBase CE19180 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1583024_AT sterol regulatory element binding transcription factor 1 cfa
CANINE:1582829_AT sterol regulatory element binding transcription factor 1 cfa
CANINE_2:CFA.189.1.S1_S_AT sterol regulatory element binding transcription factor 1 cfa
CANINE_2:CFA.189.2.S1_S_AT sterol regulatory element binding transcription factor 1 cfa
CANINE_2:CFAAFFX.28201.1.S1_AT sterol regulatory element binding transcription factor 1 cfa
CANINE:1583023_AT sterol regulatory element binding transcription factor 1 cfa
CANINE_2:CFA.189.2.A1_AT sterol regulatory element binding transcription factor 1 cfa
DROSOPHILA_2:1628292_S_AT Helix loop helix protein 106 dm
DROSGENOME1:143786_AT Helix loop helix protein 106 dm
HG-U133_PLUS_2:202308_AT sterol regulatory element binding transcription factor 1 hs
HG-U133A:202308_AT sterol regulatory element binding transcription factor 1 hs
HG-FOCUS:202308_AT sterol regulatory element binding transcription factor 1 hs
HG-U133A_2:202308_AT sterol regulatory element binding transcription factor 1 hs
HUGENEFL:U00968_AT sterol regulatory element binding transcription factor 1 hs
U133_X3P:G4759167_3P_AT sterol regulatory element binding transcription factor 1 hs
U133_X3P:HS2.424536.1.A1_3P_AT sterol regulatory element binding transcription factor 1 hs
HG-U133_PLUS_2:1558875_AT sterol regulatory element binding transcription factor 1 hs
HG-U95AV2:32135_AT sterol regulatory element binding transcription factor 1 hs
HG-U95E:73364_R_AT sterol regulatory element binding transcription factor 1 hs
HG-U95E:88057_AT sterol regulatory element binding transcription factor 1 hs
HU35KSUBD:RC_W94594_AT Sterol regulatory element binding transcription factor 1 hs
HG-U95B:59252_AT Sterol regulatory element binding transcription factor 1 hs
HU35KSUBD:RC_AA232663_AT Sterol regulatory element binding transcription factor 1 hs
MOE430A:1426690_A_AT sterol regulatory element binding factor 1 mm
MOUSE430_2:1426690_A_AT sterol regulatory element binding factor 1 mm
MOUSE430A_2:1426690_A_AT sterol regulatory element binding factor 1 mm
MU11KSUBB:MSA.27761.0_S_AT sterol regulatory element binding factor 1 mm
MU11KSUBB:MSA.27633.0_S_AT sterol regulatory element binding factor 1 mm
MU11KSUBB:MSA.26077.0_S_AT sterol regulatory element binding factor 1 mm
MU11KSUBB:MSA.24483.0_S_AT sterol regulatory element binding factor 1 mm
MG-U74AV2:93264_AT sterol regulatory element binding factor 1 mm
MU19KSUBC:TC39714_AT sterol regulatory element binding factor 1 mm
RG-U34A:L16995_AT sterol regulatory element binding factor 1 rn
RG-U34B:RC_AI013042_AT sterol regulatory element binding factor 1 rn
RAE230A:1371104_AT sterol regulatory element binding factor 1 rn
RAT230_2:1371104_AT sterol regulatory element binding factor 1 rn
RAE230A:1388426_AT sterol regulatory element binding factor 1 rn
RAT230_2:1388426_AT sterol regulatory element binding factor 1 rn
Protein Similarities
Method ID Description E-Value
blast CAA21042 Hypothetical protein Y47D3B.7 [Caenorhabditis elegans] ref|NP_499472.1| Sterol regulatory element Binding Protein family member (sbp-1) [Caenorhabditis elegans] 0.0
blast CAE67710 Hypothetical protein CBG13284 [Caenorhabditis briggsae] 0.0
blast CAG03157 unnamed protein product [Tetraodon nigroviridis] 8.0E-47
Protein Domains
Database ID Description E-Value
Pfam IPR001092 EMBL-EBI Basic helix-loop-helix dimerization domain bHLH 4.0E-16
Pfam IPR001092 EMBL-EBI Basic helix-loop-helix dimerization domain bHLH 4.0E-16
Pfam IPR001092 EMBL-EBI Basic helix-loop-helix dimerization domain bHLH 2.8E-7
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_499472.1 2 480-502,539-561
Y47D3B.7 2 480-502,539-561
GENEFINDER00000004522 2 465-487,524-546
SNAP00000004516 2 430-452,489-511
Sequence
Target Sequence 
>C. ELEGANS:192735_S_AT
tggcacggcaacactattcactgatcaggaactgtccgccgaagattttgacagacaatc
tgggtttggcggttggccacgcgttgtgtgctcgcaagatttgcatagatgaccgagatt
ccccgaaagtcagtcaatacgtgtgcattcacacaaagaagtcgctcgaatccctccgac
tattctccacatcatcgcgagcatcaggtgtggtgtctggaattcaggaaggtacacgcc
gaatggcctacgaatggattatgaactcgctgctcgacgcgtggcgttccaatctattcg
catcgaaaccctactggacacaaagcttcaagggacaatccacgtttagtacgctttatc
aagaggcgtataatcattatgcgattattaatgggacaaggggagattgttggagactat
ttgtctacgagctcacgtgccgaatgctcaacggagccaacccacaagccacgtggtcag
g

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGCACGGCAACACTATTCACTGAT 44 547 2747 Antisense
TCACTGATCAGGAACTGTCCGCCGA 484 625 2764 Antisense
CCACGCGTTGTGTGCTCGCAAGATT 45 275 2823 Antisense
GACCGAGATTCCCCGAAAGTCAGTC 634 381 2857 Antisense
ACAAAGAAGTCGCTCGAATCCCTCC 151 111 2899 Antisense
CATCGCGAGCATCAGGTGTGGTGTC 425 211 2939 Antisense
GAAGGTACACGCCGAATGGCCTACG 627 333 2974 Antisense
AATGGATTATGAACTCGCTGCTCGA 423 163 2999 Antisense
TTCGCATCGAAACCCTACTGGACAC 19 697 3043 Antisense
GCTCACGTGCCGAATGCTCAACGGA 318 301 3177 Antisense
CCAACCCACAAGCCACGTGGTCAGG 495 275 3203 Antisense
Sequence Source Affymetrix Proprietary Database