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[191973_s_at]

Description F02E9.2B /REP_DB=WormBase Gene ID /WP=CE24880 /GEN=lin-28 /TR=Q9U3K6 /GB=CAB61009.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=cold shock domain
Cluster 6grp_high1_10_10 > 17      6grp_total > 07      4grp_total > 39      6grp_cgc > 11      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 486
1 2 3 4 range
A 493.2
(3)
P 		80.9
(-2.4)
A 		33.2
(-3)
A 		121.2
(-1.9)
P 		460
B 388
(3)
P 		72.5
(-2)
A 		11.3
(-3)
A 		202.5
(0)
P 		377
C 497.5
(3)
P 		90.8
(-2.5)
A 		57.3
(-3)
A 		148.9
(-1.8)
P 		440
avr 459.6
(3) 		81.4
(-2.3) 		33.9
(-3) 		157.5
(-1.3) 		426

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 487
1 2 3 4 5 6 range
A 291.7
(3)
P 		151.6
(-0.2)
P 		139.5
(-0.5)
P 		144.9
(-0.3)
P 		27.3
(-3)
A 		85.3
(-1.7)
A 		264
B 295.1
(3)
P 		129.7
(-1.4)
P 		100.5
(-2.2)
P 		90.6
(-2.5)
P 		107.1
(-2.1)
P 		71.9
(-3)
P 		223
C 513.8
(3)
P 		189.5
(-1.3)
P 		102.5
(-2.4)
A 		64.9
(-2.9)
A 		59
(-3)
A 		91.5
(-2.6)
M 		455
avr 366.9
(3) 		156.9
(-1.2) 		114.2
(-2) 		100.1
(-2.3) 		64.5
(-3) 		82.9
(-2.6) 		302
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 177
1 2 3 4 range
A 179.6
(3)
P 		17.6
(-2.7)
A 		8.7
(-3)
A 		17.7
(-2.7)
P 		171
B 123.7
(3)
P 		17.9
(-2.2)
A 		2.6
(-3)
A 		43.2
(-1)
P 		121
C 164.7
(3)
P 		26.1
(-2.7)
A 		20
(-3)
A 		25.1
(-2.8)
P 		145
avr 156
(3) 		20.5
(-2.6) 		10.4
(-3) 		28.7
(-2.2) 		146

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 182
1 2 3 4 5 6 range
A 53.8
(3)
P 		53.9
(3)
P 		30.4
(-0.1)
P 		36.8
(0.8)
P 		8.3
(-3)
A 		20.8
(-1.4)
A 		46
B 102.7
(3)
P 		43.2
(-1.5)
P 		24.4
(-3)
P 		24
(-3)
P 		43.5
(-1.5)
P 		26.8
(-2.8)
P 		79
C 190.4
(3)
P 		57.8
(-1.5)
P 		26.1
(-2.6)
A 		13.1
(-3)
A 		19.1
(-2.8)
A 		30.6
(-2.4)
M 		177
avr 115.6
(3) 		51.6
(-1.2) 		27
(-2.8) 		24.6
(-2.9) 		23.6
(-3) 		26.1
(-2.8) 		92
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 191973_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2126
Sequence Type Exemplar sequence
Representative Public ID F02E9.2B NCBI
Target Description F02E9.2B /REP_DB=WormBase Gene ID /WP=CE24880 /GEN=lin-28 /TR=Q9U3K6 /GB=CAB61009.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=cold shock 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_001025914(11), NM_059880(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001025914 NCBI Caenorhabditis elegans abnormal cell LINeage family member (lin-28) (lin-28) mRNA, complete cds. 11/11 None
NM_059880 NCBI Caenorhabditis elegans abnormal cell LINeage family member (lin-28) (lin-28) mRNA, complete cds. 11/11 A 
GENEFINDER00000012712 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:8416025:8418928:-1 11/11 None
SNAP00000012705 ENSEMBL cdna:SNAP chromosome:CEL140:I:8416286:8417856:-1 11/11 None
F02E9.2a ENSEMBL cdna:known chromosome:CEL140:I:8415759:8418929:-1 gene:F02E9.2 11/11 A 
F02E9.2b ENSEMBL cdna:known chromosome:CEL140:I:8416286:8418001:-1 gene:F02E9.2 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
chrI:8416216-8417787(-) 100.0 100.0
Public Domain and Genome References
Ensembl F02E9.2
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAB61008 Hypothetical protein F02E9.2a [Caenorhabditis elegans] ref|NP_001021085.1| abnormal cell LINeage family member (lin-28) [Caenorhabditis elegans] gb|AAC47476.1| LIN-28 [Caenorhabditis elegans] gb|AAB49759.1| Lin-28 [Caenorhabditis elegans] 1.0E-123
blast CAB61008 Hypothetical protein F02E9.2a [Caenorhabditis elegans] ref|NP_001021085.1| abnormal cell LINeage family member (lin-28) [Caenorhabditis elegans] gb|AAC47476.1| LIN-28 [Caenorhabditis elegans] gb|AAB49759.1| Lin-28 [Caenorhabditis elegans] 1.0E-120
blast CAB61009 Hypothetical protein F02E9.2b [Caenorhabditis elegans] ref|NP_492281.2| abnormal cell LINeage family member (lin-28) [Caenorhabditis elegans] 1.0E-104
blast AAC47478 LIN-28 [Caenorhabditis vulgaris] 1.0E-103
blast AAC47477 LIN-28 [Caenorhabditis remanei] 1.0E-101
Protein Domains
Database ID Description E-Value
Pfam IPR002059 EMBL-EBI Cold-shock DNA-binding domain 2.7E-32
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 3.0E-5
Pfam IPR002059 EMBL-EBI Cold-shock DNA-binding domain 2.7E-32
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 3.0E-5
Sequence
Target Sequence 
>C. ELEGANS:191973_S_AT
gtcaccaacacctcgatactttggctcatgcaaatggtttaatgtgtcgaaaggatatgg
ttttgtgatcgatgacatcaccggtgaagatctattcgttcatcagtctaatctcaatat
gcaaggatttcggagtcttgatgaaggagaacgtgtatcatactacattcaagagcgatc
gaatggaaaaggtagagaagcttatgcggtatcaggagaagtagaaggacaaggactgaa
aggaagccgaattcatccattgggtcgtaagaaggctgtctcactacgttgcttcagatg
tggaaagtttgcgactcacaaggcgaaaagttgtccaaacgtaaaaaccgatgcaaaagt
gtgttatacctgtggatccgaggagcacgtgagctcaatctgtcctgaaagacgacgaaa
gcatcgaccggaacaagttgccgcagaggaagcagaagctgcgagaatggcagctgaaaa
atcatcaccgactacatctgacgat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTCACCAACACCTCGATACTTTGGC 554 465 60 Antisense
GATCTATTCGTTCATCAGTCTAATC 398 419 148 Antisense
GAAGCCGAATTCATCCATTGGGTCG 607 343 302 Antisense
GGGTCGTAAGAAGGCTGTCTCACTA 339 497 321 Antisense
TGTCTCACTACGTTGCTTCAGATGT 516 557 336 Antisense
GGAAAGTTTGCGACTCACAAGGCGA 261 527 361 Antisense
AAGTGTGTTATACCTGTGGATCCGA 405 159 416 Antisense
TGTGGATCCGAGGAGCACGTGAGCT 359 553 430 Antisense
ACGTGAGCTCAATCTGTCCTGAAAG 445 95 446 Antisense
GCATCGACCGGAACAAGTTGCCGCA 709 307 480 Antisense
ATCATCACCGACTACATCTGACGAT 145 31 540 Antisense
Sequence Source Affymetrix Proprietary Database