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[172855_x_at]

Description F02E9.2A /REP_DB=WormBase Gene ID /WP=CE24879 /GEN=lin-28 /TR=P92186 /GB=CAB61008.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=cold shock domain
Cluster 6grp_total > 07      4grp_total > 39      6grp_cgc > 11      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 346
1 2 3 4 range
A 340.9
(3)
P 		9.8
(-3)
A 		41.1
(-2.4)
A 		87.6
(-1.6)
A 		331
B 315.7
(3)
P 		41.2
(-2.4)
A 		11.4
(-3)
A 		50
(-2.2)
A 		304
C 354.6
(3)
P 		22
(-2.8)
A 		8.3
(-3)
A 		118.5
(-1.1)
P 		346
avr 337.1
(3) 		24.3
(-2.9) 		20.3
(-3) 		85.4
(-1.8) 		317

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 305
1 2 3 4 5 6 range
A 206.8
(3)
P 		92.8
(-0.5)
A 		116.1
(0.2)
P 		53.4
(-1.7)
P 		59.7
(-1.5)
A 		12.6
(-3)
A 		194
B 180.4
(3)
P 		115.8
(0)
P 		109.5
(-0.3)
A 		78.2
(-1.7)
A 		51.1
(-3)
A 		88.2
(-1.3)
P 		129
C 316
(3)
P 		159.9
(-0.1)
P 		66.3
(-1.9)
A 		82.7
(-1.6)
P 		11.4
(-3)
A 		76.2
(-1.7)
A 		305
avr 234.4
(3) 		122.8
(-0.5) 		97.3
(-1.2) 		71.4
(-2) 		40.7
(-3) 		59
(-2.4) 		194
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 122
1 2 3 4 range
A 124.1
(3)
P 		2.1
(-3)
A 		10.8
(-2.6)
A 		12.8
(-2.5)
A 		122
B 100.7
(3)
P 		10.2
(-2.5)
A 		2.6
(-3)
A 		10.7
(-2.5)
A 		98
C 117.4
(3)
P 		6.3
(-2.8)
A 		2.9
(-3)
A 		20
(-2.1)
P 		115
avr 114.1
(3) 		6.2
(-3) 		5.4
(-3) 		14.5
(-2.5) 		109

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 114
1 2 3 4 5 6 range
A 38.1
(3)
P 		33
(2.1)
A 		25.3
(0.8)
P 		13.6
(-1.2)
P 		18
(-0.4)
A 		3.1
(-3)
A 		35
B 62.8
(3)
P 		38.5
(-0.5)
P 		26.6
(-2.2)
A 		20.7
(-3)
A 		20.8
(-3)
A 		32.9
(-1.3)
P 		42
C 117.1
(3)
P 		48.8
(-0.6)
P 		16.9
(-2.3)
A 		16.6
(-2.3)
P 		3.7
(-3)
A 		25.5
(-1.8)
A 		113
avr 72.7
(3) 		40.1
(-0.3) 		22.9
(-2.1) 		17
(-2.7) 		14.2
(-3) 		20.5
(-2.4) 		59
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172855_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2143
Sequence Type Exemplar sequence
Representative Public ID F02E9.2A NCBI
Target Description F02E9.2A /REP_DB=WormBase Gene ID /WP=CE24879 /GEN=lin-28 /TR=P92186 /GB=CAB61008.1 /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(10)
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. 10/11 A 
GENEFINDER00000012712 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:8416025:8418928:-1 11/11 None
SNAP00000012705 ENSEMBL cdna:SNAP chromosome:CEL140:I:8416286:8417856:-1 10/11 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 10/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000012706 1/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:8416216-8418859(-) 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:172855_X_AT
gaacatgagagttccttccttcgagaggctcccgtcaccaacacctcgatactttggctc
atgcaaatggtttaatgtgtcgaaaggatatggttttgtgatcgatgacatcaccggtga
agatctattcgttcatcagtctaatctcaatatgcaaggatttcggagtcttgatgaagg
agaacgtgtatcatactacattcaagagcgatcgaatggaaaaggtagagaagcttatgc
ggtatcaggagaagtagaaggacaaggactgaaaggaagccgaattcatccattgggtcg
taagaaggctgtctcactacgttgcttcagatgtggaaagtttgcgactcacaaggcgaa
aagttgtccaaacgtaaaaaccgatgcaaaagtgtgttatacctgtggatccgaggagca
cgtgagctcaatctgtcctgaaagacgacgaaagcatcgaccggaacaagttgccgcaga
ggaagcagaagctgcgagaatggcagctgaaaaatcatcaccgactacatctgacgat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAACATGAGAGTTCCTTCCTTCGAG 315 351 120 Antisense
GTCACCAACACCTCGATACTTTGGC 555 465 153 Antisense
GATCTATTCGTTCATCAGTCTAATC 399 419 241 Antisense
GAAGCCGAATTCATCCATTGGGTCG 608 343 395 Antisense
GGGTCGTAAGAAGGCTGTCTCACTA 340 497 414 Antisense
TGTCTCACTACGTTGCTTCAGATGT 517 557 429 Antisense
GGAAAGTTTGCGACTCACAAGGCGA 262 527 454 Antisense
ATACCTGTGGATCCGAGGAGCACGT 305 23 518 Antisense
GAGCACGTGAGCTCAATCTGTCCTG 667 389 535 Antisense
GCATCGACCGGAACAAGTTGCCGCA 710 307 573 Antisense
ATCATCACCGACTACATCTGACGAT 146 31 633 Antisense
Sequence Source Affymetrix Proprietary Database