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[183038_at]

Description Y39B6A.F /REP_DB=WormBase Gene ID /WP=CE21666 /TR=Q9NEI6 /GB=CAB61063.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 73      6grp_high1_10_10 > 37      4grp_highest_8_8 > 17      4grp_high_8_8 > 61      6grp_highest_nonorm > 82      6grp_total > 37      4grp_total > 59      6grp_highest_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 350
1 2 3 4 range
A 436.1
(-0.5)
P 		590
(3)
P 		520.1
(1.4)
P 		323.2
(-3)
P 		267
B 417.6
(0.9)
P 		434
(1.2)
P 		514
(3)
P 		240.3
(-3)
P 		274
C 407.1
(-1.2)
P 		460.8
(0.3)
P 		551.2
(3)
P 		346.6
(-3)
P 		205
avr 420.3
(0.1) 		494.9
(2.1) 		528.4
(3) 		303.4
(-3) 		225

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 199
1 2 3 4 5 6 range
A 391.8
(3)
P 		307.7
(-0.6)
P 		325.5
(0.2)
P 		262.4
(-2.5)
P 		251
(-3)
P 		278.9
(-1.8)
P 		141
B 357.8
(2)
P 		304.8
(-1.6)
P 		347.4
(1.3)
P 		326.1
(-0.1)
P 		284
(-3)
P 		372.1
(3)
P 		88
C 449
(3)
P 		367.9
(0.6)
P 		313.1
(-1.1)
P 		328.4
(-0.6)
P 		249.9
(-3)
P 		434.2
(2.6)
P 		199
avr 399.5
(3) 		326.8
(-0.2) 		328.7
(-0.1) 		305.6
(-1.1) 		261.6
(-3) 		361.7
(1.4) 		138
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 145
1 2 3 4 range
A 158.8
(3)
P 		128.1
(1.3)
P 		136
(1.8)
P 		47.3
(-3)
P 		112
B 133.2
(3)
P 		107.2
(1.1)
P 		119.1
(2)
P 		51.2
(-3)
P 		82
C 134.8
(0.4)
P 		132.5
(0.3)
P 		192.1
(3)
P 		58.4
(-3)
P 		134
avr 142.3
(2.6) 		122.6
(1.4) 		149.1
(3) 		52.3
(-3) 		97

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 100
1 2 3 4 5 6 range
A 72.2
(-2.2)
P 		109.4
(3)
P 		70.9
(-2.4)
P 		66.6
(-3)
P 		75.8
(-1.7)
P 		67.9
(-2.8)
P 		43
B 124.5
(1.4)
P 		101.5
(-1.1)
P 		84.4
(-3)
P 		86.4
(-2.8)
P 		115.4
(0.4)
P 		138.8
(3)
P 		54
C 166.4
(3)
P 		112.2
(-0.2)
P 		79.7
(-2.2)
P 		66
(-3)
P 		80.9
(-2.1)
P 		145.4
(1.7)
P 		100
avr 121
(3) 		107.7
(1.3) 		78.3
(-2.3) 		73
(-3) 		90.7
(-0.8) 		117.4
(2.6) 		48
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 183038_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.19435
Sequence Type Exemplar sequence
Representative Public ID Y39B6A.F NCBI
Target Description Y39B6A.F /REP_DB=WormBase Gene ID /WP=CE21666 /TR=Q9NEI6 /GB=CAB61063.1 /SUBMIT=HINXTON /CHR=5 /FEA=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_171568(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_171568 NCBI Caenorhabditis elegans Y39B6A.39 (Y39B6A.39) mRNA, complete cds. 11/11 None
SNAP00000030529 ENSEMBL cdna:SNAP chromosome:CEL140:V:18984527:19000682:1 11/11 None
GENEFINDER00000030687 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:18983892:18988188:1 11/11 None
Y39B6A.39 ENSEMBL cdna:known chromosome:CEL140:V:18983892:18988188:1 gene:Y39B6A.39 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
chrV:18983891-18988188(+) 99.82 100.0
Public Domain and Genome References
Gene Title
Ensembl Y39B6A.39
Entrez Gene 180240 Entrez gene
SwissProt Q9NEI6 EMBL-EBI
WormBase CE21666 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1590911_AT similar to mitochondrial ribosomal protein S35 cfa
CANINE_2:CFA.11153.1.A1_S_AT similar to mitochondrial ribosomal protein S35 cfa
CANINE_2:CFAAFFX.17151.1.S1_S_AT similar to mitochondrial ribosomal protein S35 cfa
DROSOPHILA_2:1632280_AT mitochondrial ribosomal protein S35 dm
DROSGENOME1:148067_AT mitochondrial ribosomal protein S35 dm
CHICKEN:GGA.5804.1.S1_S_AT mitochondrial ribosomal protein S35 gga
HG-U133_PLUS_2:217942_AT mitochondrial ribosomal protein S35 hs
HG-U133A:217942_AT mitochondrial ribosomal protein S35 hs
HG-FOCUS:217942_AT mitochondrial ribosomal protein S35 hs
HG-U133A_2:217942_AT mitochondrial ribosomal protein S35 hs
HU35KSUBA:RC_AA236018_AT mitochondrial ribosomal protein S35 hs
HU35KSUBA:D82775_AT mitochondrial ribosomal protein S35 hs
HU35KSUBD:RC_N54461_AT mitochondrial ribosomal protein S35 hs
U133_X3P:G11141894_3P_AT mitochondrial ribosomal protein S35 hs
HG-U95B:56363_AT mitochondrial ribosomal protein S35 hs
HG-U95C:63751_F_AT Mitochondrial ribosomal protein S35 hs
HU35KSUBB:RC_R02190_AT Mitochondrial ribosomal protein S35 hs
MG-U74BV2:114268_AT mitochondrial ribosomal protein S35 mm
MOE430A:1452111_AT mitochondrial ribosomal protein S35 mm
MOUSE430A_2:1452111_AT mitochondrial ribosomal protein S35 mm
MOUSE430_2:1452111_AT mitochondrial ribosomal protein S35 mm
RG-U34B:RC_AI045908_AT mitochondrial ribosomal protein S35 (predicted) rn
RAE230A:1372839_AT mitochondrial ribosomal protein S35 (predicted) rn
RAT230_2:1372839_AT mitochondrial ribosomal protein S35 (predicted) rn
Protein Similarities
Method ID Description E-Value
blast CAB61063 Hypothetical protein Y39B6A.39 [Caenorhabditis elegans] ref|NP_741658.1| Y39B6A.39 [Caenorhabditis elegans] 0.0
blast CAB61063 Hypothetical protein Y39B6A.39 [Caenorhabditis elegans] ref|NP_741658.1| Y39B6A.39 [Caenorhabditis elegans] 1.0E-169
blast CAE56190 Hypothetical protein CBG23813 [Caenorhabditis briggsae] 1.0E-155
blast CAD31828 Hypothetical protein Y39B6A.36 [Caenorhabditis elegans] ref|NP_741661.1| Y39B6A.36 [Caenorhabditis elegans] 1.0E-142
blast CAD31829 Hypothetical protein Y39B6A.37 [Caenorhabditis elegans] ref|NP_741660.1| Y39B6A.37 [Caenorhabditis elegans] 1.0E-137
blast BAE41824.1 unnamed protein product [Mus musculus] dbj|BAC36950.1| unnamed protein product [Mus musculus] 2.0E-52
Protein Domains
Database ID Description E-Value
Pfam IPR003196 EMBL-EBI Transcription initiation factor IIF, beta subunit 1.9E-7
Pfam IPR003196 EMBL-EBI Transcription initiation factor IIF, beta subunit 7.9E-41
Sequence
Target Sequence 
>C. ELEGANS:183038_AT
caccggctattcaacaacactgtcaagctatcaaaaaattctgtactccattcccaccgg
aactcctctccaatccatctgccacgtgtcaacatcttccaatttccatagaatattcta
catacattcatcagggaacttcaatccgtgacattagaagccgtgtcgtaactatgaaaa
tccacgtggcagagcttaaattgtcggaaaatcaaatggaaaaactgattcgactggccg
caaatcgatatgacgaaaaaacgggaaaaatgacaattatcactgatagatgtcatacga
gacaacagaatctcgattatgcacactatttactaactgtgttatatcatgaagctcaaa
aagtcgagaaatgggatgaattgaagaaccgcaccgacgctctgaaagttgaattcgatg
gctccaacaccaaaaccaaactcatcgatttactggaaaaagccaagttgacgcctggat
taagcccc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CACCGGCTATTCAACAACACTGTCA 405 201 482 Antisense
CAAAAAATTCTGTACTCCATTCCCA 460 189 513 Antisense
TCATCAGGGAACTTCAATCCGTGAC 63 621 609 Antisense
GGAAAAACTGATTCGACTGGCCGCA 605 527 699 Antisense
GACTGGCCGCAAATCGATATGACGA 219 377 713 Antisense
GAATCTCGATTATGCACACTATTTA 394 329 789 Antisense
GATGAATTGAAGAACCGCACCGACG 175 413 856 Antisense
CGCACCGACGCTCTGAAAGTTGAAT 494 253 871 Antisense
GTTGAATTCGATGGCTCCAACACCA 188 439 889 Antisense
CCAACACCAAAACCAAACTCATCGA 366 275 905 Antisense
CAAGTTGACGCCTGGATTAAGCCCC 183 183 945 Antisense
Sequence Source Affymetrix Proprietary Database