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[189637_at] C. elegans homeobox gene lin-39

Description C07H6.7 /REP_DB=WormBase Gene ID /WP=CE03975 /GEN=lin-39 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=C. elegans homeobox gene lin-39
Cluster 6grp_highest_10_10 > 51      6grp_high1_10_10 > 15      4grp_highest_8_8 > 63      4grp_high_8_8 > 27      6grp_highest_nonorm > 80      6grp_total > 05      4grp_total > 36      6grp_highest_sub > De      6grp_cgc > 22      6grp_high1_sub > De      6grp_cgc_sub > De      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 172
1 2 3 4 range
A 303
(1.7)
P 		334.3
(3)
P 		185.4
(-3)
P 		317.7
(2.3)
P 		149
B 299.8
(3)
P 		273.2
(1.8)
P 		162
(-3)
P 		255.7
(1.1)
P 		138
C 203.9
(-1.8)
P 		281.3
(3)
P 		218.3
(-0.9)
P 		185.3
(-3)
P 		96
avr 268.9
(1.5) 		296.3
(3) 		188.6
(-3) 		252.9
(0.6) 		108

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 167
1 2 3 4 5 6 range
A 326.9
(3)
P 		236.8
(-0.5)
P 		209.8
(-1.5)
P 		183.7
(-2.5)
P 		289.3
(1.5)
P 		171.6
(-3)
P 		155
B 292.2
(1.4)
P 		324
(3)
P 		217
(-2.3)
P 		267.3
(0.2)
P 		222.1
(-2.1)
P 		203.5
(-3)
P 		121
C 325
(3)
P 		319.9
(2.8)
P 		215.8
(-1)
P 		160
(-3)
P 		184.7
(-2.1)
P 		204.8
(-1.4)
P 		165
avr 314.7
(3) 		293.6
(2) 		214.2
(-2) 		203.7
(-2.5) 		232
(-1.1) 		193.3
(-3) 		121
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 79
1 2 3 4 range
A 110.3
(3)
P 		72.6
(-0.5)
P 		48.5
(-2.8)
P 		46.5
(-3)
P 		64
B 95.6
(3)
P 		67.5
(0.1)
P 		37.5
(-3)
P 		54.5
(-1.2)
P 		58
C 67.5
(1.4)
P 		80.9
(3)
P 		76.1
(2.4)
P 		31.2
(-3)
P 		50
avr 91.1
(3) 		73.7
(0.8) 		54
(-1.7) 		44.1
(-3) 		47

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 88
1 2 3 4 5 6 range
A 60.3
(-0.6)
P 		84.2
(2.6)
P 		45.7
(-2.5)
P 		46.6
(-2.4)
P 		87.3
(3)
P 		41.8
(-3)
P 		46
B 101.7
(2.3)
P 		107.8
(3)
P 		52.7
(-3)
P 		70.8
(-1)
P 		90.3
(1.1)
P 		75.9
(-0.5)
P 		55
C 120.5
(3)
P 		97.6
(1.4)
P 		54.9
(-1.5)
P 		32.2
(-3)
P 		59.8
(-1.1)
P 		68.5
(-0.5)
P 		88
avr 94.2
(2.7) 		96.5
(3) 		51.1
(-2.8) 		49.9
(-3) 		79.1
(0.8) 		62.1
(-1.4) 		47
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189637_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6067
Sequence Type Exemplar sequence
Representative Public ID C07H6.7 NCBI
Target Description C07H6.7 /REP_DB=WormBase Gene ID /WP=CE03975 /GEN=lin-39 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=C. elegans homeobox gene lin-39
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,GenBank identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_001025993(11), L19248(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001025993 NCBI Caenorhabditis elegans abnormal cell LINeage family member (lin-39) (lin-39) mRNA, complete cds. 11/11 None
L19248 NCBI Caenorhabditis elegans homeodomain protein (lin-39) mRNA, complete cds. 11/11 None
GENEFINDER00000039498 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:7529036:7534620:-1 11/11 None
C07H6.7.2 ENSEMBL cdna:known chromosome:CEL140:III:7528588:7536552:-1 gene:C07H6.7 11/11 None
C07H6.7.1 ENSEMBL cdna:known chromosome:CEL140:III:7528591:7534725:-1 gene:C07H6.7 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000039496 3/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:7529033-7534618(-) 92.52 100.0
Public Domain and Genome References
Gene Title C. elegans homeobox gene lin-39
Gene Symbol lin-39
Ensembl C07H6.7
Entrez Gene 176068 Entrez gene
SwissProt P34684 EMBL-EBI
WormBase CE03975 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.5350.1.S1_AT similar to Homeobox protein Hox-A5 (Hox-1.3) (M2) cfa
HG-U95AV2:873_AT homeo box A5 hs
HC-G110:873_AT homeo box A5 hs
HUGENEFL:M26679_AT homeo box A5 hs
U133_X3P:HS.37034.0.S1_3P_AT homeo box A5 hs
HG-U133A_2:213844_AT homeo box A5 hs
HG-FOCUS:213844_AT homeo box A5 hs
HG-U133_PLUS_2:213844_AT homeo box A5 hs
HG-U133A:213844_AT homeo box A5 hs
MOUSE430A_2:1448926_AT homeo box A5 mm
MOE430A:1448926_AT homeo box A5 mm
MOUSE430_2:1448926_AT homeo box A5 mm
MU11KSUBA:M28021-2_S_AT homeo box A5 mm
MG-U74AV2:103086_AT homeo box A5 mm
MOE430B:1443803_X_AT homeo box A5 mm
MOUSE430_2:1443803_X_AT homeo box A5 mm
MU19KSUBA:TC23926_F_AT Homeo box A5, mRNA (cDNA clone MGC:18622 IMAGE:3985274) mm
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6355 regulation of transcription, DNA-dependent inferred from electronic annotation QuickGO AmiGO
40025 vulval development (sensu Nematoda) inferred from expression pattern QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus 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
3700 transcription factor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAK85445 Abnormal cell lineage protein 39 [Caenorhabditis elegans] ref|NP_001021164.1| abnormal cell LINeage family member (lin-39) [Caenorhabditis elegans] sp|P34684|LIN39_CAEEL Homeobox protein lin-39 (Abnormal cell lineage protein 39) gb|AAC37168.1| homeobox protein gb|AAB04137.1| homeobox protein 8.0E-94
blast AAG00456 LIN-39 [Caenorhabditis briggsae] emb|CAE64454.1| Hypothetical protein CBG09167 [Caenorhabditis briggsae] 3.0E-78
blast AAK85445 Abnormal cell lineage protein 39 [Caenorhabditis elegans] ref|NP_001021164.1| abnormal cell LINeage family member (lin-39) [Caenorhabditis elegans] sp|P34684|LIN39_CAEEL Homeobox protein lin-39 (Abnormal cell lineage protein 39) gb|AAC37168.1| homeobox protein gb|AAB04137.1| homeobox protein 5.0E-45
blast AAG00456 LIN-39 [Caenorhabditis briggsae] emb|CAE64454.1| Hypothetical protein CBG09167 [Caenorhabditis briggsae] 2.0E-44
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 1.9999999774532E-26
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 9.99999988726602E-27
Pfam IPR001356 EMBL-EBI Homeobox 3.4E-31
Pfam IPR001356 EMBL-EBI Homeobox 3.4E-31
Sequence
Target Sequence 
>C. ELEGANS:189637_AT
aatgacagcgtctgctgcactttctgctcattttggaagttattatgatccgactagttc
ttctcaaattgcttcatattttgcctcaagtcaaggactgggaggtcctcaatatccaat
actcggagatcagtcactatgctataatccatcagtaacaagtacccatcacgactggaa
gcacctggaaggagacgatgatgatgataaggatgatgacaagaaaggcatcagtggtga
tgacgatgatatggataagaattcaggcggtgcagtgtatccatggatgacacgtgttca
ttcaactacaggaggttcacgcggcgagaagcgacaacgaacagcatacacaaggaatca
agtattagagctggaaaaggaatttcatacacacaaatatctgacgaggaagcgtagaat
tgaagtagctcattcattgatgcttaccgaaagacaagtcaaaatttggtttcaaaatcg
acgaatgaagcacaaaaaagaaaataaggataaaccaatgacacctccgatgatgccatt
tggtgcaaatctaccattcggtcca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AATGACAGCGTCTGCTGCACTTTCT 298 165 180 Antisense
GATCCGACTAGTTCTTCTCAAATTG 284 417 226 Antisense
GGAGGTCCTCAATATCCAATACTCG 645 515 280 Antisense
TACTCGGAGATCAGTCACTATGCTA 19 647 299 Antisense
GTACCCATCACGACTGGAAGCACCT 318 457 341 Antisense
TCAGGCGGTGCAGTGTATCCATGGA 231 617 442 Antisense
GGATGACACGTGTTCATTCAACTAC 646 513 464 Antisense
GGAGGTTCACGCGGCGAGAAGCGAC 245 515 490 Antisense
GATAAACCAATGACACCTCCGATGA 263 423 688 Antisense
CCTCCGATGATGCCATTTGGTGCAA 37 267 703 Antisense
TGGTGCAAATCTACCATTCGGTCCA 247 551 720 Antisense
Sequence Source Affymetrix Proprietary Database