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[191686_at] homeobox protein

Description C04F1.3 /REP_DB=WormBase Gene ID /WP=CE17366 /GEN=lim-7 /TR=Q94160 /GB=AAC16985.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=homeobox protein
Cluster 6grp_highest_10_10 > 60      6grp_high1_10_10 > 17      4grp_highest_8_8 > 52      4grp_high_8_8 > 16      6grp_highest_nonorm > 80      6grp_total > 07      4grp_total > 39      6grp_highest_sub > De      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.
4 342
1 2 3 4 range
A 444.1
(3)
P 		161.4
(-2.3)
P 		124.1
(-3)
P 		322.8
(0.7)
P 		320
B 376.5
(3)
P 		161.8
(-1.7)
P 		102.5
(-3)
P 		221.7
(-0.4)
P 		274
C 380.1
(3)
P 		153.7
(-3)
P 		162.9
(-2.8)
P 		167.8
(-2.6)
P 		226
avr 400.2
(3) 		159
(-2.4) 		129.8
(-3) 		237.4
(-0.6) 		270

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 359
1 2 3 4 5 6 range
A 377.1
(3)
P 		233.7
(-0.6)
P 		214.5
(-1.1)
P 		153
(-2.7)
P 		166
(-2.4)
P 		140.8
(-3)
P 		236
B 467.2
(3)
P 		252.4
(-0.6)
P 		183.4
(-1.7)
P 		215.6
(-1.2)
P 		107.8
(-3)
P 		142
(-2.4)
P 		359
C 372.7
(3)
P 		288.6
(0.7)
P 		192.4
(-2)
P 		207.3
(-1.6)
P 		156.4
(-3)
P 		187.9
(-2.1)
P 		216
avr 405.7
(3) 		258.2
(-0.4) 		196.8
(-1.8) 		192
(-1.9) 		143.4
(-3) 		156.9
(-2.7) 		262
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 138
1 2 3 4 range
A 161.7
(3)
P 		35
(-2.9)
P 		32.4
(-3)
P 		47.3
(-2.3)
P 		129
B 120.1
(3)
P 		40
(-2)
P 		23.8
(-3)
P 		47.2
(-1.5)
P 		96
C 125.8
(3)
P 		44.2
(-2)
P 		56.8
(-1.2)
P 		28.3
(-3)
P 		98
avr 135.9
(3) 		39.7
(-2.9) 		37.7
(-3) 		40.9
(-2.8) 		98

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 128
1 2 3 4 5 6 range
A 69.5
(1.3)
P 		83.1
(3)
P 		46.7
(-1.5)
P 		38.8
(-2.4)
P 		50.1
(-1.1)
P 		34.3
(-3)
P 		49
B 162.6
(3)
P 		84
(-1)
P 		44.5
(-3)
P 		57.1
(-2.3)
P 		43.8
(-3)
P 		52.9
(-2.5)
P 		119
C 138.2
(3)
P 		88.1
(-0.1)
P 		49
(-2.5)
P 		41.7
(-3)
P 		50.6
(-2.4)
P 		62.9
(-1.7)
P 		97
avr 123.4
(3) 		85.1
(0) 		46.7
(-2.9) 		45.9
(-3) 		48.2
(-2.8) 		50
(-2.7) 		78
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191686_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1944
Sequence Type Exemplar sequence
Representative Public ID C04F1.3 NCBI
Target Description C04F1.3 /REP_DB=WormBase Gene ID /WP=CE17366 /GEN=lim-7 /TR=Q94160 /GB=AAC16985.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=homeobox protein
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_059267(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059267 NCBI Caenorhabditis elegans LIM domain family member (lim-7) (lim-7) mRNA, complete cds. 11/11 None
GENEFINDER00000002311 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:5724812:5733563:1 11/11 None
SNAP00000002306 ENSEMBL cdna:SNAP chromosome:CEL140:I:5732882:5733492:1 9/11 None
C04F1.3 ENSEMBL cdna:known chromosome:CEL140:I:5724812:5733492:1 gene:C04F1.3 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000002305 2/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:5724811-5733492(+) 100.0 100.0
Public Domain and Genome References
Gene Title homeobox protein
Gene Symbol lim-7
Ensembl C04F1.3
Entrez Gene 172236 Entrez gene
SwissProt Q94160 EMBL-EBI
WormBase CE17366 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.28228.1.S1_AT similar to Insulin gene enhancer protein ISL-1 (Islet-1) cfa
DROSOPHILA_2:1625279_A_AT tailup dm
DROSGENOME1:142284_AT tailup dm
CHICKEN:GGA.1507.1.S1_AT ISL1 transcription factor, LIM/homeodomain, (islet-1) gga
HG-U133_PLUS_2:206104_AT ISL1 transcription factor, LIM/homeodomain, (islet-1) hs
HG-U133A:206104_AT ISL1 transcription factor, LIM/homeodomain, (islet-1) hs
HG-FOCUS:206104_AT ISL1 transcription factor, LIM/homeodomain, (islet-1) hs
HG-U133A_2:206104_AT ISL1 transcription factor, LIM/homeodomain, (islet-1) hs
HUGENEFL:U07559_AT ISL1 transcription factor, LIM/homeodomain, (islet-1) hs
U133_X3P:G4504736_3P_AT ISL1 transcription factor, LIM/homeodomain, (islet-1) hs
HG-U95AV2:39990_AT ISL1 transcription factor, LIM/homeodomain, (islet-1) hs
MG-U74AV2:92515_AT ISL1 transcription factor, LIM/homeodomain (islet 1) mm
MOE430A:1450723_AT ISL1 transcription factor, LIM/homeodomain (islet 1) mm
MOUSE430A_2:1450723_AT ISL1 transcription factor, LIM/homeodomain (islet 1) mm
MOUSE430_2:1450723_AT ISL1 transcription factor, LIM/homeodomain (islet 1) mm
MOE430A:1422720_AT ISL1 transcription factor, LIM/homeodomain (islet 1) mm
MOUSE430A_2:1422720_AT ISL1 transcription factor, LIM/homeodomain (islet 1) mm
MOUSE430_2:1422720_AT ISL1 transcription factor, LIM/homeodomain (islet 1) mm
MOE430B:1444129_AT ISL1 transcription factor, LIM/homeodomain (islet 1) mm
MOUSE430_2:1444129_AT ISL1 transcription factor, LIM/homeodomain (islet 1) mm
MU19KSUBA:TC22707_AT ISL1 transcription factor, LIM/homeodomain (islet 1) (Isl1), mRNA mm
RAE230A:1369681_AT ISL1 transcription factor, LIM/homeodomain 1 rn
RAT230_2:1369681_AT ISL1 transcription factor, LIM/homeodomain 1 rn
RG-U34A:S69329_G_AT ISL1 transcription factor, LIM/homeodomain 1 rn
RG-U34A:S69329_AT ISL1 transcription factor, LIM/homeodomain 1 rn
RAE230B:1396895_AT ISL1 transcription factor, LIM/homeodomain 1 rn
RAT230_2:1396895_AT ISL1 transcription factor, LIM/homeodomain 1 rn
RG-U34B:RC_AA944599_AT ISL1 transcription factor, LIM/homeodomain 1 rn
RG-U34B:RC_AI029627_AT ISL1 transcription factor, LIM/homeodomain 1 rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6355 regulation of transcription, DNA-dependent inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation 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 AAC16985 Lim domain family protein 7 [Caenorhabditis elegans] ref|NP_491668.1| LIM domain family member (lim-7) [Caenorhabditis elegans] gb|AAB18328.1| CeLIM-7 [Caenorhabditis elegans] 0.0
blast CAE60405 Hypothetical protein CBG04010 [Caenorhabditis briggsae] 0.0
blast CAE60405 Hypothetical protein CBG04010 [Caenorhabditis briggsae] 1.0E-162
blast AAC16985 Lim domain family protein 7 [Caenorhabditis elegans] ref|NP_491668.1| LIM domain family member (lim-7) [Caenorhabditis elegans] gb|AAB18328.1| CeLIM-7 [Caenorhabditis elegans] 1.0E-59
blast NP_571045 islet2 [Danio rerio] emb|CAA61283.1| Islet-2 protein [Danio rerio] sp|P53406|ISL2_BRARE Insulin gene enhancer protein isl-2 (Islet-2) dbj|BAA07484.1| zfIsl-2 [Danio rerio] 7.0E-56
blast NP_571045 islet2 [Danio rerio] emb|CAA61283.1| Islet-2 protein [Danio rerio] sp|P53406|ISL2_BRARE Insulin gene enhancer protein isl-2 (Islet-2) dbj|BAA07484.1| zfIsl-2 [Danio rerio] 1.0E-43
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 3.00000005862444E-25
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 1.00000001954148E-25
Pfam IPR001356 EMBL-EBI Homeobox 6.7E-14
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 4.7E-16
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 2.2E-11
Pfam IPR001356 EMBL-EBI Homeobox 6.7E-14
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 5.6E-5
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 3.9E-6
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 2.2E-11
Sequence
Target Sequence 
>C. ELEGANS:191686_AT
gacacgtgtcaggactgtgctcaacgaaaatcagctcaaaattcttcgagactgctattc
gattaattctcgacctgatgcaactctgaaagaacgacttgttgagatgactggactcag
tgcacgagtgatacgagtatggttccagaataaacgatgcaaggacaagaagcgacaaat
tcaaataacagagaatcggctaaactctgaacgagaagaggtgctcaatagggtacgtgt
aaatggtatcggtcctttgatggttcaaccagctacaccacatattgataatacacttgg
tggaccaattgatattcaacattttgcacaatggaatggtacaccaccaccaccgcctcc
tcaatatgggaatcctatgatgttcaactctccttcgacatttgatgtttcggttattct
tgccccagttgctccaaacgtcacatcaccatctgaagcactgggaccacttggagcatc
cgtatttcctcatttt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACACGTGTCAGGACTGTGCTCAAC 662 367 807 Antisense
TAATTCTCGACCTGATGCAACTCTG 126 635 870 Antisense
ATGGTATCGGTCCTTTGATGGTTCA 682 45 1049 Antisense
TGATGGTTCAACCAGCTACACCACA 504 567 1064 Antisense
CACCGCCTCCTCAATATGGGAATCC 313 199 1157 Antisense
GAATCCTATGATGTTCAACTCTCCT 137 331 1176 Antisense
CAACTCTCCTTCGACATTTGATGTT 271 189 1191 Antisense
TGATGTTTCGGTTATTCTTGCCCCA 510 565 1209 Antisense
CAAACGTCACATCACCATCTGAAGC 130 193 1241 Antisense
TGAAGCACTGGGACCACTTGGAGCA 223 575 1260 Antisense
TGGAGCATCCGTATTTCCTCATTTT 113 549 1278 Antisense
Sequence Source Affymetrix Proprietary Database