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[193082_s_at] Intermediate filament proteins (2 domains)

Description DY3.2 /REP_DB=WormBase Gene ID /WP=CE15746 /TR=O62127 /GB=CAB09411.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Intermediate filament proteins (2 domains)
Cluster 6grp_highest_10_10 > 41      6grp_high1_10_10 > 03      4grp_highest_8_8 > 40      4grp_high_8_8 > 50      6grp_highest_nonorm > 14      6grp_total > 25      4grp_total > 53      6grp_highest_sub > De      6grp_cgc > 31      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3778
1 2 3 4 range
A 4506.5
(3)
P 		4127
(2.4)
P 		3440
(1.2)
P 		948.6
(-3)
P 		3558
B 4726.2
(3)
P 		3919.4
(1.6)
P 		3321.5
(0.6)
P 		1228.7
(-3)
P 		3498
C 4524.1
(3)
P 		3737.5
(1.6)
P 		3462.8
(1.2)
P 		1075.1
(-3)
P 		3449
avr 4585.6
(3) 		3928
(1.9) 		3408.1
(1) 		1084.1
(-3) 		3502

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2770
1 2 3 4 5 6 range
A 5085.2
(3)
P 		4350.3
(1.3)
P 		2736.7
(-2.6)
P 		2779.5
(-2.5)
P 		2563.8
(-3)
P 		2828.3
(-2.4)
P 		2521
B 3529.4
(1.1)
P 		4085.3
(3)
P 		3635.6
(1.5)
P 		3154.3
(-0.2)
P 		2469.1
(-2.5)
P 		2315.2
(-3)
P 		1770
C 5064
(3)
P 		3931.7
(0.3)
P 		3923.8
(0.3)
P 		3015.6
(-1.9)
P 		2535.2
(-3)
P 		2555.7
(-3)
P 		2529
avr 4559.5
(3) 		4122.4
(1.7) 		3432
(-0.3) 		2983.1
(-1.6) 		2522.7
(-3) 		2566.4
(-2.9) 		2037
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1502
1 2 3 4 range
A 1640.8
(3)
P 		895.9
(0)
P 		899.3
(0)
P 		138.9
(-3)
P 		1502
B 1507.2
(3)
P 		968
(0.4)
P 		769.7
(-0.6)
P 		261.8
(-3)
P 		1245
C 1497.6
(3)
P 		1074.6
(1.1)
P 		1206.9
(1.7)
P 		181.3
(-3)
P 		1316
avr 1548.5
(3) 		979.5
(0.5) 		958.6
(0.4) 		194
(-3) 		1355

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1281
1 2 3 4 5 6 range
A 937.4
(-0.8)
P 		1547.2
(3)
P 		596
(-3)
P 		704.9
(-2.3)
P 		773.6
(-1.9)
P 		688.6
(-2.4)
P 		951
B 1228.1
(1.5)
P 		1359.8
(3)
P 		882.8
(-2.5)
P 		835.5
(-3)
P 		1003.2
(-1.1)
P 		863.3
(-2.7)
P 		524
C 1877
(3)
P 		1199.7
(-0.2)
P 		998.7
(-1.1)
P 		606.4
(-3)
P 		820.4
(-2)
P 		855.5
(-1.8)
P 		1271
avr 1347.5
(2.8) 		1368.9
(3) 		825.8
(-2) 		715.6
(-3) 		865.7
(-1.6) 		802.5
(-2.2) 		653
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193082_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.794
Sequence Type Exemplar sequence
Representative Public ID DY3.2 NCBI
Target Description DY3.2 /REP_DB=WormBase Gene ID /WP=CE15746 /TR=O62127 /GB=CAB09411.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Intermediate filament proteins (2 domains)
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_059970(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059970 NCBI Caenorhabditis elegans nuclear LaMiN family member (lmn-1) (lmn-1) mRNA, complete cds. 11/11 None
GENEFINDER00000022846 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:8770204:8773309:1 11/11 None
SNAP00000022833 ENSEMBL cdna:SNAP chromosome:CEL140:I:8771357:8773309:1 11/11 None
DY3.2.3 ENSEMBL cdna:known chromosome:CEL140:I:8771113:8773736:1 gene:DY3.2 11/11 None
DY3.2.2 ENSEMBL cdna:known chromosome:CEL140:I:8771164:8773754:1 gene:DY3.2 11/11 None
DY3.2.1 ENSEMBL cdna:known chromosome:CEL140:I:8771166:8773754:1 gene:DY3.2 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
chrI:8771111-8773240(+) 100.0 100.0
Public Domain and Genome References
Gene Title Intermediate filament proteins (2 domains)
Gene Symbol lmn-1
Ensembl DY3.2
Entrez Gene 172687 Entrez gene
SwissProt Q21443 EMBL-EBI
WormBase CE15746 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFA.17731.1.S1_S_AT similar to Lamin B1 cfa
CANINE_2:CFA.19447.1.S1_AT similar to Lamin B1 cfa
CANINE_2:CFAAFFX.1813.1.S1_S_AT similar to Lamin B1 cfa
DROSOPHILA_2:1629981_AT Lamin C dm
DROSGENOME1:154588_AT Lamin C dm
CHICKEN:GGA.1368.1.S1_AT lamin B1 gga
CHICKEN:GGA.1368.1.S2_AT lamin B1 gga
HG-U133A_2:203276_AT lamin B1 hs
HG-U133_PLUS_2:203276_AT lamin B1 hs
HG-FOCUS:203276_AT lamin B1 hs
HG-U133A:203276_AT lamin B1 hs
HU35KSUBA:L37747_S_AT lamin B1 hs
HUGENEFL:M34458_RNA1_S_AT lamin B1 hs
U133_X3P:G5031876_3P_X_AT lamin B1 hs
U133_X3P:G5031876_3P_AT lamin B1 hs
HG-U95AV2:37985_AT lamin B1 hs
HG-U95B:42702_AT Lamin B1 hs
HU35KSUBB:RC_R05816_AT Lamin B1 hs
MU11KSUBA:M35153_S_AT lamin B1 mm
MG-U74AV2:160517_AT lamin B1 mm
MOE430A:1423520_AT lamin B1 mm
MOUSE430A_2:1423520_AT lamin B1 mm
MOUSE430_2:1423520_AT lamin B1 mm
MOE430A:1423521_AT Lamin B1 (Lmnb1), mRNA mm
MOUSE430A_2:1423521_AT Lamin B1 (Lmnb1), mRNA mm
MOUSE430_2:1423521_AT Lamin B1 (Lmnb1), mRNA mm
MOE430B:1444459_AT Lamin B1 (Lmnb1), mRNA mm
MOUSE430_2:1444459_AT Lamin B1 (Lmnb1), mRNA mm
MU19KSUBB:TC30755_S_AT Lamin B1 (Lmnb1), mRNA mm
RG-U34A:RC_AA957201_S_AT hypothetical gene supported by NM_053905 rn
RAE230A:1368812_AT hypothetical gene supported by NM_053905 rn
RAT230_2:1368812_AT hypothetical gene supported by NM_053905 rn
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
5638 lamin filament inferred from sequence similarity QuickGO AmiGO
5635 nuclear membrane inferred from direct assay QuickGO AmiGO
5654 nucleoplasm inferred from direct assay QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5198 structural molecule activity inferred from electronic annotation QuickGO AmiGO
5198 structural molecule activity inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB09411 Hypothetical protein DY3.2 [Caenorhabditis elegans] ref|NP_492371.1| nuclear LaMiN family member (lmn-1) [Caenorhabditis elegans] sp|Q21443|LMN1_CAEEL Lamin 1 (CeLam-1) (Ce-lamin) 0.0
blast CAA52188 lamin [Caenorhabditis elegans] 0.0
blast CAE66968 Hypothetical protein CBG12363 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001664 EMBL-EBI Intermediate filament protein 9.9E-11
Pfam IPR001664 EMBL-EBI Intermediate filament protein 3.3E-11
Pfam IPR001322 EMBL-EBI Intermediate filament, C-terminal 1.2E-53
Pfam IPR001664 EMBL-EBI Intermediate filament protein 9.9E-11
Pfam IPR001664 EMBL-EBI Intermediate filament protein 3.3E-11
Pfam IPR001322 EMBL-EBI Intermediate filament, C-terminal 1.2E-53
Pfam IPR001664 EMBL-EBI Intermediate filament protein 6.0E-13
Pfam IPR001664 EMBL-EBI Intermediate filament protein 3.3E-11
Pfam IPR001322 EMBL-EBI Intermediate filament, C-terminal 1.2E-53
Sequence
Target Sequence 
>C. ELEGANS:193082_S_AT
gagttccacgatcttcttgatgttaaaatccaattggacgccgaactcaagacctaccaa
gctctccttgagggtgaggaggagcgtctcaatcttactcaggaggcgccacaaaacact
tcagttcatcacgtctcgttttcatccggaggagcaagcgctcagcgcggagtgaagcgt
cgtcgcgttgtcgatgtaaatggagaggaccaagacattgattatctcaaccgtcgctcc
aaactcaacaaagagactgttggcccagttggaatcgacgaggttgatgaggaaggaaag
tgggtccgtgttgcaaacaactctgaagaagaacaatccatcggaggatacaagttggtg
gtcaaagctggaaacaaagaagcctccttccaattttcatctcgtatgaagctcgctcca
catgctagcgccaccgtttggtctgcggatgctggtgccgttcaccacccaccagaagtc
tacgttatgaagaagcaacagtggccaattggagataacccatcagctcgtcttgaggat
agtgaaggagacactgtttcttctatcacc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGTTCCACGATCTTCTTGATGTTA 377 397 1084 Antisense
AATTGGACGCCGAACTCAAGACCTA 10 179 1115 Antisense
GAGGAGGAGCGTCTCAATCTTACTC 685 403 1159 Antisense
AAAACACTTCAGTTCATCACGTCTC 658 129 1196 Antisense
GTCTCGTTTTCATCCGGAGGAGCAA 195 469 1216 Antisense
AGTGAAGCGTCGTCGCGTTGTCGAT 519 59 1254 Antisense
AAAGAAGCCTCCTTCCAATTTTCAT 257 123 1459 Antisense
CACCGTTTGGTCTGCGGATGCTGGT 408 197 1515 Antisense
CCACCCACCAGAAGTCTACGTTATG 137 275 1548 Antisense
ATAACCCATCAGCTCGTCTTGAGGA 99 25 1598 Antisense
AGGAGACACTGTTTCTTCTATCACC 181 57 1629 Antisense
Sequence Source Affymetrix Proprietary Database