[Home] | [Total List]

[189051_at] LIM domains

Description F07C6.1 /REP_DB=WormBase Gene ID /WP=CE05562 /TR=SW:Q19157 /GB=CAA93483.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=LIM domains
Cluster 6grp_highest_10_10 > 48      6grp_high1_10_10 > 73      4grp_highest_8_8 > 22      4grp_high_8_8 > 06      6grp_highest_nonorm > 91      6grp_total > 74      4grp_total > 01      6grp_cgc > 66      6grp_high1_sub > 03_04      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1079
1 2 3 4 range
A 170.3
(-2.7)
P 		128.1
(-3)
P 		176.6
(-2.7)
P 		1034.9
(3)
P 		907
B 210
(-2.6)
P 		147.9
(-3)
P 		237.2
(-2.4)
P 		982.4
(3)
P 		835
C 159.4
(-3)
P 		194.7
(-2.8)
P 		216.1
(-2.7)
P 		1206.9
(3)
P 		1048
avr 179.9
(-2.8) 		156.9
(-3) 		210
(-2.7) 		1074.7
(3) 		918

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 194
1 2 3 4 5 6 range
A 156.6
(-3)
P 		201.5
(-1.5)
P 		336.8
(3)
P 		305.6
(2)
P 		197.9
(-1.6)
P 		189.7
(-1.9)
P 		180
B 143.2
(-3)
P 		224.6
(0.6)
P 		260.9
(2.2)
P 		234.6
(1)
P 		279.5
(3)
P 		274.5
(2.8)
P 		136
C 164.2
(-3)
P 		225.9
(-0.6)
P 		201.5
(-1.5)
P 		311.5
(2.7)
P 		199.3
(-1.6)
P 		318.5
(3)
P 		154
avr 154.7
(-3) 		217.3
(-0.1) 		266.4
(2.2) 		283.9
(3) 		225.6
(0.3) 		260.9
(1.9) 		129
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 182
1 2 3 4 range
A 62
(-1.3)
P 		27.8
(-3)
P 		46.2
(-2.1)
P 		151.5
(3)
P 		124
B 67
(-1.9)
P 		36.5
(-3)
P 		55
(-2.4)
P 		209.4
(3)
P 		173
C 52.8
(-3)
P 		56
(-2.9)
P 		75.3
(-2.1)
P 		203.5
(3)
P 		151
avr 60.6
(-2.2) 		40.1
(-3) 		58.8
(-2.2) 		188.1
(3) 		148

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 85
1 2 3 4 5 6 range
A 28.9
(-3)
P 		71.7
(2.3)
P 		73.3
(2.5)
P 		77.5
(3)
P 		59.7
(0.8)
P 		46.2
(-0.9)
P 		49
B 49.8
(-3)
P 		74.8
(-0.6)
P 		63.4
(-1.7)
P 		62.1
(-1.8)
P 		113.5
(3)
P 		102.3
(1.9)
P 		64
C 60.8
(-2)
P 		68.9
(-1.1)
P 		51.3
(-3)
P 		62.6
(-1.8)
P 		64.5
(-1.6)
P 		106.6
(3)
P 		55
avr 46.5
(-3) 		71.8
(0.9) 		62.7
(-0.5) 		67.4
(0.3) 		79.2
(2.1) 		85
(3) 		39
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189051_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9634
Sequence Type Exemplar sequence
Representative Public ID F07C6.1 NCBI
Target Description F07C6.1 /REP_DB=WormBase Gene ID /WP=CE05562 /TR=SW:Q19157 /GB=CAA93483.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=LIM 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_070039(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070039 NCBI Caenorhabditis elegans PINch protein family member (pin-2) (pin-2) mRNA, complete cds. 11/11 None
F07C6.1 ENSEMBL cdna:known chromosome:CEL140:IV:12793906:12796078:1 gene:F07C6.1 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000006500 1/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:12793911-12796084(+) 100.0 100.0
Public Domain and Genome References
Gene Title LIM domains
Gene Symbol pin-2
Ensembl F07C6.1
Entrez Gene 178234 Entrez gene
SwissProt Q19157 EMBL-EBI
WormBase CE05562 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA93483 Hypothetical protein F07C6.1 [Caenorhabditis elegans] ref|NP_502440.1| PINch protein family member (pin-2) [Caenorhabditis elegans] sp|Q19157|PIN2_CAEEL LIM protein pin-2 0.0
blast CAE74554 Hypothetical protein CBG22312 [Caenorhabditis briggsae] 1.0E-168
blast XP_793010 PREDICTED: similar to LIM and senescent cell antigen-like domains 2 [Strongylocentrotus purpuratus] 9.0E-73
Protein Domains
Database ID Description E-Value
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 6.2E-12
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 7.3E-9
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 1.6E-4
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 3.1E-13
Sequence
Target Sequence 
>C. ELEGANS:189051_AT
ggcactattttatgctttctttgcaatcagaaaaaaccgaaaatgagaatttataattgt
aataaatgcaaacaacacgtggataacagtgatctactaacatatcaagagaatccttat
cacgcttatcatttcaaatgtactacatgcaaaaaagtactggaatctgatgctcgaaca
attaaagatgatttattctgtccgagatgttttgatttcaaatgtgaagtttgttttgat
tgcaagaaggttattgatccacaagttgagcagagtattttcacgatgaacaagcattgg
catactgatcatttccgatgtgccacttgtgctcgtccatttttcggtcacgaacattat
gagaagaatggaaaagcatattgtagagatgattttttggaacttattgggcatcattgt
ttcatttgcgacaggaatgtgggtggtggtatggttcatgtatttggaaaagctttttgt
ccggaatgttatcgatgtagaggatgtgataaggttttacattacaaagacaaagtaatg
gagcttgacctgatgccttta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGCACTATTTTATGCTTTCTTTGCA 255 535 382 Antisense
AGAGAATCCTTATCACGCTTATCAT 30 69 489 Antisense
AGTACTGGAATCTGATGCTCGAACA 477 61 537 Antisense
TTCTGTCCGAGATGTTTTGATTTCA 655 693 577 Antisense
GCATTGGCATACTGATCATTTCCGA 380 307 675 Antisense
TCATTTCCGATGTGCCACTTGTGCT 566 619 690 Antisense
TGCTCGTCCATTTTTCGGTCACGAA 501 581 711 Antisense
TGGGCATCATTGTTTCATTTGCGAC 69 555 789 Antisense
TGTGGGTGGTGGTATGGTTCATGTA 267 555 819 Antisense
AAGCTTTTTGTCCGGAATGTTATCG 481 149 851 Antisense
AATGGAGCTTGACCTGATGCCTTTA 609 161 918 Antisense
Sequence Source Affymetrix Proprietary Database