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[173432_at] SWI/SNF protein

Description g10312095-REP_DB=GenBank Identifier /5_PRIME_EXT_ID=g10312095 /5_PRIME_EXT_DB=GenBank Identifier /CHR=5 /FEA=Genomic Cluster /GEN=psa-1 /DEF=SWI3-like protein
Cluster 6grp_high1_10_10 > 08      4grp_highest_8_8 > 58      4grp_high_8_8 > 33      6grp_total > 09      4grp_total > 46      6grp_cgc > 01      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 243
1 2 3 4 range
A 418.8
(3)
P 		206.2
(-3)
P 		301.4
(-0.3)
P 		240.7
(-2)
P 		213
B 363.6
(3)
P 		301.3
(1)
P 		175.7
(-3)
P 		214.2
(-1.8)
P 		188
C 260
(2.9)
P 		260.6
(3)
P 		191.2
(-3)
P 		214.8
(-1)
P 		69
avr 347.5
(3) 		256
(-1.4) 		222.8
(-3) 		223.2
(-3) 		125

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 312
1 2 3 4 5 6 range
A 305.4
(0.5)
P 		173.8
(-2.4)
P 		415.4
(3)
P 		146.9
(-3)
P 		229.2
(-1.2)
P 		287.7
(0.1)
P 		269
B 397.4
(3)
P 		129.7
(-2.5)
P 		103.4
(-3)
P 		300.7
(1)
P 		243.3
(-0.1)
P 		119.8
(-2.7)
P 		294
C 310.9
(3)
P 		131.3
(-3)
P 		198.3
(-0.8)
P 		169.2
(-1.7)
P 		210.5
(-0.4)
P 		280.2
(2)
A 		180
avr 337.9
(3) 		144.9
(-3) 		239
(-0.1) 		205.6
(-1.1) 		227.7
(-0.4) 		229.2
(-0.4) 		193
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 117
1 2 3 4 range
A 152.5
(3)
P 		44.8
(-2.5)
P 		78.8
(-0.8)
P 		35.2
(-3)
P 		117
B 115.9
(3)
P 		74.4
(-0.3)
P 		40.7
(-3)
P 		45.6
(-2.6)
P 		75
C 86.1
(3)
P 		74.9
(1.7)
P 		66.7
(0.7)
P 		36.2
(-3)
P 		50
avr 118.2
(3) 		64.7
(-1.1) 		62.1
(-1.3) 		39
(-3) 		79

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 113
1 2 3 4 5 6 range
A 56.3
(-0.9)
P 		61.8
(-0.2)
P 		90.5
(3)
P 		37.3
(-3)
P 		69.2
(0.6)
P 		70
(0.7)
P 		53
B 138.3
(3)
P 		43.2
(-2)
P 		25.1
(-3)
P 		79.7
(-0.1)
P 		98.9
(0.9)
P 		44.7
(-2)
P 		113
C 115.2
(3)
P 		40.1
(-2.5)
P 		50.5
(-1.8)
P 		34
(-3)
P 		68.1
(-0.5)
P 		93.8
(1.4)
A 		81
avr 103.3
(3) 		48.4
(-3) 		55.4
(-2.2) 		50.3
(-2.8) 		78.7
(0.3) 		69.5
(-0.7) 		55
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173432_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.25485
Sequence Type Exemplar sequence
Representative Public ID 10312095 NCBI
Target Description g10312095-REP_DB=GenBank Identifier /5_PRIME_EXT_ID=g10312095 /5_PRIME_EXT_DB=GenBank Identifier /CHR=5 /FEA=Genomic Cluster /GEN=psa-1 /DEF=SWI3-like protein
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_075505(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_075505 NCBI Caenorhabditis elegans Phasmid Socket Absent family member (psa-1) (psa-1) mRNA, complete cds. 11/11 A 
Y113G7B.23 ENSEMBL cdna:known chromosome:CEL140:V:20237241:20247481:-1 gene:Y113G7B.23 11/11 A 
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:20237242-20247480(-) 88.26 100.0
Public Domain and Genome References
Gene Title SWI/SNF protein
Gene Symbol psa-1
Ensembl Y113G7B.23
Entrez Gene 180324 Entrez gene
SwissProt Q9U2W6 EMBL-EBI
WormBase CE25208 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1603955_AT similar to SWI/SNF-related matrix-associated actin-dependent regulator of chromatin c2 isoform b cfa
CANINE:1604203_AT similar to SWI/SNF-related matrix-associated actin-dependent regulator of chromatin c2 isoform b cfa
CANINE:1599908_AT similar to SWI/SNF-related matrix-associated actin-dependent regulator of chromatin c2 isoform b cfa
CANINE_2:CFA.10539.1.A1_S_AT similar to SWI/SNF-related matrix-associated actin-dependent regulator of chromatin c2 isoform b cfa
CANINE_2:CFA.10539.2.A1_AT similar to SWI/SNF-related matrix-associated actin-dependent regulator of chromatin c2 isoform b cfa
CANINE_2:CFA.16860.1.S1_AT similar to SWI/SNF-related matrix-associated actin-dependent regulator of chromatin c2 isoform b cfa
CANINE_2:CFA.16860.1.S1_S_AT similar to SWI/SNF-related matrix-associated actin-dependent regulator of chromatin c2 isoform b cfa
CANINE_2:CFA.19374.1.S1_S_AT similar to SWI/SNF-related matrix-associated actin-dependent regulator of chromatin c2 isoform b cfa
CANINE_2:CFA.6803.1.A1_AT similar to SWI/SNF-related matrix-associated actin-dependent regulator of chromatin c2 isoform b cfa
CANINE_2:CFAAFFX.1130.1.S1_S_AT similar to SWI/SNF-related matrix-associated actin-dependent regulator of chromatin c2 isoform b cfa
DROSOPHILA_2:1640418_AT moira dm
DROSGENOME1:153570_AT moira dm
HG-U95AV2:453_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 hs
HC-G110:453_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 hs
HG-U133A:201321_S_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 hs
HG-U133_PLUS_2:201321_S_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 hs
HG-FOCUS:201321_S_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 hs
HG-U133A_2:201321_S_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 hs
HUGENEFL:U66616_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 hs
U133_X3P:G4507080_3P_A_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 hs
U133_X3P:HS.236030.0.S2_3P_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 hs
HG-U133A_2:201320_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 hs
HG-U133_PLUS_2:201320_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 hs
HG-U133A:201320_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 hs
HG-U95AV2:34690_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 hs
U133_X3P:HS2.376911.1.S1_3P_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 hs
HG-U133_PLUS_2:1561973_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 hs
HG-U95C:65482_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 hs
HU35KSUBD:RC_AA236396_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 hs
MU11KSUBB:MSA.17084.0_S_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 mm
MG-U74BV2:106590_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 mm
MOE430B:1428382_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 mm
MOUSE430_2:1428382_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 mm
MU19KSUBA:TC16182_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2, mRNA (cDNA clone IMAGE:5686195) mm
MU19KSUBB:TC28058_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2, mRNA (cDNA clone IMAGE:5686195) mm
MU19KSUBB:TC30542_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2, mRNA (cDNA clone IMAGE:5686195) mm
YEAST_2:1779487_AT One of 11 subunits of the SWI/SNF chromatin remodeling complex that regulates transcription by remodeling chromosomes; required for transcription of many genes, including ADH1, ADH2, GAL1, HO, INO1 and SUC2 Sc
Gene Ontology
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
Protein Similarities
Method ID Description E-Value
blast CAB54337 Hypothetical protein Y113G7B.23 [Caenorhabditis elegans] ref|NP_507906.1| Phasmid Socket Absent family member (psa-1) [Caenorhabditis elegans] gb|AAG16654.1| SWI3-like protein; PSA-1 [Caenorhabditis elegans] 0.0
blast CAE67424 Hypothetical protein CBG12912 [Caenorhabditis briggsae] 0.0
blast XP_393008 PREDICTED: similar to ENSANGP00000027316 [Apis mellifera] 1.0E-139
Protein Domains
Database ID Description E-Value
Pfam IPR001005 EMBL-EBI Myb DNA-binding domain 1.9E-10
Pfam IPR007526 EMBL-EBI SWIRM 2.9E-42
Sequence
Target Sequence 
>C. ELEGANS:173432_AT
aaatcgctgaatttttctgatttttttgcgaattttttggtatattttggacatttttca
gattttttttctcaaaatttttagaaaattcgctgattttttcccaaaatttatccgaat
tttctaaaattttctggattttttcaaaaattccctattttttcagattttttgcgaatt
tttgagcattttttggaaattttgtcctcaaaattttccattttttctcgaatttttttt
acaaaatttttcactgaattttcccaattttaatcctatttcctccgatcgcatttttta
aaatgttttaccacccccttatatacatatttacccccattctgtttcccccgtaaaaaa
accaccaaaatgatctttttttctctctctgaaatatatatatatgtaacacccctccga
actccacgctgctggtatctcctttttttcatggtt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAATCGCTGAATTTTTCTGATTTTT 330 119 2506 Antisense
TAGAAAATTCGCTGATTTTTTCCCA 250 651 2587 Antisense
TCAAAAATTCCCTATTTTTTCAGAT 46 629 2649 Antisense
CAATTTTAATCCTATTTCCTCCGAT 233 181 2770 Antisense
CTATTTCCTCCGATCGCATTTTTTA 675 221 2781 Antisense
TATTTCCTCCGATCGCATTTTTTAA 321 661 2782 Antisense
TTATATACATATTTACCCCCATTCT 650 679 2824 Antisense
TATACATATTTACCCCCATTCTGTT 113 661 2827 Antisense
TTTCTCTCTCTGAAATATATATATA 430 671 2885 Antisense
AATATATATATATGTAACACCCCTC 160 173 2898 Antisense
CTGGTATCTCCTTTTTTTCATGGTT 355 241 2937 Antisense
Sequence Source GenBank