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[173648_s_at]

Description CEC5213_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F53G2.6 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C10521 /WB_GENE_ID=F53G2.6 /WP=CE11000 /CHR=2 /FEA=Genomic Cluster /GEN=tsr-1 /DEF=C.elegans cDNA clone yk147g3 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 71      6grp_high1_10_10 > 27      4grp_high_8_8 > 42      6grp_highest_nonorm > 90      6grp_total > 27      4grp_total > 53      6grp_highest_sub > De      6grp_cgc > 05      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 219
1 2 3 4 range
A 249.1
(3)
P 		169
(-0.2)
P 		103.9
(-2.9)
P 		100.8
(-3)
P 		148
B 243
(3)
P 		194.5
(1.5)
P 		171.6
(0.8)
P 		47.5
(-3)
A 		196
C 266.4
(3)
P 		179.7
(0.2)
P 		161.6
(-0.3)
P 		77.9
(-3)
P 		189
avr 252.8
(3) 		181.1
(0.6) 		145.7
(-0.6) 		75.4
(-3) 		177

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 159
1 2 3 4 5 6 range
A 258.3
(3)
P 		142.3
(-2.5)
P 		154.7
(-1.9)
P 		130.9
(-3)
P 		198.3
(0.2)
P 		199.7
(0.2)
P 		127
B 219.9
(3)
P 		200.8
(1.9)
P 		164
(-0.2)
P 		134.6
(-1.9)
P 		116.5
(-3)
P 		163.5
(-0.3)
P 		103
C 272.5
(3)
P 		218.9
(1)
P 		135.8
(-2.2)
P 		113.5
(-3)
P 		116.8
(-2.9)
P 		122.6
(-2.7)
P 		159
avr 250.2
(3) 		187.3
(-0) 		151.5
(-1.8) 		126.3
(-3) 		143.9
(-2.1) 		161.9
(-1.3) 		124
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 81
1 2 3 4 range
A 90.7
(3)
P 		36.7
(-1.3)
P 		27.2
(-2)
P 		14.8
(-3)
P 		76
B 77.5
(3)
P 		48
(0.4)
P 		39.8
(-0.4)
P 		10.1
(-3)
A 		67
C 88.2
(3)
P 		51.7
(0.1)
P 		56.3
(0.5)
P 		13.1
(-3)
P 		75
avr 85.5
(3) 		45.5
(-0.3) 		41.1
(-0.7) 		12.7
(-3) 		73

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 78
1 2 3 4 5 6 range
A 47.6
(0.2)
P 		50.6
(0.9)
P 		33.7
(-2.9)
P 		33.2
(-3)
P 		59.8
(3)
P 		48.6
(0.5)
P 		27
B 76.5
(3)
P 		66.8
(1.6)
P 		39.8
(-2.4)
P 		35.6
(-3)
P 		47.3
(-1.3)
P 		61
(0.7)
P 		41
C 101
(3)
P 		66.8
(0.4)
P 		34.6
(-2.1)
P 		22.8
(-3)
P 		37.8
(-1.8)
P 		41
(-1.6)
P 		78
avr 75
(3) 		61.4
(1.2) 		36
(-2.3) 		30.5
(-3) 		48.3
(-0.6) 		50.2
(-0.3) 		45
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173648_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.23787
Sequence Type Exemplar sequence
Representative Public ID CEC5213 NCBI
Target Description CEC5213_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F53G2.6 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C10521 /WB_GENE_ID=F53G2.6 /WP=CE11000 /CHR=2 /FEA=Genomic Cluster /GEN=tsr-1 /DEF=C.elegans cDNA clone yk147g3 : 3prime end, single read.
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_061878(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_061878 NCBI Caenorhabditis elegans Transporter of SR proteins family member (tsr-1) (tsr-1) mRNA, complete cds. 11/11 None
SNAP00000030758 ENSEMBL cdna:SNAP chromosome:CEL140:II:2461194:2481190:-1 9/11 None
GENEFINDER00000030762 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:2461101:2473360:-1 9/11 None
F53G2.6 ENSEMBL cdna:known chromosome:CEL140:II:2460867:2472863:-1 gene:F53G2.6 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
chrII:2460931-2472863(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol tsr-1
Ensembl F53G2.6
Entrez Gene 173601 Entrez gene
SwissProt O17244 EMBL-EBI
WormBase CE37021 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:247428_AT transportin-SR-related at
CANINE_2:CFA.3962.1.A1_AT similar to transportin 3 cfa
CANINE_2:CFA.3962.1.A1_S_AT similar to transportin 3 cfa
CANINE_2:CFAAFFX.3208.1.S1_AT similar to transportin 3 cfa
CANINE_2:CFAAFFX.3208.1.S1_S_AT similar to transportin 3 cfa
DROSOPHILA_2:1630732_AT Transportin-Serine/Arginine rich dm
DROSGENOME1:154021_AT Transportin-Serine/Arginine rich dm
CHICKEN:GGA.15699.1.S1_AT transportin 3 gga
CHICKEN:GGAAFFX.8788.1.S1_AT transportin 3 gga
HG-U133_PLUS_2:214550_S_AT transportin 3 hs
HG-U133A_2:214550_S_AT transportin 3 hs
HG-U133A:214550_S_AT transportin 3 hs
HG-U95AV2:35812_AT transportin 3 hs
HU35KSUBA:AA090622_AT transportin 3 hs
HU35KSUBA:RC_AA100521_AT transportin 3 hs
HU35KSUBC:RC_AA455456_AT transportin 3 hs
U133_X3P:HS.69235.1.S1_3P_A_AT transportin 3 hs
U133_X3P:HS.69235.0.S2_3P_AT transportin 3 hs
U133_X3P:HS.69235.0.S1_3P_X_AT transportin 3 hs
HG-U133A_2:212317_AT transportin 3 hs
HG-U133_PLUS_2:212317_AT transportin 3 hs
HG-U133A:212317_AT transportin 3 hs
HG-U133A_2:212318_AT transportin 3 hs
HG-FOCUS:212318_AT transportin 3 hs
HG-U133_PLUS_2:212318_AT transportin 3 hs
HG-U133A:212318_AT transportin 3 hs
HG-U95AV2:35813_AT transportin 3 hs
HG-U95B:46147_AT transportin 3 hs
HG-U95AV2:31377_R_AT Transportin 3 hs
HG-U95C:63897_AT Transportin 3 hs
HG-U95D:83138_AT Transportin 3 hs
HU35KSUBC:RC_D20925_AT Transportin 3 hs
MU11KSUBA:AA537569_S_AT transportin 3 mm
MG-U74AV2:96674_AT transportin 3 mm
MOE430A:1453124_AT transportin 3 mm
MOUSE430A_2:1453124_AT transportin 3 mm
MOUSE430_2:1453124_AT transportin 3 mm
MOE430A:1429369_AT transportin 3 mm
MOUSE430A_2:1429369_AT transportin 3 mm
MOUSE430_2:1429369_AT transportin 3 mm
MOE430A:1419950_S_AT transportin 3 mm
MOUSE430A_2:1419950_S_AT transportin 3 mm
MOUSE430_2:1419950_S_AT transportin 3 mm
MU19KSUBB:TC31921_AT MKIAA4133 protein mm
MU19KSUBB:TC31921_G_AT MKIAA4133 protein mm
RG-U34B:RC_AI008911_AT transportin 3 (predicted) rn
RG-U34B:RC_AI012523_AT transportin 3 (predicted) rn
RAE230A:1389979_AT transportin 3 (predicted) rn
RAT230_2:1389979_AT transportin 3 (predicted) rn
RG-U34B:RC_AI011608_AT Transportin 3 (predicted) rn
RG-U34C:RC_AI071164_AT Transportin 3 (predicted) rn
YEAST_2:1777266_AT Nuclear import receptor, mediates the nuclear localization of proteins involved in mRNA-nucleus export Sc
Protein Similarities
Method ID Description E-Value
blast AAB71016 Transporter of sr proteins protein 1 [Caenorhabditis elegans] ref|NP_494279.3| Transporter of SR proteins family member (tsr-1) [Caenorhabditis elegans] 0.0
blast CAE73069 Hypothetical protein CBG20440 [Caenorhabditis briggsae] 0.0
blast AAB71017 Mnat (menage a trois) tfiih subunit protein 1 [Caenorhabditis elegans] ref|NP_494280.3| F53G2.7 [Caenorhabditis elegans] 1.0E-157
blast NP_036602 transportin 3 [Homo sapiens] gb|EAL24106.1| transportin 3 [Homo sapiens] emb|CAB42643.1| nuclear transport receptor [Homo sapiens] 7.0E-94
Protein Domains
Database ID Description E-Value
Pfam IPR004575 EMBL-EBI Cdk-activating kinase assembly factor (MAT1) 9.8E-111
Pfam IPR008011 EMBL-EBI Complex 1 LYR protein 1.6E-7
Sequence
Target Sequence 
>C. ELEGANS:173648_S_AT
tgtagacgacctattccggttggctcaacgcttcacaatgcgtgccacgtcgatattctt
cacggatcctgtttcggagcttctgttcatctgtgccgtgttgaacattcgattggacca
tcctgatgcgaatcgcagcgttaataagttcattatggaggtgctcgagcagttggccac
tgcgaaaaaggcttcctacactgacgctggcgtcaccgcagcccaaactcttgtcaatcg
gaacgcgcaaagcatcgtcaccaacgcactctccatgtgccttttcagtcattccggaca
aattcgacgagaaatggccgatgttgtgctgcaagttgggcgaaatgacccatcgaaata
caagcaaatcctgactcaagctgtcgccgcacttccaaatgatcccgttaaagcgacacc
gcaacaattgacagaattcgtggaggcgggtttcatcgatttttacctcgtttcttttat
ttttttttcgtttttcaattttttcccccacattttccctcggctatctgtaatattcaa
tttttttttcgagttttttttgttggatttttctctctttctc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGTAGACGACCTATTCCGGTTGGCT 502 557 2371 Antisense
GGCTCAACGCTTCACAATGCGTGCC 539 537 2392 Antisense
GTGCCACGTCGATATTCTTCACGGA 212 477 2412 Antisense
TCTTCACGGATCCTGTTTCGGAGCT 275 617 2427 Antisense
GGACCATCCTGATGCGAATCGCAGC 390 523 2485 Antisense
GAAAAAGGCTTCCTACACTGACGCT 642 353 2554 Antisense
TCGGAACGCGCAAAGCATCGTCACC 251 607 2608 Antisense
GCAAATCCTGACTCAAGCTGTCGCC 672 317 2734 Antisense
AATGATCCCGTTAAAGCGACACCGC 6 159 2768 Antisense
TTTCCCTCGGCTATCTGTAATATTC 707 669 2884 Antisense
TTTGTTGGATTTTTCTCTCTTTCTC 544 667 2929 Antisense
Sequence Source Affymetrix Proprietary Database