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[191872_at] TRA-2 like protein

Description F54F7.4 /REP_DB=WormBase Gene ID /WP=CE03419 /GEN=trx-1 /TR=Q20791 /GB=CAA91757.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=TRA-2 like protein
Cluster 6grp_highest_10_10 > 14      6grp_high1_10_10 > 41      4grp_high_8_8 > 49      6grp_highest_nonorm > 52      6grp_total > 41      4grp_total > 53      6grp_cgc > 71      6grp_high1_sub > 03      6grp_cgc_sub > 03      6grp_total_sub > Hat      6grp_rule_based > S3      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 558
1 2 3 4 range
A 554.2
(3)
P 		321.2
(-0.1)
P 		260.8
(-0.9)
A 		105
(-3)
A 		449
B 579.7
(3)
P 		332.6
(0.3)
P 		327
(0.3)
P 		21.7
(-3)
A 		558
C 499.2
(3)
P 		282.4
(-0.3)
P 		322.2
(0.3)
P 		99.8
(-3)
P 		399
avr 544.4
(3) 		312.1
(0) 		303.3
(-0.1) 		75.5
(-3) 		469

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 882
1 2 3 4 5 6 range
A 697
(2.9)
P 		702
(3)
P 		654.4
(2.5)
P 		650.2
(2.4)
P 		281.5
(-1.7)
P 		170.4
(-3)
P 		532
B 472.2
(-0.5)
P 		626.6
(0.6)
P 		939
(3)
P 		636.6
(0.7)
P 		276.4
(-2)
P 		145.6
(-3)
P 		793
C 540.3
(-0.4)
P 		637.6
(0.3)
P 		1027.8
(3)
P 		631.5
(0.3)
P 		294
(-2.1)
P 		159.9
(-3)
P 		868
avr 569.8
(0.5) 		655.4
(1.2) 		873.7
(3) 		639.4
(1) 		284
(-1.9) 		158.6
(-3) 		715
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 197
1 2 3 4 range
A 201.8
(3)
P 		69.7
(-1.3)
P 		68.2
(-1.3)
A 		15.4
(-3)
A 		186
B 184.9
(3)
P 		82.1
(-0.4)
P 		75.8
(-0.6)
P 		4.6
(-3)
A 		180
C 165.2
(3)
P 		81.2
(-0.4)
P 		112.3
(0.9)
P 		16.8
(-3)
P 		148
avr 184
(3) 		77.7
(-0.7) 		85.4
(-0.4) 		12.3
(-3) 		172

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 220
1 2 3 4 5 6 range
A 128.5
(-0.5)
P 		249.7
(3)
P 		142.5
(-0.1)
P 		164.9
(0.6)
P 		84.9
(-1.7)
P 		41.5
(-3)
P 		208
B 164.3
(0.8)
P 		208.6
(2.3)
P 		228
(3)
P 		168.6
(0.9)
P 		112.3
(-1)
P 		54.3
(-3)
P 		174
C 200.3
(1.2)
P 		194.5
(1.1)
P 		261.6
(3)
P 		127
(-0.9)
P 		95.1
(-1.8)
P 		53.5
(-3)
P 		208
avr 164.4
(1.1) 		217.6
(3) 		210.7
(2.8) 		153.5
(0.7) 		97.4
(-1.3) 		49.8
(-3) 		168
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191872_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16097
Sequence Type Exemplar sequence
Representative Public ID F54F7.4 NCBI
Target Description F54F7.4 /REP_DB=WormBase Gene ID /WP=CE03419 /GEN=trx-1 /TR=Q20791 /GB=CAA91757.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=TRA-2 like 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_077578(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077578 NCBI Caenorhabditis elegans MX region of TRA-2 Related family member (xtr-1) (xtr-1) mRNA, complete cds. 11/11 None
SNAP00000009558 ENSEMBL cdna:SNAP chromosome:CEL140:X:11852741:11853384:1 10/11 None
GENEFINDER00000009568 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:11852741:11853544:1 10/11 None
F54F7.4 ENSEMBL cdna:known chromosome:CEL140:X:11850689:11853384:1 gene:F54F7.4 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
chrX:11850688-11853384(+) 100.0 100.0
Public Domain and Genome References
Gene Title TRA-2 like protein
Gene Symbol xtr-1
Ensembl F54F7.4
Entrez Gene 192057 Entrez gene
SwissProt Q20791 EMBL-EBI
WormBase CE03419 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA91757 Hypothetical protein F54F7.4 [Caenorhabditis elegans] ref|NP_509979.1| MX region of TRA-2 Related family member (xtr-1) [Caenorhabditis elegans] 1.0E-169
blast CAA91757 Hypothetical protein F54F7.4 [Caenorhabditis elegans] ref|NP_509979.1| MX region of TRA-2 Related family member (xtr-1) [Caenorhabditis elegans] 5.0E-80
blast CAA91757 Hypothetical protein F54F7.4 [Caenorhabditis elegans] ref|NP_509979.1| MX region of TRA-2 Related family member (xtr-1) [Caenorhabditis elegans] 2.0E-75
blast AAF39755 Transformer : xx animals transformed into males protein 2, isoform a [Caenorhabditis elegans] ref|NP_495426.1| TRAnsformer : XX animals transformed into males family member (tra-2) [Caenorhabditis elegans] gb|AAB22845.1| pTra2A [Caenorhabditis elegans] sp|P34709|TRA2_CAEEL Sex-determining transformer protein 2 precursor (Ce-Tra-2) gb|AAA28150.1| membrane protein 5.0E-17
blast AAF39755 Transformer : xx animals transformed into males protein 2, isoform a [Caenorhabditis elegans] ref|NP_495426.1| TRAnsformer : XX animals transformed into males family member (tra-2) [Caenorhabditis elegans] gb|AAB22845.1| pTra2A [Caenorhabditis elegans] sp|P34709|TRA2_CAEEL Sex-determining transformer protein 2 precursor (Ce-Tra-2) gb|AAA28150.1| membrane protein 6.0E-17
blast AAF39755 Transformer : xx animals transformed into males protein 2, isoform a [Caenorhabditis elegans] ref|NP_495426.1| TRAnsformer : XX animals transformed into males family member (tra-2) [Caenorhabditis elegans] gb|AAB22845.1| pTra2A [Caenorhabditis elegans] sp|P34709|TRA2_CAEEL Sex-determining transformer protein 2 precursor (Ce-Tra-2) gb|AAA28150.1| membrane protein 1.0E-16
blast AAF71403 TRA-2B [Caenorhabditis remanei] 4.0E-12
blast AAF71403 TRA-2B [Caenorhabditis remanei] 5.0E-12
Protein Domains
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_509979.1 3 20-42,57-79,124-146
F54F7.4 3 20-42,57-79,124-146
Sequence
Target Sequence 
>C. ELEGANS:191872_AT
gtacttctaacagcgttgtcagccaaactcaaactttggtggagacagccattcaaggaa
acaaaaaagctgtcggaaagctgtcataaatctcaagaatcgatgaatggagatctttta
ataaacaccgaaaagcaacacgcaaagattcaaaacaaacatccacggaattatttcaca
gaacccccatcgattgaatgttgtgtccgagagaaccaaggattgccaccacatccacgc
gcaaatcagtacccagcccatttctgcaaggcaatggtggcctactgtgaagatccgtat
tggacagaacgcacagtgccacttccgccagggcttgttgtaccacgtcgccctctagac
tactacaatatcataccaaacttgtcgccaccaccagaggatttcaattggattcctcct
aatgagcctcctccaattgaaatacc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTACTTCTAACAGCGTTGTCAGCCA 201 459 457 Antisense
GGAATTATTTCACAGAACCCCCATC 507 529 623 Antisense
GAACCCCCATCGATTGAATGTTGTG 663 343 637 Antisense
GAGAGAACCAAGGATTGCCACCACA 397 393 665 Antisense
ACCCAGCCCATTTCTGCAAGGCAAT 224 91 707 Antisense
ATGGTGGCCTACTGTGAAGATCCGT 37 51 730 Antisense
GGACAGAACGCACAGTGCCACTTCC 699 525 758 Antisense
GTCGCCCTCTAGACTACTACAATAT 516 475 803 Antisense
ATATCATACCAAACTTGTCGCCACC 241 19 824 Antisense
ATTGGATTCCTCCTAATGAGCCTCC 655 3 863 Antisense
ATGAGCCTCCTCCAATTGAAATACC 122 45 878 Antisense
Sequence Source Affymetrix Proprietary Database