[Home] | [Total List]

[191654_at] splicing factor

Description W07E6.4 /REP_DB=WormBase Gene ID /WP=CE17296 /GEN=prp-21 /TR=Q10577 /GB=AAC78179.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=splicing factor
Cluster 6grp_highest_10_10 > 86      6grp_high1_10_10 > 67      4grp_highest_8_8 > 26      4grp_high_8_8 > 59      6grp_highest_nonorm > 85      6grp_total > 68      4grp_total > 60      6grp_highest_sub > Da      6grp_cgc > 39      6grp_high1_sub > Da      6grp_cgc_sub > Cu      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 200
1 2 3 4 range
A 763.3
(1.5)
P 		732.5
(0.5)
P 		810.1
(3)
P 		623
(-3)
P 		187
B 800.5
(3)
P 		786.5
(2.3)
P 		786.9
(2.4)
P 		671.8
(-3)
P 		129
C 724.3
(-0.9)
P 		704
(-1.7)
P 		822.5
(3)
P 		670.9
(-3)
P 		152
avr 762.7
(1.3) 		741
(0.4) 		806.5
(3) 		655.2
(-3) 		151

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 490
1 2 3 4 5 6 range
A 761
(-0.9)
P 		697
(-2.2)
P 		656.6
(-3)
P 		710.1
(-1.9)
P 		886
(1.7)
P 		948.5
(3)
P 		292
B 923.7
(1)
P 		739.5
(-2.2)
P 		716.6
(-2.6)
P 		696.2
(-2.9)
P 		692.4
(-3)
P 		1039.4
(3)
P 		347
C 605.5
(-3)
P 		778.4
(-0.9)
P 		672.9
(-2.2)
P 		667.7
(-2.2)
P 		696.4
(-1.9)
P 		1095.9
(3)
P 		490
avr 763.4
(-1.6) 		738.3
(-2) 		682
(-3) 		691.3
(-2.8) 		758.3
(-1.7) 		1027.9
(3) 		346
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 196
1 2 3 4 range
A 277.9
(3)
P 		159
(-0.8)
P 		211.8
(0.9)
P 		91.2
(-3)
P 		187
B 255.3
(3)
P 		194.2
(-0.3)
P 		182.3
(-0.9)
P 		143.2
(-3)
P 		112
C 239.8
(1.4)
P 		202.4
(0.1)
P 		286.7
(3)
P 		113.1
(-3)
P 		174
avr 257.7
(3) 		185.2
(-0.1) 		226.9
(1.7) 		115.8
(-3) 		142

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 253
1 2 3 4 5 6 range
A 140.3
(-3)
P 		247.9
(2.1)
P 		143
(-2.9)
P 		180.1
(-1.1)
P 		267.3
(3)
P 		230.9
(1.3)
P 		127
B 321.4
(1.1)
P 		246.2
(-1)
P 		174
(-3)
P 		184.4
(-2.7)
P 		281.3
(0)
P 		387.6
(3)
P 		214
C 224.4
(-0.7)
P 		237.5
(-0.3)
P 		171.3
(-2)
P 		134.3
(-3)
P 		225.3
(-0.7)
P 		366.9
(3)
P 		233
avr 228.7
(-0.6) 		243.9
(-0.1) 		162.8
(-3) 		166.3
(-2.9) 		258
(0.4) 		328.5
(3) 		166
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191654_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5792
Sequence Type Exemplar sequence
Representative Public ID W07E6.4 NCBI
Target Description W07E6.4 /REP_DB=WormBase Gene ID /WP=CE17296 /GEN=prp-21 /TR=Q10577 /GB=AAC78179.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=splicing factor
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_061345(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_061345 NCBI Caenorhabditis elegans yeast PRP (splicing factor) related family member (prp-21) (prp-21) mRNA, complete cds. 11/11 None
SNAP00000002747 ENSEMBL cdna:SNAP chromosome:CEL140:II:484868:497599:1 11/11 None
GENEFINDER00000002750 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:484868:490278:1 11/11 None
W07E6.4.2 ENSEMBL cdna:known chromosome:CEL140:II:484863:490402:1 gene:W07E6.4 11/11 None
W07E6.4.3 ENSEMBL cdna:known chromosome:CEL140:II:484863:490342:1 gene:W07E6.4 11/11 None
W07E6.4.1 ENSEMBL cdna:known chromosome:CEL140:II:484865:490402:1 gene:W07E6.4 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
chrII:484867-490278(+) 100.0 100.0
Public Domain and Genome References
Gene Title splicing factor
Gene Symbol prp-21
Ensembl W07E6.4
Entrez Gene 173440 Entrez gene
SwissProt Q10577 EMBL-EBI
WormBase CE17296 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:260779_AT SWAP (Suppressor-of-White-APricot)/surp domain-containing protein / ubiquitin family protein at
CANINE:1583582_AT similar to splicing factor 3a, subunit 1, 120kDa isoform 2 cfa
CANINE_2:CFA.11069.1.A1_S_AT similar to splicing factor 3a, subunit 1, 120kDa isoform 2 cfa
CANINE_2:CFA.18055.1.S1_S_AT similar to splicing factor 3a, subunit 1, 120kDa isoform 2 cfa
CANINE_2:CFAAFFX.19574.1.S1_AT similar to splicing factor 3a, subunit 1, 120kDa isoform 2 cfa
CANINE_2:CFAAFFX.19635.1.S1_S_AT similar to splicing factor 3a, subunit 1, 120kDa isoform 2 cfa
DROSOPHILA_2:1639977_AT dm
DROSGENOME1:151919_AT dm
CHICKEN:GGA.9742.1.S1_S_AT splicing factor 3a, subunit 1, 120kDa gga
CHICKEN:GGAAFFX.11603.1.S1_AT splicing factor 3a, subunit 1, 120kDa gga
HG-U133A:201356_AT splicing factor 3a, subunit 1, 120kDa hs
HG-U133_PLUS_2:201356_AT splicing factor 3a, subunit 1, 120kDa hs
HG-U133A_2:201356_AT splicing factor 3a, subunit 1, 120kDa hs
HG-FOCUS:201356_AT splicing factor 3a, subunit 1, 120kDa hs
HG-U133A:201357_S_AT splicing factor 3a, subunit 1, 120kDa hs
HG-U133_PLUS_2:201357_S_AT splicing factor 3a, subunit 1, 120kDa hs
HG-U133A_2:201357_S_AT splicing factor 3a, subunit 1, 120kDa hs
HG-U133_PLUS_2:216457_S_AT splicing factor 3a, subunit 1, 120kDa hs
HG-U133A_2:216457_S_AT splicing factor 3a, subunit 1, 120kDa hs
HG-U133A:216457_S_AT splicing factor 3a, subunit 1, 120kDa hs
HG-U133_PLUS_2:227516_AT splicing factor 3a, subunit 1, 120kDa hs
HG-U133B:227516_AT splicing factor 3a, subunit 1, 120kDa hs
HU35KSUBC:RC_T72628_F_AT splicing factor 3a, subunit 1, 120kDa hs
HUGENEFL:X85237_AT splicing factor 3a, subunit 1, 120kDa hs
U133_X3P:G5032086_3P_A_AT splicing factor 3a, subunit 1, 120kDa hs
U133_X3P:HS.288883.2.A1_3P_A_AT splicing factor 3a, subunit 1, 120kDa hs
U133_X3P:HS.288883.1.S1_3P_AT splicing factor 3a, subunit 1, 120kDa hs
U133_X3P:HS.288883.0.A2_3P_AT splicing factor 3a, subunit 1, 120kDa hs
U133_X3P:HS.288883.0.A2_3P_A_AT splicing factor 3a, subunit 1, 120kDa hs
HG-U95AV2:34733_AT splicing factor 3a, subunit 1, 120kDa hs
HG-U95E:78615_AT splicing factor 3a, subunit 1, 120kDa hs
HG-U95E:91167_S_AT splicing factor 3a, subunit 1, 120kDa hs
HG-U95E:91508_AT splicing factor 3a, subunit 1, 120kDa hs
U133_X3P:1568796_3P_AT Splicing factor 3a, subunit 1, 120kDa hs
HG-U133_PLUS_2:1568796_AT Splicing factor 3a, subunit 1, 120kDa hs
HG-U95C:66152_AT Splicing factor 3a, subunit 1, 120kDa hs
HU35KSUBD:RC_R08318_AT Splicing factor 3a, subunit 1, 120kDa hs
MOUSE430A_2:1449333_AT splicing factor 3a, subunit 1 mm
MOE430A:1449333_AT splicing factor 3a, subunit 1 mm
MOUSE430_2:1449333_AT splicing factor 3a, subunit 1 mm
MOUSE430A_2:1419087_S_AT splicing factor 3a, subunit 1 mm
MOE430A:1419087_S_AT splicing factor 3a, subunit 1 mm
MOUSE430_2:1419087_S_AT splicing factor 3a, subunit 1 mm
MU11KSUBA:AA106955_S_AT splicing factor 3a, subunit 1 mm
MG-U74AV2:96027_AT splicing factor 3a, subunit 1 mm
MG-U74BV2:117259_AT splicing factor 3a, subunit 1 mm
MOE430B:1446687_AT splicing factor 3a, subunit 1 mm
MOUSE430_2:1446687_AT splicing factor 3a, subunit 1 mm
MOE430B:1445719_AT Splicing factor 3a, subunit 1, mRNA (cDNA clone MGC:6887 IMAGE:2651773) mm
MOUSE430_2:1445719_AT Splicing factor 3a, subunit 1, mRNA (cDNA clone MGC:6887 IMAGE:2651773) mm
MU19KSUBA:TC19917_AT Splicing factor 3a, subunit 1, mRNA (cDNA clone MGC:6887 IMAGE:2651773) mm
MU19KSUBA:TC21554_AT Splicing factor 3a, subunit 1, mRNA (cDNA clone MGC:6887 IMAGE:2651773) mm
MU19KSUBB:TC29070_AT Splicing factor 3a, subunit 1, mRNA (cDNA clone MGC:6887 IMAGE:2651773) mm
RG-U34C:RC_AI230180_AT splicing factor 3a, subunit 1 (predicted) rn
RAE230A:1374668_AT splicing factor 3a, subunit 1 (predicted) rn
RAT230_2:1374668_AT splicing factor 3a, subunit 1 (predicted) rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6396 RNA processing inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3723 RNA binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAC78179 Yeast prp (splicing factor) related protein 21 [Caenorhabditis elegans] ref|NP_493746.1| yeast PRP (splicing factor) related family member (prp-21) [Caenorhabditis elegans] gb|AAA82164.1| similar to yeast pre-mRNA splicing factor PRP21, Swiss-Prot Accession Number P32524; similar to D. melanogaster suppressor-of-white-apricot, Swiss-Prot Accession Number P12297; ubiquitin-like domain; putative splicing factor 0.0
blast CAE62877 Hypothetical protein CBG07063 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000626 EMBL-EBI Ubiquitin 1.7E-10
Pfam IPR000061 EMBL-EBI SWAP/Surp 6.8E-26
Pfam IPR000061 EMBL-EBI SWAP/Surp 2.1E-22
Pfam IPR000626 EMBL-EBI Ubiquitin 1.0E-11
Pfam IPR000626 EMBL-EBI Ubiquitin 1.0E-11
Sequence
Target Sequence 
>C. ELEGANS:191654_AT
accgtcaacacggattcgttgccgatccatcaaaggaaaagattggagctcagcaggtgc
cacgtcatcaatcgacccagggaaatgtgacaattactcaaggaataacgaatattcctg
gacaaatgccatccggatggccgccggttccaccaatgggaatgcctgggatgccgaatc
aagcgcttcctccaatccgacaaatggactttggcggtggacctccagcgaagcgtcctc
gtaccgaagatgatttgataccagaagctgattggcttaaaaaggtcaacggagcaattt
cgcttaatgttcatcttccacaggctcccgaacacggaatggatggctcaattgtgcagt
ttacaattcaagttactgcaccgatgtccgaactcaaacaacaaatccaggatcgttacg
gaatgcctgttggaaagcagaagctgatgtctgatggccttttcgtgaaggataatatga
gctcggccttctacaatttggc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACCGTCAACACGGATTCGTTGCCGA 290 87 1424 Antisense
AGATTGGAGCTCAGCAGGTGCCACG 403 65 1463 Antisense
CCACGTCATCAATCGACCCAGGGAA 258 273 1483 Antisense
CCGCCGGTTCCACCAATGGGAATGC 293 261 1564 Antisense
CTGGGATGCCGAATCAAGCGCTTCC 363 241 1589 Antisense
CAAATGGACTTTGGCGGTGGACCTC 608 189 1624 Antisense
GAAGCGTCCTCGTACCGAAGATGAT 504 341 1653 Antisense
AAGTTACTGCACCGATGTCCGAACT 232 157 1793 Antisense
GGATCGTTACGGAATGCCTGTTGGA 345 511 1833 Antisense
GAAGCTGATGTCTGATGGCCTTTTC 620 341 1863 Antisense
TGAGCTCGGCCTTCTACAATTTGGC 697 567 1901 Antisense
Sequence Source Affymetrix Proprietary Database