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[181418_at] synbindin TRS23 family

Description F36D4.2 /REP_DB=WormBase Gene ID /WP=CE07190 /TR=Q20100 /GB=AAA93486.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 38      6grp_high1_10_10 > 72      4grp_highest_8_8 > 31      4grp_high_8_8 > 12      6grp_highest_nonorm > 64      6grp_total > 71      4grp_total > 12      6grp_highest_sub > 04      6grp_high1_sub > 04      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 536
1 2 3 4 range
A 579.6
(-1.1)
P 		575.1
(-1.1)
P 		455.1
(-3)
P 		843.4
(3)
P 		388
B 677.1
(-0.9)
P 		533.2
(-2.7)
P 		505.5
(-3)
P 		991.4
(3)
P 		486
C 588.6
(-2.2)
P 		581.8
(-2.3)
P 		541.7
(-3)
P 		883.7
(3)
P 		342
avr 615.1
(-1.3) 		563.4
(-2.1) 		500.8
(-3) 		906.2
(3) 		405

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 392
1 2 3 4 5 6 range
A 765.2
(-1.6)
P 		704
(-3)
P 		963.4
(3)
P 		916.3
(1.9)
P 		844.1
(0.2)
P 		708.1
(-2.9)
P 		259
B 724.9
(-1.8)
P 		841.9
(1.4)
P 		720.5
(-1.9)
P 		899.9
(3)
P 		767.6
(-0.6)
P 		679.7
(-3)
P 		220
C 571.3
(-3)
P 		723.3
(-0.6)
P 		722.8
(-0.6)
P 		957.9
(3)
P 		729.4
(-0.5)
P 		886.5
(1.9)
P 		387
avr 687.1
(-3) 		756.4
(-1.3) 		802.2
(-0.1) 		924.7
(3) 		780.4
(-0.6) 		758.1
(-1.2) 		238
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 99
1 2 3 4 range
A 211
(3)
P 		124.8
(-2.6)
P 		119
(-3)
P 		123.5
(-2.7)
P 		92
B 215.9
(3)
P 		131.7
(-2.1)
P 		117.1
(-3)
P 		211.3
(2.7)
P 		99
C 194.8
(3)
P 		167.3
(-0.6)
P 		188.8
(2.2)
P 		149
(-3)
P 		46
avr 207.2
(3) 		141.3
(-3) 		141.6
(-3) 		161.3
(-1.2) 		66

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 171
1 2 3 4 5 6 range
A 141.1
(-3)
P 		250.4
(2.8)
P 		209.8
(0.6)
P 		232.4
(1.8)
P 		254.7
(3)
P 		172.4
(-1.3)
P 		114
B 252.2
(0.4)
P 		280.2
(1.6)
P 		175
(-3)
P 		238.4
(-0.2)
P 		311.9
(3)
P 		253.4
(0.4)
P 		137
C 211.7
(-1.5)
P 		220.7
(-1)
P 		184
(-3)
P 		192.6
(-2.5)
P 		236
(-0.2)
P 		296.8
(3)
P 		113
avr 201.7
(-2.1) 		250.4
(1.7) 		189.6
(-3) 		221.1
(-0.6) 		267.5
(3) 		240.9
(1) 		78
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 181418_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12512
Sequence Type Exemplar sequence
Representative Public ID F36D4.2 NCBI
Target Description F36D4.2 /REP_DB=WormBase Gene ID /WP=CE07190 /TR=Q20100 /GB=AAA93486.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=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_073034(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073034 NCBI Caenorhabditis elegans F36D4.2 (F36D4.2) mRNA, complete cds. 11/11 None
SNAP00000027390 ENSEMBL cdna:SNAP chromosome:CEL140:V:9399112:9404344:1 11/11 None
GENEFINDER00000027395 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:9402918:9404344:1 11/11 None
F36D4.2 ENSEMBL cdna:known chromosome:CEL140:V:9402918:9404344:1 gene:F36D4.2 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
chrV:9402917-9404344(+) 100.0 100.0
Public Domain and Genome References
Gene Title synbindin TRS23 family
Ensembl F36D4.2
Entrez Gene 185357 Entrez gene
SwissProt Q20100 EMBL-EBI
WormBase CE07190 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:250993_AT synbindin, putative at
CANINE:1592114_AT similar to Trafficking protein particle complex subunit 4 (Synbindin) (TRS23 homolog) (Hematopoietic stem/progenitor cell protein 172) cfa
CANINE_2:CFA.10710.1.S1_A_AT similar to Trafficking protein particle complex subunit 4 (Synbindin) (TRS23 homolog) (Hematopoietic stem/progenitor cell protein 172) cfa
CANINE_2:CFAAFFX.19224.1.S1_S_AT similar to Trafficking protein particle complex subunit 4 (Synbindin) (TRS23 homolog) (Hematopoietic stem/progenitor cell protein 172) cfa
DROSOPHILA_2:1641214_AT dm
DROSGENOME1:146045_AT dm
CHICKEN:GGAAFFX.13161.1.S1_S_AT trafficking protein particle complex 4 gga
HG-U133_PLUS_2:234456_AT trafficking protein particle complex 4 hs
HG-U133B:234456_AT trafficking protein particle complex 4 hs
HG-U133A:217958_AT trafficking protein particle complex 4 hs
HG-U133_PLUS_2:217958_AT trafficking protein particle complex 4 hs
HG-U133A_2:217958_AT trafficking protein particle complex 4 hs
HG-U133A:217959_S_AT trafficking protein particle complex 4 hs
HG-U133_PLUS_2:217959_S_AT trafficking protein particle complex 4 hs
HG-U133A_2:217959_S_AT trafficking protein particle complex 4 hs
U133_X3P:G7706666_3P_AT trafficking protein particle complex 4 hs
U133_X3P:HS.279901.1.A1_3P_AT trafficking protein particle complex 4 hs
HG-U95E:91724_AT trafficking protein particle complex 4 hs
MOUSE430_2:1429632_AT trafficking protein particle complex 4 mm
MOUSE430A_2:1429632_AT trafficking protein particle complex 4 mm
MOE430A:1429632_AT trafficking protein particle complex 4 mm
MU11KSUBA:AA051641_S_AT trafficking protein particle complex 4 mm
MG-U74AV2:160361_AT trafficking protein particle complex 4 mm
MOE430A:1415674_A_AT trafficking protein particle complex 4 mm
MOE430B:1415674_A_AT trafficking protein particle complex 4 mm
MOUSE430A_2:1415674_A_AT trafficking protein particle complex 4 mm
MOUSE430_2:1415674_A_AT trafficking protein particle complex 4 mm
MU19KSUBA:TC23042_S_AT Trafficking protein particle complex 4, mRNA (cDNA clone MGC:49061 IMAGE:5401311) mm
MU19KSUBC:TC39685_AT Trafficking protein particle complex 4, mRNA (cDNA clone MGC:49061 IMAGE:5401311) mm
MU19KSUBC:TC39685_G_AT Trafficking protein particle complex 4, mRNA (cDNA clone MGC:49061 IMAGE:5401311) mm
RG-U34B:RC_AI008536_AT trafficking protein particle complex 4 rn
RG-U34B:RC_AA924765_G_AT trafficking protein particle complex 4 rn
RG-U34B:RC_AA924765_AT trafficking protein particle complex 4 rn
RG-U34C:RC_AI230945_S_AT trafficking protein particle complex 4 rn
RAE230A:1373907_AT trafficking protein particle complex 4 rn
RAT230_2:1373907_AT trafficking protein particle complex 4 rn
YEAST_2:1774837_AT One of 10 subunits of the transport protein particle (TRAPP) complex of the cis-Golgi which mediates vesicle docking and fusion; involved in endoplasmic reticulum (ER) to Golgi membrane traffic; human homolog is TRAPPC4 Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6888 ER to Golgi transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5801 Golgi cis-face inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast T29311 hypothetical protein F36D4.3 - Caenorhabditis elegans 0.0
blast AAO12438 Heavy chain, unconventional myosin protein 2, isoform e [Caenorhabditis elegans] ref|NP_001023887.1| Heavy chain, Unconventional Myosin family member (hum-2) [Caenorhabditis elegans] 0.0
blast AAM29688 Heavy chain, unconventional myosin protein 2, isoform c [Caenorhabditis elegans] ref|NP_741590.1| Heavy chain, Unconventional Myosin family member (hum-2) [Caenorhabditis elegans] 0.0
blast AAA93486 Hypothetical protein F36D4.2 [Caenorhabditis elegans] ref|NP_505435.1| F36D4.2 [Caenorhabditis elegans] 1.0E-123
blast CAE72167 Hypothetical protein CBG19270 [Caenorhabditis briggsae] 7.0E-61
blast AAH98628 Trafficking protein particle complex 4 [Rattus norvegicus] ref|XP_579105.1| PREDICTED: trafficking protein particle complex 4 [Rattus norvegicus] 5.0E-53
Protein Domains
Database ID Description E-Value
Pfam IPR007233 EMBL-EBI Sybindin-like protein 1.0E-126
Pfam IPR002710 EMBL-EBI Dilute (DIL) domain 1.2E-45
Pfam IPR007233 EMBL-EBI Sybindin-like protein 9.5E-125
Sequence
Target Sequence 
>C. ELEGANS:181418_AT
gagactgtatccggaacgagacttcaacttggtgcacaacaagtaaatgtactcgaatat
ctacaagaagaagatcactatccggtaaccgttaaatttgctgctccgaccgtatcgaca
aacgagaaaattattctttcatccatgtttcattcacttttcacaattgccgttcaactg
tcaccgtgtcaaaaaagttcaggagtcgaagttctcgaaacaacacagttcaaattattc
tgcctacaaagtcggacaggtgtgaagttcgttgtaatcacatctgctgcatcaaatatc
gcagctgattcacttctgtcaaaaatgtatgaactctacacggatttcgctctcaagaat
cccttttatt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGACTGTATCCGGAACGAGACTTC 588 391 223 Antisense
ACGAGACTTCAACTTGGTGCACAAC 285 91 238 Antisense
GAAGATCACTATCCGGTAACCGTTA 163 337 292 Antisense
TAACCGTTAAATTTGCTGCTCCGAC 577 637 308 Antisense
TGCTCCGACCGTATCGACAAACGAG 535 575 324 Antisense
CATCCATGTTTCATTCACTTTTCAC 480 211 362 Antisense
TCACAATTGCCGTTCAACTGTCACC 96 629 383 Antisense
GTTGTAATCACATCTGCTGCATCAA 705 437 493 Antisense
ATCGCAGCTGATTCACTTCTGTCAA 538 37 520 Antisense
ATGAACTCTACACGGATTTCGCTCT 18 45 551 Antisense
TTCGCTCTCAAGAATCCCTTTTATT 379 697 568 Antisense
Sequence Source Affymetrix Proprietary Database