[Home] | [Total List]

[173541_at]

Description CEK072C7F /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F28B3.7 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D69642 /WB_GENE_ID=F28B3.7 /WP=CE09745 /CHR=1 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk72c7 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 84      6grp_high1_10_10 > 58      4grp_highest_8_8 > 42      4grp_high_8_8 > 49      6grp_highest_nonorm > 87      6grp_total > 48      4grp_total > 54      6grp_highest_sub > Cu      6grp_cgc > 28      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 994
1 2 3 4 range
A 1151.4
(3)
P 		1026
(1.9)
P 		1043.7
(2)
P 		486.8
(-3)
P 		665
B 1481
(3)
P 		900.3
(-1.4)
P 		688.4
(-3)
P 		776.4
(-2.3)
P 		793
C 1305.7
(3)
P 		843.3
(-1.8)
P 		1058.8
(0.5)
P 		721.7
(-3)
P 		584
avr 1312.7
(3) 		923.2
(-0.6) 		930.3
(-0.5) 		661.6
(-3) 		651

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 986
1 2 3 4 5 6 range
A 1444.1
(1.9)
P 		1257
(0.6)
P 		730.8
(-3)
P 		937.7
(-1.6)
P 		1044.4
(-0.9)
P 		1608.7
(3)
P 		878
B 1123.2
(-1)
P 		1038.8
(-1.6)
P 		836.4
(-3)
P 		920
(-2.4)
P 		1076.7
(-1.4)
P 		1716.4
(3)
P 		880
C 1426.3
(2.1)
P 		1216
(-0.1)
P 		1089.2
(-1.4)
P 		1031.1
(-2.1)
P 		943.2
(-3)
P 		1506.2
(3)
P 		563
avr 1331.2
(0.7) 		1170.6
(-0.6) 		885.5
(-3) 		962.9
(-2.4) 		1021.4
(-1.9) 		1610.4
(3) 		725
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 401
1 2 3 4 range
A 419.2
(3)
P 		222.7
(-0.4)
P 		272.8
(0.5)
P 		71.3
(-3)
P 		348
B 472.3
(3)
P 		222.4
(-1.8)
P 		159.5
(-3)
P 		165.5
(-2.9)
P 		313
C 432.2
(3)
P 		242.4
(-0.7)
P 		369
(1.8)
P 		121.7
(-3)
P 		311
avr 441.2
(3) 		229.2
(-1) 		267.1
(-0.2) 		119.5
(-3) 		322

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 481
1 2 3 4 5 6 range
A 266.2
(-0.8)
P 		447.1
(3)
P 		159.2
(-3)
P 		237.8
(-1.4)
P 		315.2
(0.3)
P 		391.7
(1.8)
P 		288
B 390.8
(-0.4)
P 		345.8
(-1)
P 		203.1
(-3)
P 		243.7
(-2.4)
P 		437.4
(0.2)
P 		640
(3)
P 		437
C 528.7
(3)
P 		371
(0.1)
P 		277.2
(-1.7)
P 		207.4
(-3)
P 		305.2
(-1.2)
P 		504.2
(2.5)
P 		321
avr 395.2
(0.7) 		388
(0.5) 		213.2
(-3) 		229.6
(-2.7) 		352.6
(-0.2) 		512
(3) 		299
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173541_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.22670
Sequence Type Exemplar sequence
Representative Public ID CEK072C7F NCBI
Target Description CEK072C7F /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F28B3.7 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D69642 /WB_GENE_ID=F28B3.7 /WP=CE09745 /CHR=1 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk72c7 : 5prime 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_059085(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059085 NCBI Caenorhabditis elegans High Incidence of Males (increased X chromosome loss) family member (him-1) (him-1) mRNA, complete cds. 11/11 None
F28B3.7.3 ENSEMBL cdna:known chromosome:CEL140:I:4951244:4957670:-1 gene:F28B3.7 11/11 None
F28B3.7.1 ENSEMBL cdna:known chromosome:CEL140:I:4951580:4957668:-1 gene:F28B3.7 11/11 A 
F28B3.7.2 ENSEMBL cdna:known chromosome:CEL140:I:4951580:4957670:-1 gene:F28B3.7 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
chrI:4951590-4958068(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol him-1
Ensembl F28B3.7
Entrez Gene 172116 Entrez gene
SwissProt O01789 EMBL-EBI
WormBase CE29497 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:251851_AT structural maintenance of chromosomes (SMC) family protein at
CANINE_2:CFAAFFX.24935.1.S1_AT similar to Structural maintenance of chromosome 1-like 1 protein (SMC1alpha protein) (SB1.8/DXS423E protein) (Sb1.8) cfa
CANINE_2:CFAAFFX.24935.1.S1_S_AT similar to Structural maintenance of chromosome 1-like 1 protein (SMC1alpha protein) (SB1.8/DXS423E protein) (Sb1.8) cfa
DROSOPHILA_2:1628112_AT dm
DROSGENOME1:141490_AT dm
HG-U95AV2:32849_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
HU35KSUBB:RC_R43262_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
HUGENEFL:S78271_S_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
HUGENEFL:D80000_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
U133_X3P:HS.22130.0.A1_3P_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
U133_X3P:HS.211602.0.S2_3P_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
U133_X3P:HS.132153.0.A1_3P_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
U133_X3P:1555677_3P_S_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
HG-U133_PLUS_2:1555677_S_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
HG-U133A_2:201589_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
HG-FOCUS:201589_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
HG-U133_PLUS_2:201589_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
HG-U133A:201589_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
HG-U133A_2:217555_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
HG-U133_PLUS_2:217555_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
HG-U133A:217555_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
HG-U133_PLUS_2:239688_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
HG-U133B:239688_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
HG-U95AV2:35546_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
HG-U95C:63519_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
HG-U95C:66821_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
HG-U133_PLUS_2:244150_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
HG-U133B:244150_AT SMC1 structural maintenance of chromosomes 1-like 1 (yeast) hs
MG-U74BV2:106277_AT SMC (structural maintenance of chromosomes 1)-like 1 (S. cerevisiae) mm
MG-U74BV2:163269_AT SMC (structural maintenance of chromosomes 1)-like 1 (S. cerevisiae) mm
MG-U74CV2:166333_AT SMC (structural maintenance of chromosomes 1)-like 1 (S. cerevisiae) mm
MOE430A:1417832_AT SMC (structural maintenance of chromosomes 1)-like 1 (S. cerevisiae) mm
MOUSE430A_2:1417832_AT SMC (structural maintenance of chromosomes 1)-like 1 (S. cerevisiae) mm
MOUSE430_2:1417832_AT SMC (structural maintenance of chromosomes 1)-like 1 (S. cerevisiae) mm
MOE430A:1417831_AT SMC (structural maintenance of chromosomes 1)-like 1 (S. cerevisiae) mm
MOUSE430A_2:1417831_AT SMC (structural maintenance of chromosomes 1)-like 1 (S. cerevisiae) mm
MOUSE430_2:1417831_AT SMC (structural maintenance of chromosomes 1)-like 1 (S. cerevisiae) mm
MOE430A:1417830_AT SMC (structural maintenance of chromosomes 1)-like 1 (S. cerevisiae) mm
MOUSE430A_2:1417830_AT SMC (structural maintenance of chromosomes 1)-like 1 (S. cerevisiae) mm
MOUSE430_2:1417830_AT SMC (structural maintenance of chromosomes 1)-like 1 (S. cerevisiae) mm
MU19KSUBB:TC29029_AT SMC (structural maintenance of chromosomes 1)-like 1 (S. cerevisiae) (Smc1l1), mRNA mm
MU19KSUBB:TC29029_G_AT SMC (structural maintenance of chromosomes 1)-like 1 (S. cerevisiae) (Smc1l1), mRNA mm
RG-U34A:AJ005113_G_AT structural maintenance of chromosomes 1 like 1 (S. cerevisiae) rn
RG-U34A:AJ005113_AT structural maintenance of chromosomes 1 like 1 (S. cerevisiae) rn
RAE230A:1387026_AT structural maintenance of chromosomes 1 like 1 (S. cerevisiae) rn
RAT230_2:1387026_AT structural maintenance of chromosomes 1 like 1 (S. cerevisiae) rn
RG-U34B:RC_AA964157_AT Structural maintenance of chromosomes 1 like 1 (S. cerevisiae) rn
RG-U34B:RC_AI058741_AT Structural maintenance of chromosomes 1 like 1 (S. cerevisiae) rn
YEAST_2:1771900_AT Subunit of the multiprotein cohesin complex, essential protein involved in chromosome segregation and in double-strand DNA break repair; SMC chromosomal ATPase family member, binds DNA with a preference for DNA with secondary structure Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6810 transport inferred from electronic annotation QuickGO AmiGO
7059 chromosome segregation inferred from electronic annotation QuickGO AmiGO
7064 mitotic sister chromatid cohesion inferred from sequence similarity QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
16020 membrane inferred from electronic annotation QuickGO AmiGO
8278 cohesin complex inferred from sequence similarity QuickGO AmiGO
5634 nucleus inferred from direct assay QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5524 ATP binding inferred from electronic annotation QuickGO AmiGO
3677 DNA binding inferred from direct assay QuickGO AmiGO
5515 protein binding inferred from direct assay QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAK21378 High incidence of males (increased x chromosome loss) protein 1 [Caenorhabditis elegans] ref|NP_491486.1| High Incidence of Males (increased X chromosome loss) family member (him-1) [Caenorhabditis elegans] 0.0
blast T34063 chromosome segregation protein smc1 F28B3.7 [similarity] - Caenorhabditis elegans 0.0
blast CAE73105 Hypothetical protein CBG20485 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR003405 EMBL-EBI Structural maintenance of chromosome protein SMC, C-terminal 3.5E-42
Pfam IPR003395 EMBL-EBI SMC protein, N-terminal 3.1E-71
Pfam IPR010935 EMBL-EBI SMCs flexible hinge 1.2E-37
Sequence
Target Sequence 
>C. ELEGANS:173541_AT
aaatttttgacaaccgcgactatcaaatcatctgtataatttcattattactattccctt
acccctcattatttcttaattatcaaaaaccgattcactcagtcacacagttccccgcat
ttaaaggtctcaaacgtttttccctcttctctcttatacattactgtttttatgttccca
a

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAATTTTTGACAACCGCGACTATCA 344 115 3954 Antisense
GACAACCGCGACTATCAAATCATCT 491 365 3962 Antisense
ACCGCGACTATCAAATCATCTGTAT 17 91 3966 Antisense
AAATCATCTGTATAATTTCATTATT 336 117 3978 Antisense
TACCCCTCATTATTTCTTAATTATC 174 649 4013 Antisense
TCAAAAACCGATTCACTCAGTCACA 693 629 4036 Antisense
AACCGATTCACTCAGTCACACAGTT 386 147 4041 Antisense
CACACAGTTCCCCGCATTTAAAGGT 117 195 4057 Antisense
TCCCCGCATTTAAAGGTCTCAAACG 654 593 4065 Antisense
CTCTTCTCTCTTATACATTACTGTT 145 231 4097 Antisense
TACATTACTGTTTTTATGTTCCCAA 172 643 4110 Antisense
Sequence Source Affymetrix Proprietary Database