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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTAAATCTACAACATGTGTTGCCTTTATTCTTGCAATGTACAAGGAGGCTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacctaactacttgtccaagttgcaggaaaacactgtgttcttcaacatgtttgaattcatttcgttgccatcattcttccattggttgatgccaaaagttccgaaattccctacaccaatctgactgtctacttctgcctcag

Basic information

species Oryza sativa
transcript LOC_Os09g22440.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g22440.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G031824_T01 (Zea mays), 5'ss of exon 6
TGGTAAATCTACAACATGTGTTGCCTTTATTCTTGCAATGTACAAGGAGGCTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacctaactacttgtccaagttgcaggaaaacactgtgttcttcaacatgtttgaattcatttcgttgccatcattcttccattggttgatgccaaaagttccgaaattccctacaccaatctgactgtctacttctgcctcag
||||||||| || || ||||| ||||| ||||||||||||||||||||||||||||||||||| |||||  | |||||||| ||||| ||||||||||||||||||  |     |    |      |  |      ||   |  | ||  || ||  | | |   | | ||  | | | || |  |||| | |  |||      | ||  |                                      
TGGTAAATCAACTACTTGTGTCGCCTTCATTCTTGCAATGTACAAGGAGGCTGGAATATTCACCCCTTTCTCGGAGTCGATCCAGGTCACCGAGTTCACTgtaagtgacatctcatgcttagtctctctatctcttcatccttctgtttgacgtgcattactaagtctagt--caaaccttgtgtcatttgattctgcttcttctgcctcag-------------------------------------

upper sequence: LOC_Os09g22440.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA01G04400.1 (Glycine max), 5'ss of exon 6
TGGTAAATCTACAACATGTGTTGCCTTTATTCTTGCAATGTACAAGGAGGCTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacctaactacttgtccaagttgcaggaaaacactg-tgttcttcaacatgtttgaattcatttcgttgccatcattcttccattggttgatgccaaaagttccgaaattccctacaccaatctgactgtctacttctgcctcag
||| ||||| |||||||||||||||||||||||| ||||||| || | |||||||||||||   ||| || |    || ||||| || || || ||||| |||||  || | || | | |     ||  |   || | ||| |  |  | |     |||   |   ||||  || | | || || |                                                                
TGGGAAATCAACAACATGTGTTGCCTTTATTCTTTCAATGTATAAAGCGGCTGGAATATTCGGCCCTATTTCTAGCTCCATTCAAGTAACTGAATTCACAgtaag--ccaagcttcct-tagtgcttataaccaacctctgatagttataattgctttttcttatgtttctatgtcgttat-ctgcag--------------------------------------------------------------

upper sequence: LOC_Os09g22440.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA02G03160.1 (Glycine max), 5'ss of exon 6
TGGTAAATCTACAACATGTGTTGCCTTTATTCTTGCAATGTACAAGGAGGCTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacctaactacttgtccaagttgcaggaaaacactgtgttcttcaac-atgtttgaattcatttcgttgccatcattcttccattggttgatgccaaaagttccgaaattccctacaccaatctgactgtctacttctgcctcag
||| ||||| |||||||||||||||||||||||| ||||||| || | |||||||||||||   ||| || |    || ||||| || || || ||||| |||||  || | || | | |     ||  |   || | |||     |  ||     |||   |   ||||  ||   | | ||| |                                                                
TGGGAAATCAACAACATGTGTTGCCTTTATTCTTTCAATGTATAAAGCGGCTGGAATATTCGGCCCTATTTCTAGCTCCATTCAAGTAACTGAATTCACAgtaag--ccaagcttcct-tagtgcttataaccaacctctgatcgttataattgccttttcttatgtttctatgttgt-aatctgcag--------------------------------------------------------------

upper sequence: LOC_Os09g22440.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G70160.1 (Arabidopsis thaliana), 5'ss of exon 6
TGGTAAATCTACAACATGTGTTGCCTTTATTCTTGCAATGTACAAGGAGGCTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacctaactacttgtccaagttgcaggaaaacactgtgttcttcaacat-gtttgaattcatttcgttgccatcattcttccattggttgatgccaaaagttccgaaattccctacaccaatctgactgtctacttctgcctcag
 |||||||| |||||||||||||| || || |||||||||||||| |  ||||| ||||||   ||| | || ||    ||||| || || || |||||||| |||  ||   |  || |     || ||  |  | |   | | | | |||||   |      | |||   | |  || |  || ||                                                              
CGGTAAATCGACAACATGTGTTGCTTTCATCCTTGCAATGTACAAAGCTGCTGGTATATTCGACCCTCTCGCTGATCACATTCAAGTCACTGAATTCACTgtgagtttctttttttttct-----tttcaatatcaaatctt-tccattaacattactcatgaacgtttatcttctttcgtattttcag-------------------------------------------------------------

upper sequence: LOC_Os09g22440.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv01s0026g00920.t01 (Vitis vinifera), 5'ss of exon 6
TGGTAAATCTACAACATGTGTTGCCTTTATTCTTGCAATGTACAAGGAGGCTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacctaactacttgtccaagttgcaggaaaacactgtgttcttcaacatgtttgaattcatttcgttgccatcattcttccattggttgatgccaaaagttccgaaattccctacaccaatctgactgtctacttctgcctcag
||| ||||| |||||||||||||||||||| || | |||||| || ||||| ||||| ||    ||   | |    || ||||| || || |||||||||||||||| | |||| | | | |    | |  | |  ||   |     ||   |   |||   | |  | | |    |  | ||  ||                                                              
TGGGAAATCGACAACATGTGTTGCCTTTATCCTGGAAATGTATAAAGAGGCAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACTgtaagtatc-aactgcct-tgctgtatacgtggatgcatctttcctctccttacaattgctgtaacatggctttactactgctcacag-------------------------------------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86881795|gb|CI324091.1|CI324091
EST:     GCAGAGTCGATTCAGGTGACCGAGTTCACT                         ATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
genomic: GCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacct ... tctgcctcagATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
EST: gi|58691578|gb|CK080265.1|CK080265
EST:     CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACT                         ATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
genomic: CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacct ... tctgcctcagATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
EST: gi|89182785|gb|CI045543.1|CI045543
EST:     TCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACT                         ATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
genomic: TCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacct ... tctgcctcagATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
EST: gi|86887600|gb|CI294234.1|CI294234
EST:     CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACT                         ATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
genomic: CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacct ... tctgcctcagATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
EST: gi|87017872|gb|CI273894.1|CI273894
EST:     CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACT                         ATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
genomic: CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacct ... tctgcctcagATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
EST: gi|87027155|gb|CI278187.1|CI278187
EST:     CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACT                         ATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
genomic: CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacct ... tctgcctcagATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
EST: gi|29616538|gb|CB621550.1|CB621550
EST:     CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACT                         ATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
genomic: CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacct ... tctgcctcagATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
EST: gi|8859189|gb|AU096507.1|AU096507
EST:     CGATTCAGGTGACCGAGTTCACT                         ATACGCAGACGCAGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGAC
genomic: CGATTCAGGTGACCGAGTTCACTgtaagtacct ... tctgcctcagATACGC-GACGC-GTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGAC
EST: gi|58587758|gb|CF986066.1|CF986066
EST:     CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACT                         ATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
genomic: CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacct ... tctgcctcagATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
EST: gi|218498562|gb|FG955783.1|FG955783
EST:     CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACT                         ATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
genomic: CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacct ... tctgcctcagATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
EST: gi|25806597|gb|CA762558.1|CA762558
EST:     CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACT                         ATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
genomic: CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacct ... tctgcctcagATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
EST: gi|29683637|gb|CB679912.1|CB679912
EST:     CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACT                         ATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
genomic: CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacct ... tctgcctcagATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
EST: gi|38481125|gb|CF965214.1|CF965214
EST:     CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACT                         ATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
genomic: CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacct ... tctgcctcagATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
EST: gi|88226080|gb|CI225996.1|CI225996
EST:     GCAGAGTCGATTCAGGTGACCGAGTTCACT                         ATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
genomic: GCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacct ... tctgcctcagATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
EST: gi|89187379|gb|CI047446.1|CI047446
EST:     CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACT                         ATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
genomic: CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacct ... tctgcctcagATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
EST: gi|7134677|gb|AU082617.1|AU082617
EST:     CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACT                         ATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT
genomic: CTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacct ... tctgcctcagATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 69 (upstream exon), 73 (downstream exon)
Score: 46

TGGTAAATCTACAACATGTGTTGCCTTTATTCTTGCAATGTACAAGGAGGCTGGAATATTCACGCCTTTTGCAGAGTCGATTCAGGTGACCGAGTTCACTgtaagtacct ... tctgcctcagATACGCGACGCGTACATGCTCAAGATTTTCGAAGATAACCAGGCCAGACTTCCAAGCTGGTGCAACACAGAATCTGACAAGCTCCCCTTCTGCCAGATCC




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