Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattattgagtgttgaaagagctattattatgtttctttattccagtcactatttctcactggactttctcttaaatgtattagGAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTAAAGACTGAGAACCGCATAGGAATTTTCAAATCTGAATTTGATGTCCAGTCCACATTTGAGGGTGATA

Basic information

species Zea mays
transcript GRMZM2G014136_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014136_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g24704.1 (Oryza sativa), 3'ss of exon 8
-------gtattattgagtgttgaaagagc----tattatt----atgtttctttattccagtcactatttctcactggactttctcttaaatgtattagGAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTAAAGACTGAGAACCGCATAGGAATTTTCAAATCTGAATTTGATGTCCAGTCCACATTTGAGGGTGATA
        |||| | |   |  |  ||       |||||||    |     | || |     ||  |||  |   ||||| ||  | ||| || ||||||||||| || || || ||||| || |||||| | ||||| ||||| |||||||||||||||||| ||||||||||||||||||| ||||||||||| || |
aatgcttatattttgggacggagggagtatatcttattattccaaacaagcccttttcttgatcgatatcacattctggatttctttttacatctattagGAGTGCCGTGAAGCTTGTGGTGGCCAAGGTTTGAAGACAGAGAATCGCATAGGAATTTTCAAAGCTGAATTTGATGTCCAGTCTACATTTGAGGGCGACA
















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|213191931|gb|FM185346.1|FM185346
EST:     NNNNNNTNNNNAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAG                         GAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTAAAGACTGAGAACCGCATA
genomic: TAGTGCT-CTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAGgtattattga ... aatgtattagGAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTAAAGACTGAGAACCGCATA
EST: gi|32922953|gb|CF027765.1|CF027765
EST:     CTAGTGTTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAG                         GAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTGAAGACTGAGAACCGCATA
genomic: CTAGTGCTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAGgtattattga ... aatgtattagGAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTAAAGACTGAGAACCGCATA
EST: gi|32923445|gb|CF028257.1|CF028257
EST:     CTAGTGTTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAG                         GAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTGAAGACTGAGACCCGCATA
genomic: CTAGTGCTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAGgtattattga ... aatgtattagGAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTAAAGACTGAGAACCGCATA
EST: gi|32921856|gb|CF026668.1|CF026668
EST:     CTAGTGTTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAG                         GAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTGAAGACTGAGAACCGCATA
genomic: CTAGTGCTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAGgtattattga ... aatgtattagGAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTAAAGACTGAGAACCGCATA
EST: gi|32920309|gb|CF025121.1|CF025121
EST:     CTAGTGTTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAG                         GAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTGAAGACTGAGAACCGCATA
genomic: CTAGTGCTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAGgtattattga ... aatgtattagGAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTAAAGACTGAGAACCGCATA
EST: gi|211534372|gb|FL093852.1|FL093852
EST:     CTAGTGCTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAG                         GAGTGTCGCGAGGCCTGTGGAGGTC
genomic: CTAGTGCTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAGgtattattga ... aatgtattagGAGTGTCGCGAGGCCTGTGGAGGTC
EST: gi|32923051|gb|CF027863.1|CF027863
EST:     CTAGTGTTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAG                         GAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTGAAGACTGAGAACCGCATA
genomic: CTAGTGCTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAGgtattattga ... aatgtattagGAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTAAAGACTGAGAACCGCATA
EST: gi|61119686|gb|DN560647.1|DN560647
EST:     CTAGTGCTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAG                         GAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTGAAGACTGAGAACCGCATA
genomic: CTAGTGCTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAGgtattattga ... aatgtattagGAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTAAAGACTGAGAACCGCATA
EST: gi|32921929|gb|CF026741.1|CF026741
EST:     CTAGTGTTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAG                         GAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTGAAGACTGAGAACCGCATA
genomic: CTAGTGCTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAGgtattattga ... aatgtattagGAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTAAAGACTGAGAACCGCATA
EST: gi|32922523|gb|CF027335.1|CF027335
EST:     CTAGTGTTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAG                         GAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTGAAGACTGAGAACCGCATA
genomic: CTAGTGCTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAGgtattattga ... aatgtattagGAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTAAAGACTGAGAACCGCATA
EST: gi|32923374|gb|CF028186.1|CF028186
EST:     CTAGTGTTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAG                         GAGTGTCGCGAGGCCTGTGCAGGTCAAGGTCTGAAGACTGAGAACCGCATA
genomic: CTAGTGCTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAGgtattattga ... aatgtattagGAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTAAAGACTGAGAACCGCATA
EST: gi|32922304|gb|CF027116.1|CF027116
EST:     CTAGTGTTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAG                         GAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTGAAGACTGAGAACCGCATA
genomic: CTAGTGCTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAGgtattattga ... aatgtattagGAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTAAAGACTGAGAACCGCATA

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 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 67

TATGTATGTAAAGAGAACTCCTGAAATGAGCAAAGACATACACATTTACTCTAGTGCTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAGgtattattga ... aatgtattagGAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTAAAGACTGAGAACCGCATAGGAATTTTCAAATCTGAATTTGATGTCCAGTCCACATTTGAGGGTGATA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 333

TATGTATGTAAAGAGAACTCCTGAAATGAGCAAAGACATACACATTTACTCTAGTGCTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAGgtattattga ... aatgtattagGAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTAAAGACTGAGAACCGCATAGGAATTTTCAAATCTGAATTTGATGTCCAGTCCACATTTGAGGGTGATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 327

TATGTATGTAAAGAGAACTCCTGAAATGAGCAAAGACATACACATTTACTCTAGTGCTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAGgtattattga ... aatgtattagGAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTAAAGACTGAGAACCGCATAGGAATTTTCAAATCTGAATTTGATGTCCAGTCCACATTTGAGGGTGATA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 171

TATGTATGTAAAGAGAACTCCTGAAATGAGCAAAGACATACACATTTACTCTAGTGCTCTGAAGGCGACACTAACTTGGCAGAATATGATTACGATTCAGgtattattga ... aatgtattagGAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTAAAGACTGAGAACCGCATAGGAATTTTCAAATCTGAATTTGATGTCCAGTCCACATTTGAGGGTGATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttctttattccagtcactatttctcactggactttctcttaaatgtattagGAGTGTCGCGAGGCCTGTGGAGGTCAAGGTCTAAAGACTGAGAACCGCATAGGAATTTTCAAATCTGAATTTGATGTCCAGTCCACATTTGAGGGTGATA
                        ttctcac  putative branch site (score: 171)
                                        tcttaaatgtatta  TA-rich tract