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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattacatattgacctactactcagattccttttttatgtaatcaaatcttcttttgatgaatgttgtgttctgttttttttctgcagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAA

Basic information

species Zea mays
transcript GRMZM2G051043_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051043_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g11120.1 (Oryza sativa), 3'ss of exon 4
gtattacatattgacctactactcagattccttttttatgtaatcaaatcttcttttgatgaatgttgtgttctgttttttttctgcagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAA
||| || |  || |||| ||||| |  | |||| |     || | ||    | |||||||| ||||   ||| | ||| ||  ||  ||||||||| |||||||| |||||||| || ||||||||  |||||||||||||||||||||| || || |||||||||||||| || ||||| ||||||||
gtaatatagtttcaccttctactgaagtgccttctcc-catagtgaatctattttttgatgtatgtaa-gttttatttgtt--ctaaagAGGGCGCAAGAACTGCACTTAACCTTGGTGGCACAATGCTTGGTTTCTACCCTGTTAGAGTCTTACCTTCAAAGACAGCTATATTGCCTGTGAATCCAAA
















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|108823990|gb|EC277998.1|EC277998
EST:     TGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAG                         AGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACC
genomic: TGATCCCCACTCAGTTCTTAGGTTTGCATTCATTGAGTTCTCTGATGAAGgtattacata ... ttttctgcagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACC
EST: gi|108953255|gb|EC364659.1|EC364659
EST:     TGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAG                         AGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACC
genomic: TGATCCCCACTCAGTTCTTAGGTTTGCATTCATTGAGTTCTCTGATGAAGgtattacata ... ttttctgcagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACC
EST: gi|4730461|gb|AI649627.1|AI649627
EST:     TGATCCCCACTCAGTTCTTAGGTTTGCATTCATTGAGTTCTCTGATGAAG                         AGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACC
genomic: TGATCCCCACTCAGTTCTTAGGTTTGCATTCATTGAGTTCTCTGATGAAGgtattacata ... ttttctgcagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACC
EST: gi|38502629|gb|CF972489.1|CF972489
EST:     TGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAG                         AGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACC
genomic: TGATCCCCACTCAGTTCTTAGGTTTGCATTCATTGAGTTCTCTGATGAAGgtattacata ... ttttctgcagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACC
EST: gi|4730460|gb|AI649626.1|AI649626
EST:     TGATCCCCACTCAGTTCTTAGGTTTGCATTCATTGAGTTCTCTGATGAAG                         AGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACC
genomic: TGATCCCCACTCAGTTCTTAGGTTTGCATTCATTGAGTTCTCTGATGAAGgtattacata ... ttttctgcagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACC
EST: gi|33771172|gb|CF272833.1|CF272833
EST:     TGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAG                         AGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACC
genomic: TGATCCCCACTCAGTTCTTAGGTTTGCATTCATTGAGTTCTCTGATGAAGgtattacata ... ttttctgcagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACC
EST: gi|78077711|gb|DV506143.1|DV506143
EST:     TGATCCCCACTCAGTTCTTAGGTTTGCATTCATTGAGTTCTCTGATGAAG                         AGGGCGCCAGAGCTGCGCTTAACCTGCAACGCACAATTTTCGGTTTCTACC
genomic: TGATCCCCACTCAGTTCTTAGGTTTGCATTCATTGAGTTCTCTGATGAAGgtattacata ... ttttctgcagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACC

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: 46 (upstream exon), 49 (downstream exon)
Score: 114

GTTGTTGATTGCAGAATTTGTGGTGATCCCCACTCAGTTCTTAGGTTTGCATTCATTGAGTTCTCTGATGAAGgtattacata ... ttttctgcagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

GTTGTTGATTGCAGAATTTGTGGTGATCCCCACTCAGTTCTTAGGTTTGCATTCATTGAGTTCTCTGATGAAGgtattacata ... ttttctgcagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 112

GTTGTTGATTGCAGAATTTGTGGTGATCCCCACTCAGTTCTTAGGTTTGCATTCATTGAGTTCTCTGATGAAGgtattacata ... ttttctgcagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 194

GTTGTTGATTGCAGAATTTGTGGTGATCCCCACTCAGTTCTTAGGTTTGCATTCATTGAGTTCTCTGATGAAGgtattacata ... ttttctgcagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgtaatcaaatcttcttttgatgaatgttgtgttctgttttttttctgcagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAA
                   ttttgat  putative branch site (score: 194)
                                  tgttctgttttttttc  putative PPT
                                       tgtttttttt  TA-rich tract