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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattacatattgacctactcagatgcctttttctgtaatcaatcttcttttgatgaattttgggttccattttctctgtagAGGGTGCAAGAACTGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAA

Basic information

species Zea mays
transcript GRMZM2G069816_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069816_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g11120.1 (Oryza sativa), 3'ss of exon 4
gtattacatattgacct---actcagatgcctttttctgtaatcaatct-tcttttgatgaattttgggttccattttctctgtagAGGGTGCAAGAACTGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAA
||| || |  || ||||   ||| |  |||||| | |  || | ||||| | |||||||| || |   |||  ||||  |||  |||||| |||||||||||||||||||| || ||||||||  |||||||||||||||||||||| || ||||||||||||||||| || || || ||||||||
gtaatatagtttcaccttctactgaagtgccttctcccatagtgaatctattttttgatgtatgt-aagttttatttgttctaaagAGGGCGCAAGAACTGCACTTAACCTTGGTGGCACAATGCTTGGTTTCTACCCTGTTAGAGTCTTACCTTCAAAGACAGCTATATTGCCTGTGAATCCAAA
















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|78092729|gb|DV521103.1|DV521103
EST:     TGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAG                         AGGGTGCAAGAACTGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACC
genomic: TGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAGgtattacata ... ttctctgtagAGGGTGCAAGAACTGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACC
EST: gi|37385479|gb|CF629884.1|CF629884
EST:     TGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAG                         AGGGTGCAAGAACTGCACTTAACCTTGGAGGCACAATTTTTGGTTTCTACC
genomic: TGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAGgtattacata ... ttctctgtagAGGGTGCAAGAACTGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACC
EST: gi|166600684|gb|EG236388.1|EG236388
EST:     TGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAG                         AGGGTGCAAGAAC
genomic: TGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAGgtattacata ... ttctctgtagAGGGTGCAAGAAC
EST: gi|148948792|gb|EC894194.2|EC894194
EST:     GATCCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAG                         AGGGTGCAAGAACTGCACTTAACCTCGGAGGCACAATTTTTGGTTTC
genomic: GATCCCC-ACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAGgtattacata ... ttctctgtagAGGGTGCAAGAACTGCACTTAACCTCGGAGGCACAATTTTTGGTTTC
EST: gi|60352077|gb|DN219050.1|DN219050
EST:     TGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAG                         AGGGTGCAAGAACTGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACC
genomic: TGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAGgtattacata ... ttctctgtagAGGGTGCAAGAACTGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACC
EST: gi|149097331|gb|EE183163.2|EE183163
EST:     TGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAG                         AGGGTGCAAGAACTGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACC
genomic: TGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAGgtattacata ... ttctctgtagAGGGTGCAAGAACTGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACC
EST: gi|78092728|gb|DV521102.1|DV521102
EST:     GCATTTATGGAGTTCTCTGATGAAG                         AGGGTGCAAGAACTGCACTTAACCTGGGAGGCACAATTTTTGGTTTCTACC
genomic: GCATTTATTGAGTTCTCTGATGAAGgtattacata ... ttctctgtagAGGGTGCAAGAACTGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACC
EST: gi|149096648|gb|EE182414.2|EE182414
EST:     TGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAG                         AGGGTGCAAGAACTGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACC
genomic: TGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAGgtattacata ... ttctctgtagAGGGTGCAAGAACTGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACC

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), 49 (downstream exon)
Score: 65

GTTGTTGATTGCAGAATTTGTGGTGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAGgtattacata ... ttctctgtagAGGGTGCAAGAACTGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 105

GTTGTTGATTGCAGAATTTGTGGTGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAGgtattacata ... ttctctgtagAGGGTGCAAGAACTGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 108

GTTGTTGATTGCAGAATTTGTGGTGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAGgtattacata ... ttctctgtagAGGGTGCAAGAACTGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 84

GTTGTTGATTGCAGAATTTGTGGTGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAGgtattacata ... ttctctgtagAGGGTGCAAGAACTGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttctgtaatcaatcttcttttgatgaattttgggttccattttctctgtagAGGGTGCAAGAACTGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAA
                     ttttgat  putative branch site (score: 84)
                                      ttccattttctctgt  putative PPT
                     ttttgatgaatttt  TA-rich tract