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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttttgtagtttttgcactctactagcctgattcaaggtatacttaatttttatgttgtatatacttttttgcagATGGACCTTTTATACAAGGGAACTATGCGAGTTCTGCTTGTACTACTGCATGACTTTCCTGAATTTCTTTGTGATTATCACTTCAGTTTCTGCGATGTGA

Basic information

species Zea mays
transcript GRMZM2G065130_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065130_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 36
gtaa-gtttttgt----------agtttttgcactcta---ctagcctgattcaaggtatacttaatttttatgttgtatatacttttttgcagATGGACCTTTTATACAAGGGAACTATGCGAGTTCTGCTTGTACTACTGCATGACTTTCCTGAATTTCTTTGTGATTATCACTTCAGTTTCTGCGATGTGA
||||  |||||||          ||  ||  | ||  |   ||    || ||     |   |  | || |||| |  | | | |||||    |||||   ||| | ||||| ||||||||| | || || ||| |||||||||||||||||||||||||||| ||  |||| |||||||||||||| ||  |||
gtaatatttttgtctctaaactaagcattatcgcttcagttcttatatgtttttcttttgccccagttcttatatgtttttttcttttccatagATGTGTCTTATGTACAAAGGAACTATGAGGGTGCTACTTATACTACTGCATGACTTTCCTGAATTTCTGTGCAATTACCACTTCAGTTTCTGTGACATGA
















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|211183840|gb|FL001297.1|FL001297
EST:     TTCTCAAGTTCATGGAACCATATCTGAGAAATGCTGAACTCCCAGAGGCG                         ATGGACCTTTTATACAAGGGAACTATGCGAGTTCTGCTTGTACTACTGCAT
genomic: TTCTCAAGTTCATGGAACCATATCTGAGAAATGCTGAACTCCCAGAGGCGgtaagttttt ... ttttttgcagATGGACCTTTTATACAAGGGAACTATGCGAGTTCTGCTTGTACTACTGCAT
EST: gi|211183842|gb|FL001299.1|FL001299
EST:     TTCTCAAGTTCATGGAACCATATCTGAGAAATGCTGAACTCCCAGAGGCG                         ATGGACCTTTTATACAAGGGAACTATGCGAGTTCTGCTTGTACTACTGCAT
genomic: TTCTCAAGTTCATGGAACCATATCTGAGAAATGCTGAACTCCCAGAGGCGgtaagttttt ... ttttttgcagATGGACCTTTTATACAAGGGAACTATGCGAGTTCTGCTTGTACTACTGCAT
EST: gi|74243504|gb|DT651418.1|DT651418
EST:     TTCTCAAGTTCATGGAACCATATCTGAGAAATGCTGAACTCCCAGAGGCG                         ATGGACCTTTTATACAAGGGAACTATGCGAGTTCTGCTTGTACTACTGCAT
genomic: TTCTCAAGTTCATGGAACCATATCTGAGAAATGCTGAACTCCCAGAGGCGgtaagttttt ... ttttttgcagATGGACCTTTTATACAAGGGAACTATGCGAGTTCTGCTTGTACTACTGCAT
EST: gi|211190227|gb|FL310797.1|FL310797
EST:     TTCTCAAGTTCATGGAACCATATCTGAGAAATGCTGAACTCCCAGARGCG                         ATGGACCTTTTATACAAGGGAACTATGCGAGTTCTGCTTGTACTACTGCAT
genomic: TTCTCAAGTTCATGGAACCATATCTGAGAAATGCTGAACTCCCAGAGGCGgtaagttttt ... ttttttgcagATGGACCTTTTATACAAGGGAACTATGCGAGTTCTGCTTGTACTACTGCAT
EST: gi|211183841|gb|FL001298.1|FL001298
EST:     TTCTCAAGTTCATGGAACCATATCTGAGAAATGCTGAACTCCCAGAGGCG                         ATGGACCTTTTATACAAGGGAACTATGCGAGTTCTGCTTGTACTACTGCAT
genomic: TTCTCAAGTTCATGGAACCATATCTGAGAAATGCTGAACTCCCAGAGGCGgtaagttttt ... ttttttgcagATGGACCTTTTATACAAGGGAACTATGCGAGTTCTGCTTGTACTACTGCAT

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: 49 (upstream exon), 49 (downstream exon)
Score: 159

GTGCAATTCACAGAAAGGTTGGCCATTTTTTCAGCGACTGCTTGTTGCTCTTCTCAAGTTCATGGAACCATATCTGAGAAATGCTGAACTCCCAGAGGCGgtaagttttt ... ttttttgcagATGGACCTTTTATACAAGGGAACTATGCGAGTTCTGCTTGTACTACTGCATGACTTTCCTGAATTTCTTTGTGATTATCACTTCAGTTTCTGCGATGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 89

GTGCAATTCACAGAAAGGTTGGCCATTTTTTCAGCGACTGCTTGTTGCTCTTCTCAAGTTCATGGAACCATATCTGAGAAATGCTGAACTCCCAGAGGCGgtaagttttt ... ttttttgcagATGGACCTTTTATACAAGGGAACTATGCGAGTTCTGCTTGTACTACTGCATGACTTTCCTGAATTTCTTTGTGATTATCACTTCAGTTTCTGCGATGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

GTGCAATTCACAGAAAGGTTGGCCATTTTTTCAGCGACTGCTTGTTGCTCTTCTCAAGTTCATGGAACCATATCTGAGAAATGCTGAACTCCCAGAGGCGgtaagttttt ... ttttttgcagATGGACCTTTTATACAAGGGAACTATGCGAGTTCTGCTTGTACTACTGCATGACTTTCCTGAATTTCTTTGTGATTATCACTTCAGTTTCTGCGATGTGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 80

GTGCAATTCACAGAAAGGTTGGCCATTTTTTCAGCGACTGCTTGTTGCTCTTCTCAAGTTCATGGAACCATATCTGAGAAATGCTGAACTCCCAGAGGCGgtaagttttt ... ttttttgcagATGGACCTTTTATACAAGGGAACTATGCGAGTTCTGCTTGTACTACTGCATGACTTTCCTGAATTTCTTTGTGATTATCACTTCAGTTTCTGCGATGTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactagcctgattcaaggtatacttaatttttatgttgtatatacttttttgcagATGGACCTTTTATACAAGGGAACTATGCGAGTTCTGCTTGTACTACTGCATGACTTTCCTGAATTTCTTTGTGATTATCACTTCAGTTTCTGCGATGTGA
                     acttaat  putative branch site (score: 80)
                                          tactttttt  putative PPT
                  tatacttaatttttat  TA-rich tract