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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgcagtccccatagttgggttgtgttgactactattacacttttgacctcttttcaatacctaaaacagGGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAG

Basic information

species Zea mays
transcript GRMZM2G086489_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086489_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g55960.1 (Oryza sativa), 3'ss of exon 4
gtttgtgcagtccccatagttgggttgtgttgac-tact---attacactttt----gacctcttt-tcaataccta------aaacagGGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAG
|| |||  ||||    |   |   ||  |||||| || |   | |||| | ||    || ||| || | |||   |       || ||||| || || |||||||| ||| | ||||||||||| |||| | |||||||||| ||||| ||||| || || || |||||||||
gtgtgtaaagtcattttgactccatttcgttgacatattctaactacattattttatgatctccttattaatttttggcattgaagcagGGGAAGGAAAAGGAAGTCTGGCTTAAGGATCTTAAGTATGCTGTTTTTGGCCTGGGAAATAGGCAGTATGAGCACTTTAATAAG
















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|148941319|gb|EC886225.2|EC886225
EST:     ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAG                         GGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGC
genomic: ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAGgtttgtgcag ... cctaaaacagGGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGC
EST: gi|22472411|gb|BU036891.1|BU036891
EST:     ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAG                         GGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGC
genomic: ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAGgtttgtgcag ... cctaaaacagGGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGC
EST: gi|148961269|gb|EE011991.2|EE011991
EST:     ATGGGGAGCCAACTGATAATGCAGCACGATTCTACCAATGGTTTACTGAG                         GGGAAAAGAGAAGGAAGTTTGGGTGAAGGATCTTAAATATGGTATTTTTGG
genomic: ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAGgtttgtgcag ... cctaaaacagGG-AAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGG
EST: gi|26558402|gb|CA830637.1|CA830637
EST:     ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAG                         GGAAAAGAGAAGGAAGTTTGGGTGAAGGATCCTTAAATATGGTATTTTTGG
genomic: ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAGgtttgtgcag ... cctaaaacagGGAAAAGAGAAGGAAGTTTGGTTGAAGGATC-TTAAATATGGTATTTTTGG
EST: gi|22541992|gb|BU092430.1|BU092430
EST:     ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAG                         GGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGC
genomic: ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAGgtttgtgcag ... cctaaaacagGGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGC
EST: gi|211095653|gb|FK967022.1|FK967022
EST:     ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAG                         GGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGC
genomic: ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAGgtttgtgcag ... cctaaaacagGGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGC
EST: gi|211098118|gb|FK967027.1|FK967027
EST:     ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAG                         GGAAAAGAGAAGGCAGTTTGGGTTGAAGGATCTTAAATAATGGGTATTTTT
genomic: ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAGgtttgtgcag ... cctaaaacagGGAAAAGAGAAGGAAGTTTGG-TTGAAGGATCTTAAATA-TGG-TATTTTT
EST: gi|148940766|gb|EC885587.2|EC885587
EST:     ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAG                         GGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGC
genomic: ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAGgtttgtgcag ... cctaaaacagGGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGC
EST: gi|148970820|gb|EE021584.2|EE021584
EST:     ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAG                         GGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGC
genomic: ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAGgtttgtgcag ... cctaaaacagGGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGC
EST: gi|19437265|gb|BM953675.1|BM953675
EST:     ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAG                         GGTAATGTGATGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGC
genomic: ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAGgtttgtgcag ... cctaaaacagGGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGC

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: 558

ATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAGgtttgtgcag ... cctaaaacagGGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 743

ATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAGgtttgtgcag ... cctaaaacagGGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 648

ATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAGgtttgtgcag ... cctaaaacagGGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1397

ATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAGgtttgtgcag ... cctaaaacagGGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgggttgtgttgactactattacacttttgacctcttttcaatacctaaaacagGGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAG
                                            acctaaa  putative branch site (score: 1397)
                                    ttttcaata  TA-rich tract