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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcttctccgcccctagctgtcgatcgatcgatagattattcgattatacgatcgccgaatttggtggtgttcttttttttttttttgggtctactcgtcgatctgagccgtgagggtttgttgcgagattggcgtgctgtgttgtggggtggtgttgattttttgtgtttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG

Basic information

species Oryza sativa
transcript LOC_Os08g09240.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g09240.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G134613_T07 (Zea mays), 3'ss of exon 1
gtaagtcttctccgcccctagctgtcgatcgatcgatagattattcgattatacgatcgccgaatttggtggtgttcttttttttttttttgggtctactcgtcgatctgagccgtgagggtttgttgcga-gattgg-cgtgctgtgttgtggggtggtgttgattttttgtgtttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG-----------
                                                                 |  | |  |  |    |   |   || | | |  ||||    ||   ||| |     | ||| |   ||   | ||  | |  || |    || |   | |   || | | ||||          ||   |  ||  | | |||   |||  | |   |||||||||||| ||||||||| ||||||||||  |||           
----------------------------------------------------------------gtgagcgccggccaccgtcaatcgattcgatttgatcgttccccttccccgcgcctcctcgttcccctgaccagtcgccccgattttttttctgttccagGTCGCTTCTCTCTGTTC------CGCGTGCGATCGAGTAGATCAAA--AGGAGGAGGAGGATGGCGAGGAGTTCGTTCAAGTTGGAGCACCCCTTCGGTTCGTCTCTC

upper sequence: LOC_Os08g09240.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G134613_T03 (Zea mays), 3'ss of exon 1
gtaagtcttctccgcccctagctgtcgatcgatcgatagattattcgattatacgatcgccgaatttggtggtgttcttttttttttttttgggtctactcgtcgatctgagccgtgagggtttgttgcga-gattgg-cgtgctgtgttgtggggtggtgttgattttttgtgtttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG
||||  |  |  | |    ||| | ||||| | |  |   |   || ||    | |||       |  | |  |  |    |   |   || | | |  ||||    ||   ||| |     | ||| |   ||   | ||  | |  || |    || |   | |   || | | ||||          ||   |  ||  | | |||   |||  | |   |||||||||||| ||||||||| ||||||||||  |||
gtaatcccacgtc-ctatcagccgccgatccagccttgcttccatccatccatccatccatctcgtgagcgccggccaccgtcaatcgattcgatttgatcgttccccttccccgcgcctcctcgttcccctgaccagtcgccccgattttttttctgttccagGTCGCTTCTCTCTGTTC------CGCGTGCGATCGAGTAGATCAAA--AGGAGGAGGAGGATGGCGAGGAGTTCGTTCAAGTTGGAGCACCCCTTCG

upper sequence: LOC_Os08g09240.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G134613_T05 (Zea mays), 3'ss of exon 1
gtaagtcttctccgcccctagctgtcgatcgatcgatagattattcgattatacgatcgccgaatttggtggtgttcttttttttttttttgggtctactcgtcgatctgagccgtgagggtttgttgcga-gattgg-cgtgctgtgttgtggggtggtgttgattttttgtgtttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG
                                                                 |  | |  |  |    |   |   || | | |  ||||    ||   ||| |     | ||| |   ||   | ||  | |  || |    || |   | |   || | | ||||          ||   |  ||  | | |||   |||  | |   |||||||||||| ||||||||| ||||||||||  |||
----------------------------------------------------------------gtgagcgccggccaccgtcaatcgattcgatttgatcgttccccttccccgcgcctcctcgttcccctgaccagtcgccccgattttttttctgttccagGTCGCTTCTCTCTGTTC------CGCGTGCGATCGAGTAGATCAAA--AGGAGGAGGAGGATGGCGAGGAGTTCGTTCAAGTTGGAGCACCCCTTCG

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|55434634|gb|CV730441.1|CV730441
EST:     GCCGCCGCGATCCCCAATCCGATCTC                         GAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
genomic: GCCGCCGCGATCCCCAATCCGATCTCgtaagtcttc ... ttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
EST: gi|55436298|gb|CV731287.1|CV731287
EST:     GCCGCCGCGATCCCCAATCCGATCTC                         GAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
genomic: GCCGCCGCGATCCCCAATCCGATCTCgtaagtcttc ... ttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
EST: gi|58590250|gb|CF988558.1|CF988558
EST:     TCCTCCTCCTCCTCCGCCGCGATCCCCAATCCGATCTC                         GAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
genomic: TCCTCCTCCTCCGCCGCCGCGATCCCCAATCCGATCTCgtaagtcttc ... ttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
EST: gi|218487512|gb|FG953689.1|FG953689
EST:     GCCGCGATCCCCAATCCGATCTC                         GAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
genomic: GCCGCGATCCCCAATCCGATCTCgtaagtcttc ... ttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
EST: gi|25802781|gb|CA758742.1|CA758742
EST:     GCCGCCGCGATCCCCAATCCGATCTC                         GAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
genomic: GCCGCCGCGATCCCCAATCCGATCTCgtaagtcttc ... ttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
EST: gi|88721866|gb|CI743378.1|CI743378
EST:     GCCGCCGCGATCCCCAATCCGATCTC                         GAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
genomic: GCCGCCGCGATCCCCAATCCGATCTCgtaagtcttc ... ttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
EST: gi|88428393|gb|CI564861.1|CI564861
EST:     GCCGCCGCGATCCCCAATCCGATCTC                         GAAAGGTATTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
genomic: GCCGCCGCGATCCCCAATCCGATCTCgtaagtcttc ... ttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
EST: gi|58695129|gb|CK083816.1|CK083816
EST:     GCCGCGATCCCCAATCCGATCTC                         GAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
genomic: GCCGCGATCCCCAATCCGATCTCgtaagtcttc ... ttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
EST: gi|88963125|gb|CI026798.1|CI026798
EST:     CGATCCCCAATCCGATCTC                         GAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
genomic: CGATCCCCAATCCGATCTCgtaagtcttc ... ttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
EST: gi|33671347|gb|CF299586.1|CF299586
EST:     ATCCCCAATCCGATCTC                         GAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
genomic: ATCCCCAATCCGATCTCgtaagtcttc ... ttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
EST: gi|58593892|gb|CF992200.1|CF992200
EST:     CGCGATCCCCAATCCGATCTG                         GGGAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
genomic: CGCGATCCCCAATCCGATCTCgtaagtcttc ... ttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
EST: gi|55431390|gb|CV728708.1|CV728708
EST:     GCCGCCGCGATCCCCAATCCGATCTC                         GAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
genomic: GCCGCCGCGATCCCCAATCCGATCTCgtaagtcttc ... ttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
EST: gi|218486561|gb|FG954049.1|FG954049
EST:     GCCGCGATCCCCAATCCGATCTC                         GAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
genomic: GCCGCGATCCCCAATCCGATCTCgtaagtcttc ... ttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
EST: gi|163926759|gb|EG715047.1|EG715047
EST:     AATCCGATCTC                         GAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
genomic: AATCCGATCTCgtaagtcttc ... ttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
EST: gi|33682438|gb|CF310677.1|CF310677
EST:     GCCGCCGCGATCCCCAATCCGATCTC                         GAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
genomic: GCCGCCGCGATCCCCAATCCGATCTCgtaagtcttc ... ttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
EST: gi|87012764|gb|CI295208.1|CI295208
EST:     GCCGCCGCGATCCCCAATCCGATCTC                         GAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
genomic: GCCGCCGCGATCCCCAATCCGATCTCgtaagtcttc ... ttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
EST: gi|88424094|gb|CI689796.1|CI689796
EST:     GCCGCCGCGATCCCCAATCCGATCTC                         GAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
genomic: GCCGCCGCGATCCCCAATCCGATCTCgtaagtcttc ... ttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
EST: gi|58599898|gb|CK010426.1|CK010426
EST:     GCCGCGATCCCCAATCCGATCTC                         GAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC
genomic: GCCGCGATCCCCAATCCGATCTCgtaagtcttc ... ttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgagattggcgtgctgtgttgtggggtggtgttgattttttgtgtttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG
                             tgttgat  putative branch site (score: 4)
                                            tttgttt  putative PPT
                               ttgatttttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcttctccgcccctagctgtcgatcgatcgatagattattcgattatacgatcgccgaatttggtggtgttcttttttttttttttgggtctactcgtcgatctgagccgtgagggtttgttgcgagattggcgtgctgtgttgtggggtggtgttgattttttgtgtttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA