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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggcgaattgccgatacccttggaatacaaatttatcagaaaatataatataatccactgtatatttgttttgtggtctcatatcgtccttgttttcagACAGGCAGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACACAACGAGGCGGAGATGTGATCATCGTCCTTGTTGGAAATAAAACAGACCT

Basic information

species Oryza sativa
transcript LOC_Os03g09140.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g09140.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AC166636.1_FGT008 (Zea mays), 3'ss of exon 3
ttggcgaattgccgatacccttggaa-tacaaatttatcagaa--aatataatataatccactgtatatttgttt---tgtggtctcatatc--gtccttgtttt-cagACAGGCAGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACACAACGAGGCGGAGATGTGATCATCGTCCTTGTTGGAAATAAAACAGACCT
           |   ||  |||  |  ||   |||||| |||   | |  | |  ||  | || || || |  |    |   ||||||| ||  ||| || |||| ||||||||||||| || ||||  |  || |||||||| || || ||||| || ||| |||| ||||| ||| ||||| |||| |||||||||||||| |||||
---------cactagtaatcttttagctaactatttattagatctagtgcatttaaacaccctctaaatataatagtatccagtctcatctcatgtcgttcttttgcagACAGGCAGTCATTCTTGAACACGTCAAAGTGGATCGAGGAAGTAAACACGCAAAGAGGTGGAGACGTGCTCATCTTCCTCGTTGGAAATAAAACTGACCT
















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|33682509|gb|CF310748.1|CF310748
EST:     GTGGCAGTGATTGTTTACGATGTGACTG                         ACAGGCAGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACAC
genomic: GTGGCAGTGATTGTTTACGATGTGACTGgcaagttaac ... ttgttttcagACAGGCAGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACAC
EST: gi|16577976|gb|BI812071.1|BI812071
EST:     GCAGTGATTGTTTACGATGTGACTG                         ACA-GCACGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACA
genomic: GCAGTGATTGTTTACGATGTGACTGgcaagttaac ... ttgttttcagACAGGCA-GTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACA
EST: gi|33684735|gb|CF312974.1|CF312974
EST:     AAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTG                         ACAGGCAGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACAC
genomic: AAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTGgcaagttaac ... ttgttttcagACAGGCAGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACAC
EST: gi|33688710|gb|CF316949.1|CF316949
EST:     AAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTG                         ACAGGCAGTCCTTTTTGAGT-TATCGAAGTGGATTGAAGAGGTAAATACAC
genomic: AAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTGgcaagttaac ... ttgttttcagACAGGCAGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACAC
EST: gi|33682508|gb|CF310747.1|CF310747
EST:     AAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTG                         ACAGGCAGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACAC
genomic: AAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTGgcaagttaac ... ttgttttcagACAGGCAGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatataatccactgtatatttgttttgtggtctcatatcgtccttgttttcagACAGGCAGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACACAACGAGGCGGAGATGTGATCATCGTCCTTGTTGGAAATAAAACAGACCT
                                       tcgtccttgttttc  CT-rich tract
              tgtatatttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggcgaattgccgatacccttggaatacaaatttatcagaaaatataatataatccactgtatatttgttttgtggtctcatatcgtccttgttttcagACAGGCAGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACACAACGAGGCGGAGATGTGATCATCGTCCTTGTTGGAAATAAAACAGACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG