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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcctgaactagattgctctttgtccagcaaacaatactataaaattttcatagcacttggaatgtccttctgtctcctgagcctgtttataatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAAGAGGAAAGAAGAAATGAAAGCAAGAGAAGCTCAGAGTCGGGCGGCTGCA

Basic information

species Oryza sativa
transcript LOC_Os01g46510.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g46510.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM5G824843_T01 (Zea mays), 3'ss of exon 2
ttcctgaactagattgctctttgtccagcaaacaatactataaaattttcata----------gcacttggaatgtccttctgtctcctgagcctgtttataatat---ccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAAGAGGAAAGAAGAAATGAAAGCAAGAGAAGCTCAGAGTCGGGCGGCTGCA
        |||| |||     |||| ||| ||||||  | | || |||| ||           || |  |||    ||||||||  | ||| | |||  | ||| |   |||||||||||||||||||||| || ||||| || ||||||||||||||||||| ||  ||| |||||||||||||||||||||||||||||||||| |||| |
--------ctaggttg-----tgtcaagcgaacaatgttttcaacttttgatgatggcagatggctcaaggacacgccttctgttccttgatcttgtaaacaatgtttcccagGTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAGGATAAAACAAGAAATGAAAGCAAGAGAAGCTCAGAGTCGGGCAGCTGAA
















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|58662672|gb|CK051358.1|CK051358
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGACATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|58664662|gb|CK053348.1|CK053348
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|58666107|gb|CK054793.1|CK054793
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|58666827|gb|CK055513.1|CK055513
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|58665271|gb|CK053957.1|CK053957
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|58587152|gb|CF985460.1|CF985460
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|58612809|gb|CK040521.1|CK040521
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|58612142|gb|CK039854.1|CK039854
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTGTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|86889062|gb|CI314678.1|CI314678
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTG
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTG
EST: gi|25804329|gb|CA760290.1|CA760290
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAAC
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAAC
EST: gi|58662716|gb|CK051402.1|CK051402
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|58666361|gb|CK055047.1|CK055047
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAA
EST: gi|88399115|gb|CI603782.1|CI603782
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCAC-ACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|58669479|gb|CK058165.1|CK058165
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcatagcacttggaatgtccttctgtctcctgagcctgtttataatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAAGAGGAAAGAAGAAATGAAAGCAAGAGAAGCTCAGAGTCGGGCGGCTGCA
                                       tgtttataatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcctgaactagattgctctttgtccagcaaacaatactataaaattttcatagcacttggaatgtccttctgtctcctgagcctgtttataatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAAGAGGAAAGAAGAAATGAAAGCAAGAGAAGCTCAGAGTCGGGCGGCTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- cctgaac
- - - - - -gattgct
- - - - - - - - - - - - -cagcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -gcacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagcctg