Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgataatgtttcttatgtcacttagcgagagctcttttaatttatatgtcttcctaattgtgtttcgatttatctccatgcattcacttccaaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g48760.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g48760.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G092152_T01 (Zea mays), 3'ss of exon 1
tgataatgtttcttatgtcacttagc-gagagctcttttaatttatatgtcttcctaattgtgt-ttcgatttatct--ccatgcattcacttcca---aattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG
       |    |||||||||||  | |  | ||  | |  | |  ||  |||    |  |||| || | |||||    |||    ||| |||| |   |||||||||||||||| |||||||||||||||||||||||||| |||||||||||||| || ||||| ||||| |||
-------gaaaattatgtcacttttctggaaacttgtatgctattcatagcttaagtaacgtgtgtttggtttatggagccactttttcgcttctatggaattgcagAAGGGTTCATTTGATGCTGAAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAG
















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|86898820|gb|CI296101.1|CI296101
EST:     GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCG
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCG
EST: gi|88334302|gb|CI642547.1|CI642547
EST:     GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|88762854|gb|CI772410.1|CI772410
EST:     GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|88349798|gb|CI634333.1|CI634333
EST:     GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|88491247|gb|CI428519.1|CI428519
EST:     CGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: CGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|88317589|gb|CI672171.1|CI672171
EST:     GCTCCGTCGAGGTTGTCATCTCGCACAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|88477298|gb|CI414569.1|CI414569
EST:     GCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: GCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|88587859|gb|CI705639.1|CI705639
EST:     GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|88577442|gb|CI674029.1|CI674029
EST:     GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|88665244|gb|CI710078.1|CI710078
EST:     GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|88308803|gb|CI654086.1|CI654086
EST:     GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|25799413|gb|CA755374.1|CA755374
EST:     GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|88210949|gb|CI212589.1|CI212589
EST:     GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|88283283|gb|CI404729.1|CI404729
EST:     CTCCGTCGAGGGTTGTCATCTCGCANAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACANTGACGCTCCAAAGCGAACTT
genomic: CTCCGTCGA-GGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|88580222|gb|CI692224.1|CI692224
EST:     GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|86850381|gb|CI307610.1|CI307610
EST:     GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAAC
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAAC
EST: gi|13165563|gb|AU174360.1|AU174360
EST:     GCTCCGTNGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|88593295|gb|CI709458.1|CI709458
EST:     GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAA
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAA
EST: gi|86417819|gb|CI032028.1|CI032028
EST:     GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|88408609|gb|CI686112.1|CI686112
EST:     GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|88514546|gb|CI442052.1|CI442052
EST:     CAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: CAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|56157672|gb|C25211.2|C25211
EST:     GCTCCGTCGAGGTTGTCATCTCGCAGA-CACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAA
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAA
EST: gi|88290434|gb|CI665223.1|CI665223
EST:     GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|88761851|gb|CI771407.1|CI771407
EST:     GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
EST: gi|88825494|gb|CI776059.1|CI776059
EST:     GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAG                         AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT
genomic: GCTCCGTCGAGGTTGTCATCTCGCAGAGCACTGGTCTGGCCGAGGTTCAGgtgagctcct ... caaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtcttcctaattgtgtttcgatttatctccatgcattcacttccaaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG
      tcctaat  putative branch site (score: 2)
                                     ttcacttcc  putative PPT
                      atttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgataatgtttcttatgtcacttagcgagagctcttttaatttatatgtcttcctaattgtgtttcgatttatctccatgcattcacttccaaattgcagAAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA