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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcacccatatttagctataggcatgcttgtttcgaatcagatcgacatgctgcagatgccacgcgtgtcttttaacaatgcgcaatcggcaatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTTGATGAGATGAATATGGGAGGAGGAGGAGGTGGTGGTTTCAATCCTTTTG

Basic information

species Oryza sativa
transcript LOC_Os02g10180.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10180.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G341404_T01 (Zea mays), 3'ss of exon 9
gtcacccatatttagctataggcatgcttgtttcgaatcagatcgacatgctgcag-atgccacgcgtgtcttttaaca-atgcgcaatcggcaatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTTGATGAGATGAATATGGGAGGAGGAGGAGGTGGTGGTTTCAATCCTTTTG------
   ||    ||||   |   ||  | |  | |  |    |  | |    |||| |   |     |||     |||  || | ||     | |||  |  ||||| ||||| || ||||| ||||||||||| || ||||| ||||||||| | || ||||||||||||||||| ||       ||||| |||||||||||||      
-atacaatcattttttttatggttttccggctctgtga-atgttgtttcgctggaatgtattgtgcgatatgtttgtcacaagcttctgctgcatgtgtcagGTGCTTGGTGATGAAGACAAACGTGTAAGGTATGACCGTGGAGAGGATGTGGAGGAGATGAATATGGGAGGCGGG------GGTGGCTTCAATCCTTTTGGGGGAG
















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|29663962|gb|CB660237.1|CB660237
EST:     AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtataaataa ... caatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|86880441|gb|CI320964.1|CI320964
EST:     AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTTCTGCAGCTTATGAG                         GTTCTTGGGGACGAAAATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtataaataa ... caatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|9864967|gb|AU100717.1|AU100717
EST:     AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtataaataa ... caatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|29624026|gb|CB629037.1|CB629037
EST:     AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtataaataa ... caatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|29685030|gb|CB681305.1|CB681305
EST:     AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtataaataa ... caatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|29624027|gb|CB629038.1|CB629038
EST:     AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtataaataa ... caatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|86483054|gb|CI125687.1|CI125687
EST:     GAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: GAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtataaataa ... caatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|86483785|gb|CI126418.1|CI126418
EST:     AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtataaataa ... caatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|29664003|gb|CB660278.1|CB660278
EST:     AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtataaataa ... caatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|58676081|gb|CK064768.1|CK064768
EST:     AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtataaataa ... caatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|88252236|gb|CI350664.1|CI350664
EST:     CAGCTTATGAG                         GTTCTTGGGGACGAAGATAAACGTGTAAAATACGACCGAGGAGAGGATCTT
genomic: CAGCTTATGAGgtataaataa ... caatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|88977922|gb|CI384404.1|CI384404
EST:     GAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGA-GAGAGGATCTT
genomic: GAAATTGCTGCAGCTTATGAGgtataaataa ... caatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|86257357|gb|CI004175.1|CI004175
EST:     AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTACAGCTTATGAG                         GTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtataaataa ... caatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|88960634|gb|CI382315.1|CI382315
EST:     GTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: GTTTCGAGAAATTGCTGCAGCTTATGAGgtataaataa ... caatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|88436919|gb|CI523869.1|CI523869
EST:     GCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: GCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtataaataa ... caatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|88993084|gb|CI108712.1|CI108712
EST:     AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtataaataa ... caatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|88961527|gb|CI096808.1|CI096808
EST:     AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtataaataa ... caatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|2310241|gb|C26396.1|C26396
EST:     AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGACGAAGATAAACGTGTAAGATACGGCCGAGGAGAGG-TCTT
genomic: AGCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtataaataa ... caatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgctgcagatgccacgcgtgtcttttaacaatgcgcaatcggcaatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTTGATGAGATGAATATGGGAGGAGGAGGAGGTGGTGGTTTCAATCCTTTTG
                         ttttaac  putative branch site (score: 2)
                         ttttaacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcacccatatttagctataggcatgcttgtttcgaatcagatcgacatgctgcagatgccacgcgtgtcttttaacaatgcgcaatcggcaatttgcagGTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTTGATGAGATGAATATGGGAGGAGGAGGAGGTGGTGGTTTCAATCCTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG