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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaagtcttataatatgaaacggaggaagtacttggtttcactagttcgtagttataagttttactaccaaaatacttaatctttctcgtcaacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG

Basic information

species Oryza sativa
transcript LOC_Os03g62640.5
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G069916_T04 (Zea mays), 3'ss of exon 4
---gaaagtcttataatatgaaacggaggaagtacttggtttcactagttcgtagttataagttttactaccaaaatacttaatctttctcgtcaacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG
    |  |     | |  || |    | |||  | | | || ||   ||    | ||       | | || |   | | |   || ||    |  ||    |||||||||||||| ||||||||| ||||| ||| ||  |||||| ||||||||  ||||| ||||||| ||||| ||||||
ctatactgcaccgtcacttgtatattaagaaa-aatggcttccatgggtgacaaattggtgaactaaatatcgtcaaattc--tcattgaaatgtactgtcagATTTTGAAGGGAGAACTGATGACAAAATAAAGGCCCAGGAAGTAGTGGAAGAGCTAAGAGCTAAAAGAGCTGATATGCAG

upper sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G118014_T02 (Zea mays), 3'ss of exon 4
gaaagtcttataatatgaaacggaggaagtac---ttggtttca----ctagttcgtagttataagttttactaccaaaatacttaatctttctcgtcaacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG
    |||| || |  |||||   ||  | | |   ||||  |||      || |   | ||      || | || ||  | | |   || ||    |  ||    |||||||||||||| ||||||||||||||| ||| ||  |||||| ||||||||| | ||| ||||||| ||||| ||||||
----gtctgatta-gtgaaatatagatattgcaatttggcctcaagtttaagctgcaaattgccgaattgattatcatcaaattc--tcattgaaatgtactgacagATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAG
















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|29681220|gb|CB677495.1|CB677495
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|88689613|gb|CI733189.1|CI733189
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29674744|gb|CB671019.1|CB671019
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29621718|gb|CB626729.1|CB626729
EST:     GTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgtagttataagttttactaccaaaatacttaatctttctcgtcaacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG
                             acttaat  putative branch site (score: 4)
                                   tctttctcgtc  CT-rich tract
                        aaaatacttaatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaagtcttataatatgaaacggaggaagtacttggtttcactagttcgtagttataagttttactaccaaaatacttaatctttctcgtcaacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA