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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaaggatggaatttcatatttttgccttataattttgaatttggttcacttagtaattcattccatagactaagttcttgtttggatttccaactatagGAACACTTCCTCCAAAGTGTATCCAGCAATGTATATTGAGAATGTGACTGAACTTGCCTTTGATGATATCACACCTGAAGATTTTGATTTTCCATTTATA

Basic information

species Oryza sativa
transcript LOC_Os03g64400.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g64400.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G077222_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------------------------------------------------------------caaaggatggaatttcatattt-ttgccttataattttgaatttggttcacttagtaattcattccatagactaagttcttgtttggatttccaactatagGAACACTTCCTCCAAAGTGTATCCAGCAATGTATATTGAGAATGTGACTGAACTTGCCTTTGATGATATCACACCTGAAGATTTTGATTTTCCATTTATA
                                                                                                   || | | |  |  |   |   | ||||  |  |||||| | ||| | || |||||    | ||||  |  || || || || |   | ||||||  || |||||||||| ||| |||||||||||||||||||||||||| ||||| ||||||||||| ||||| ||| ||||||||||||||  |||||||||||| |||
gtgcatatctattattcctttgtatcagtagacctcccaagtgtttgttgcaaatatgcagtatggtcccatttctcttttgtcctatttcatattcttcatacgtttaaggtcattgcctcttgctgttaaattttcagttttgctctcttaggtgattattctgttaaccaacttattctcgtggtttcca--tacagGAACACTTTCTCAAAAGTGTATCCAGCAATGTATATTGATAATGTCACTGAACTTGCATTTGACGATGTCACACCTGAAGATCCTGATTTTCCATTCATA

upper sequence: LOC_Os03g64400.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G140874_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------------------------------------caaaggatggaatttcatattt-ttgccttataattttgaatttggttcacttagtaattcattccatagactaagttcttgtttggatttccaactatagGAACACTTCCTCCAAAGTGTATCCAGCAATGTATATTGAGAATGTGACTGAACTTGCCTTTGATGATATCACACCTGAAGATTTTGATTTTCCATTTATA
                                                                                                   || | | |  |  |   |   | ||||  |  |||||| | ||| | || |||||    | ||||  |  || |  || || |   | ||||||  || |||||||||| ||| |||||||||| ||||||||||||||| ||||| ||||||||||| ||||| ||| ||||||||||||||  |||||||||||| |||
gtgcatatctattattcctttgtatcagtagacctcccaagtgtttgttgcaaatatgcagtatggtcccatttctcttttgtcatatttcatattcttcatacgtttaaggtcattgcctcttgctgtcaaattttcagttttgctctcttaggtgattattctgttaaccaccttattctcgtggtttcca--tacagGAACACTTTCTCAAAAGTGTATCTAGCAATGTATATTGATAATGTCACTGAACTTGCATTTGACGATGTCACACCTGAAGATCCTGATTTTCCATTCATA

upper sequence: LOC_Os03g64400.4 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G23890.1 (Arabidopsis thaliana), 3'ss of exon 4
-caaaggatgg-aatttcatatttttgccttataattttgaatttggttcacttagtaattcattccatagactaagttcttgtttggatt-tccaactat----agGAACACTTCCTCCAAAGTGTATCCAGCAATGTATATTGAGAATGTGACTGAACTTGCCTTTGATGATATCACACCTGAAGATTTTGATTTTCCATTTATA
  | |   |    ||||  |   | |  ||  |    |  || |    |   |  ||| |  |      |    | |   || | ||  || |  |||| |    || |||||  |||| ||||||||||| || ||||||||||||||||| ||||| ||||| ||||||||||| || || |||||   ||||||| | |  || 
gtatactttcatgattttgttagtgtttctggtggggtcaaaatatccttcgtatgtattagaaagtgaaattcatgcatttatgtgtgttctttaactctttgcagAAACACAACCTCAAAAGTGTATCCTGCTATGTATATTGAGAATGTTACTGAGCTTGCTTTTGATGATATTACTCCCGAAGACCCTGATTTTTCTTCCATT

upper sequence: LOC_Os03g64400.4 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G52410.1 (Arabidopsis thaliana), 3'ss of exon 5
caaaggatggaatttcatatttttgccttataattttgaatttggttcacttagtaattcattccatagactaagttcttgtttggatttcca---actatagGAACACTTCCTCCAAAGTGTATCCAGCAATGTATATTGAGAATGTGACTGAACTTGCCTTTGATGATATCACACCTGAAGATTTTGATTTTCCATTTATA
       |     |  | |  | |   |  || | |||||        || | || |   ||| ||  | || |   | ||     || | ||     ||||||||| |  | || ||||| ||||| || |||||||| || ||||| ||||||||||| ||||||||||| ||||||||||||  |||||||||||| || 
------gtaactatcaaaaaatctctttcctactcttgaa--------acattgtgaaatatttcactgccttacaacgtgaaaatatcttcattggttatagGAACTCAGCATCAAAAGTATATCCTGCCATGTATATAGAAAATGTTACTGAACTTGCATTTGATGATATTACACCTGAAGATCCTGATTTTCCATTCATT

upper sequence: LOC_Os03g64400.4 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 5
caaaggatggaatttcatatttttgccttataattttgaatttgg-ttcac-ttagtaattcattccata-gactaagttcttgtttggatttccaactatagGAACACTTCCTCCAAAGTGTATCCAGCAATGTATATTGAGAATGTGACTGAACTTGCCTTTGATGATATCACACCTGAAGATTTTGATTTTCCATTTATA
|    | | | |      ||      || |    |   ||  |   ||||| || |   || ||  |||  || |||    || | |  ||| |    | |||||| ||    || || || |||||||| ||||| || |  ||| | ||||||||||| ||||||||||| |||||||||||   ||||||| |||  || 
ctgtagcttgtagagtgcatcagcatctgaaggctaccaacataaattcacattggatgttgataacatgtgattaataatttctatccattcct---tgtagGAATACAGTTTCAAAGGTATATCCAGCTATGTACATAGGAAATATTACTGAACTTGCATTTGATGATATTACACCTGAAGACCCTGATTTTTCATCCATT

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|58689870|gb|CK078557.1|CK078557
EST:     CGACGAGAATACGCTCGATGGTTGGTGGTCGCAAGCAATTGTCTATCCAG                         GAACACTTCCTCCAAAGTGTATCCAGCAATGTATATTGAGAATGTGACTGA
genomic: CGACGAGAATACGCTCGATGGTTGGTGGTCGCAAGCAATTGTCTATCCAGgtgcttactt ... ccaactatagGAACACTTCCTCCAAAGTGTATCCAGCAATGTATATTGAGAATGTGACTGA
EST: gi|58669049|gb|CK057735.1|CK057735
EST:     AAGCAATTGTCTATCCAG                         GAACACTTCCTCCAAAGTGTATCCAGCAATGTATATTGAGAATGTGACTGA
genomic: AAGCAATTGTCTATCCAGgtgcttactt ... ccaactatagGAACACTTCCTCCAAAGTGTATCCAGCAATGTATATTGAGAATGTGACTGA
EST: gi|58669849|gb|CK058535.1|CK058535
EST:     CGACGAGAATACGCTCGATGGTTGGTGGTCGCAAGCAATTGTCTATCCAG                         GAACACTTCCTCCAAAGTGTATCCAGCAATGTATATTGAGAATGTGACTGA
genomic: CGACGAGAATACGCTCGATGGTTGGTGGTCGCAAGCAATTGTCTATCCAGgtgcttactt ... ccaactatagGAACACTTCCTCCAAAGTGTATCCAGCAATGTATATTGAGAATGTGACTGA
EST: gi|58611882|gb|CK039594.1|CK039594
EST:     CGACGAGAATACGCTCGATGGTTGGTGGTCGCAAGCAATTGTCTATCCAG                         GAACACTTCCTCCAAAGTGTATCCAGCAATGTATATTGAGAATGTGACTGA
genomic: CGACGAGAATACGCTCGATGGTTGGTGGTCGCAAGCAATTGTCTATCCAGgtgcttactt ... ccaactatagGAACACTTCCTCCAAAGTGTATCCAGCAATGTATATTGAGAATGTGACTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacttagtaattcattccatagactaagttcttgtttggatttccaactatagGAACACTTCCTCCAAAGTGTATCCAGCAATGTATATTGAGAATGTGACTGAACTTGCCTTTGATGATATCACACCTGAAGATTTTGATTTTCCATTTATA
                                          tttcc  CT-rich tract
     ttagtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaaggatggaatttcatatttttgccttataattttgaatttggttcacttagtaattcattccatagactaagttcttgtttggatttccaactatagGAACACTTCCTCCAAAGTGTATCCAGCAATGTATATTGAGAATGTGACTGAACTTGCCTTTGATGATATCACACCTGAAGATTTTGATTTTCCATTTATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - -tttttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattcca