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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcctactagttctcaaatcgctgcactgaccaatgttttattcttcttcagctaactctgtagtttctgaacttattcagACAAGAAGAATGAAAACAAGGAGGTCGCCGTGAATGAGGTACTGCCTGTGACCGCTGCTCGGGATGCCATCCAGTATTCCAT

Basic information

species Oryza sativa
transcript LOC_Os01g64670.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64670.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 7
-------------gtatgttcctactagttctcaaatcgctgcactgaccaatgttttat----tcttctt--------cagctaactctgta-gtttctgaacttatt---cagACAAGAAGAATGAAAACAAGGAGGTCGCCGTGAATGAGGTACTGCCTGTGACCGCTGCTCGGGATGCCATCCAGTATTCCAT
                | |||| |  | ||   | ||   |    | |  | |  || ||    | ||| |         |   || |  ||   ||||| ||  ||||   |||||||||||||||| ||||||||||| || || |||||  | || ||||   || ||||    ||  |||||||||| || ||
gtatccttaaaaatcttattccaataacttgatacatgagtttctttaagattacttcatagtattttcataaaaaaaataaaaaattgagtgcatttcttaatatattgatcagACAAGAAGAATGAGAACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCATCCACTGCCGTTGAATCCATCCAGTACTCAAT

upper sequence: LOC_Os01g64670.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA16G01960.1 (Glycine max), 3'ss of exon 5
------------gtatgttcctactagttctcaaatc---gctgcactgaccaatgttttat----tcttcttcagctaactctgtag--tttctgaacttatt----cagACAAGAAGAATGAAAACAAGGAGGTCGCCGTGAATGAGGTACTGCCTGTGACCGCTGCTCGGGATGCCATCCAGTATTCCAT
             | |  | | | ||  | | | | |   | |    | |  | |  |||||    | ||| | |   || |   | |  ||||| ||| ||||    |||||||||||||||| ||||||||||| || || |||||  | || ||||   || |||||   ||  |||||||||| || ||
gtatccttaaaaatcttattccaataactttgatacctaagttttctttaagattactttatagtattttcataaaaaaaattgattgcatttcttaacatatttgatcagACAAGAAGAATGAGAACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCATCCACTGCTGTTGAATCCATCCAGTACTCAAT

upper sequence: LOC_Os01g64670.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 6
gtatgttcctactagttctcaaatcg---ctgcactgaccaatgttttattcttcttcagctaactctgtagtttctga--acttattcagACAAGAAGAATGAAAACAAGGAGGTCGCCGTGAATGAGGTACTGCCTGTGACCGCTGCTCGGGATGCCATCCAGTATTCCAT
   | | | |   |  | |||  ||     | ||   |    ||||       |   ||    ||    |  ||  |||  |   ||||||| || |||||||| ||||||||||| |||||||||||  |  | |||   |   ||||||   | ||  ||||| |||||||
--gtatccttttcatctttcagttcaacctttcatgaaaatttgttaaggggatgaacaatagacaaattttttcttgacaaacaattcagATAAAAAGAATGAGAACAAGGAGGTTGCCGTGAATGATTTCTTACCTTCAAGTTCTGCTCATCAAGCTGTCCAGCATTCCAT

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|218497154|gb|FG952503.1|FG952503
EST:     TGAGCTTTCGCCTCATCGCGTCCAGGAAATCCGGCGTTTCTTTGAAGACT                         ACAAGAAGAATGAAAACAAGGAGGTCGCCGTGAATGAGGTACTTCCTGTGA
genomic: TGAGCTTTCGCCTCATCGCGTCCAGGAAATCCGGCGTTTCTTTGAAGACTgtatgttcct ... acttattcagACAAGAAGAATGAAAACAAGGAGGTCGCCGTGAATGAGGTACTGCCTGTGA
EST: gi|88206464|gb|CI206313.1|CI206313
EST:     GGAAATCCGGCGTTTCTTTGAAGACT                         ACAAGAAGAATGAAAACAAGGAGGTCGCCGTGAATGAGGTACTGCCTGTGA
genomic: GGAAATCCGGCGTTTCTTTGAAGACTgtatgttcct ... acttattcagACAAGAAGAATGAAAACAAGGAGGTCGCCGTGAATGAGGTACTGCCTGTGA
EST: gi|218503045|gb|FG970333.1|FG970333
EST:     TGAGCTTTCGCCTCATCGCGTCCAGGAAATCCGGCGTTTCTTTGAAGACT                         ACAAGACGAGTGAAAACAAGGAGGTCGCCGTGAATGAGGTACTTCCTGTGA
genomic: TGAGCTTTCGCCTCATCGCGTCCAGGAAATCCGGCGTTTCTTTGAAGACTgtatgttcct ... acttattcagACAAGAAGAATGAAAACAAGGAGGTCGCCGTGAATGAGGTACTGCCTGTGA
EST: gi|88250730|gb|CI348960.1|CI348960
EST:     TGAGCTTTCGCCTCATCGCGTCCAGGAAATCCGGCGTTTCTTTGAAGACT                         ACAAGAAGAATGAAAACAAGGAGGTCGCCGTGAATGAGGTACTGCCTGTGA
genomic: TGAGCTTTCGCCTCATCGCGTCCAGGAAATCCGGCGTTTCTTTGAAGACTgtatgttcct ... acttattcagACAAGAAGAATGAAAACAAGGAGGTCGCCGTGAATGAGGTACTGCCTGTGA
EST: gi|218499150|gb|FG960130.1|FG960130
EST:     TGAGCTTTCGCCTCATCGGGTCCAGGAAATCCGGCGTTTCTTTGAAGACT                         ACAAGAAGAATGA
genomic: TGAGCTTTCGCCTCATCGCGTCCAGGAAATCCGGCGTTTCTTTGAAGACTgtatgttcct ... acttattcagACAAGAAGAATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaccaatgttttattcttcttcagctaactctgtagtttctgaacttattcagACAAGAAGAATGAAAACAAGGAGGTCGCCGTGAATGAGGTACTGCCTGTGACCGCTGCTCGGGATGCCATCCAGTATTCCAT
                        agctaac  putative branch site (score: 2)
                                              cttattc  putative PPT
      aatgttttattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttcctactagttctcaaatcgctgcactgaccaatgttttattcttcttcagctaactctgtagtttctgaacttattcagACAAGAAGAATGAAAACAAGGAGGTCGCCGTGAATGAGGTACTGCCTGTGACCGCTGCTCGGGATGCCATCCAGTATTCCAT

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