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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtggcagtcaatgtattgtacatttgtacagtagtatgttgaacagttaggaaaagttgaatttcaagttaaatcatcacacttcaatagttgaattgattgaattcacgcagGCAAACTCCTACTGGCTTTACATTGTGCCATGGGGAATCAACAAGGCTGTGACCTATGTAAAGGAAACATATGGAAACCCTACAATGATCCTTTCTGAAA

Basic information

species Oryza sativa
transcript LOC_Os07g46280.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g46280.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G148176_T01 (Zea mays), 3'ss of exon 9
gtaagtggcagtcaatgtattg-tacatttgtacagtagtatgttgaacagttaggaaaagttgaatttcaagttaaatcatcacacttcaatagttgaattgattgaattcacgcagGCAAACTCCTACTGGCTTTACATTGTGCCATGGGGAATCAACAAGGCTGTGACCTATGTAAAGGAAACATATGGAAACCCTACAATGATCCTTTCTGAAA
          || | |||| || || || | | |||    | || ||| ||    | |||||||   ||    |   || ||   |||      ||  | ||  ||||  ||  | ||||||||||||||||||| ||||||||||| ||||| |||||||||||||| | |||||| |||||||| ||   ||| ||||||||||||||| ||||||
----------gtaagtgtactgctagatgtcttcag----acgtcgaa-agc--aggaaagttgg--tttgcctctgattatggtact------gtaaatttctttgagctc-tgtagGCAAACTCCTACTGGCTGTACATTGTGCCGTGGGGCATCAACAAGGCTGTCAGCTATGTCAAGGAAACTTACAAAAATCCTACAATGATCCTTGCTGAAA

upper sequence: LOC_Os07g46280.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv14s0006g01790.t01 (Vitis vinifera), 3'ss of exon 9
gtaagtggcagtcaatgtattgtacatttgtacagtagtatgttgaacagttaggaaaagttg--aatttcaagttaaatcatcacacttcaatagttgaattgattgaattcacgcagGCAAACTCCTACTGGCTTTACATTGTGCCATGGGGAATCAACAAGGCTGTGACCTATGTAAAGGAAACATATGGAAACCCTACAATGATCCTTTCTGAAA
                                  ||| |   |  |  |  ||  |  |  ||  |||| | | ||| |||  ||  | | |        |   | || ||     ||||||||||| |  |||||||||||||| |||||||| ||  ||||| |||||||||| || |||||    |||||||||||  | || ||| | || ||||
----------------------------------gtaatgcttatatgatctataactatctgttaattcctacttatatctacattccttat------gaccaactgtatgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTGACCTACGTGAAGGAGCAGTATGGAAACCCACCTATAATCATCTCAGAAA
















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|29674578|gb|CB670853.1|CB670853
EST:     ATGAACGAAACGGCGTGCCCATTGGAGCTCAA                         GCAAACTCCTACTGGCTTTACATTGTGCCATGGGGAATCAACAAGGCTGTG
genomic: ATGAACGAAACGGCGTGCCCATTGGAGCTCAAgtaagtggca ... attcacgcagGCAAACTCCTACTGGCTTTACATTGTGCCATGGGGAATCAACAAGGCTGTG
EST: gi|86501599|gb|CI144232.1|CI144232
EST:     ATGAACGAAACGGCGTGCCCATTGGAGCTCAA                         GCAAACTCCTACTGGCTTTACATTGTGCCATGGGGAATCAACAAGGCTGTG
genomic: ATGAACGAAACGGCGTGCCCATTGGAGCTCAAgtaagtggca ... attcacgcagGCAAACTCCTACTGGCTTTACATTGTGCCATGGGGAATCAACAAGGCTGTG
EST: gi|29664413|gb|CB660688.1|CB660688
EST:     ATGAACGAAACGGCGTGCCCATTGGAGCTCAA                         GCAAACTCCTACTGGCTTTACATTGTGCCATGGGGAATCAACAAGGCTGTG
genomic: ATGAACGAAACGGCGTGCCCATTGGAGCTCAAgtaagtggca ... attcacgcagGCAAACTCCTACTGGCTTTACATTGTGCCATGGGGAATCAACAAGGCTGTG
EST: gi|163920879|gb|EG710090.1|EG710090
EST:     ATGAACGAAACGGCGTGCCCATTGGAGCTCAA                         GCAAACTCCTACTGGCTTTACATTGTGCCATGGGGAATCAACAAGGCTGTG
genomic: ATGAACGAAACGGCGTGCCCATTGGAGCTCAAgtaagtggca ... attcacgcagGCAAACTCCTACTGGCTTTACATTGTGCCATGGGGAATCAACAAGGCTGTG
EST: gi|29665570|gb|CB661845.1|CB661845
EST:     ATGAACGAAACGGCGTGCCCATTGGAGCTCAA                         GCAAACTCCTACTGGCTTTACATTGTGCCATGGGGAATCAACAAGGCTGTG
genomic: ATGAACGAAACGGCGTGCCCATTGGAGCTCAAgtaagtggca ... attcacgcagGCAAACTCCTACTGGCTTTACATTGTGCCATGGGGAATCAACAAGGCTGTG
EST: gi|29642036|gb|CB647043.1|CB647043
EST:     ATGAACGAAACGGCGTGCCCATTGGAGCTCAA                         GCAAACTCCTACTGGCTTTACATTGTGCCATGGGGAATCAACAAGGCTGTG
genomic: ATGAACGAAACGGCGTGCCCATTGGAGCTCAAgtaagtggca ... attcacgcagGCAAACTCCTACTGGCTTTACATTGTGCCATGGGGAATCAACAAGGCTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatttcaagttaaatcatcacacttcaatagttgaattgattgaattcacgcagGCAAACTCCTACTGGCTTTACATTGTGCCATGGGGAATCAACAAGGCTGTGACCTATGTAAAGGAAACATATGGAAACCCTACAATGATCCTTTCTGAAA
                                   aattgat  putative branch site (score: 4)
       aagttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtggcagtcaatgtattgtacatttgtacagtagtatgttgaacagttaggaaaagttgaatttcaagttaaatcatcacacttcaatagttgaattgattgaattcacgcagGCAAACTCCTACTGGCTTTACATTGTGCCATGGGGAATCAACAAGGCTGTGACCTATGTAAAGGAAACATATGGAAACCCTACAATGATCCTTTCTGAAA

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