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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgttttgagaggattaaagaatgtttgatatgtgattttttactgttggtagtgagtgatgtgaaacgtaaaagtgacgctgctttgttcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGCGCTGGAGCTGGCAATGATACCACTGCAGCTGGAGTTCTTGCTGACATAC

Basic information

species Oryza sativa
transcript LOC_Os12g03190.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03190.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G151977_T01 (Zea mays), 3'ss of exon 11
tctgttttgagaggattaaagaatgtttgatatgtgattttttactgtt-ggtagtgagtgatgtgaaacgtaaaagtgacgctgctttgttct-tgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGCGCTGGAGCTGGCAATGATACCACTGCAGCTGGAGTTCTTGCTGACATAC
        |  | | |       | | |  ||| |  | | |     || |||  |   || | ||| |  | | ||  |      | ||| ||     ||||| ||||||||||||||||| ||| ||||| ||||||||||||| |||||||| ||||||||||| || |||||||| || || || |||||||||||| 
--------gtaatgttacccttctttctattattttttctctcttcatttggttatccctggtttgagattttacagaaaaaaaattatgtgctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGCGCAGGAGCTGGCAACGACACCACTGCCGCCGGCGTCCTTGCTGACATAA

upper sequence: LOC_Os12g03190.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA20G11950.1 (Glycine max), 3'ss of exon 11
----tctgttttgagaggattaaagaatgtttgatatgtgattttttactgttggtagtgagtgatgtgaaacgtaaaagtgacgctgctttgttcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGCGCTGGAGCTGGCAATGATACCACTGCAGCTGGAGTTCTTGCTGACATAC
    | || ||||  |   |  || | |          | | |  | |||               | |   |  | |  || | | || |         ||||| |||| ||||| |   |||||||    |     || ||||| ||||| || ||||||||||| ||||| || ||||| ||||| ||||||||||| ||  
cttgtttgctttgctatattgcaaaagttcagctctcctaagtaataacttcaaaggcctgactgtattctattttattgt-atgttgatacaaat---ggcagTTGGAAATATATACTCGATGCTATAGTAAACAACCACTGGTTATTCAAGGTGCTGGAGCTGGAAATGACACTACTGCTGCTGGGGTTCTTGCTGATATCG
















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|88836371|gb|CI078268.1|CI078268
EST:     AACTCCCGTAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|88538391|gb|CI467412.1|CI467412
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|88556742|gb|CI487091.1|CI487091
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|87027189|gb|CI278221.1|CI278221
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|86537637|gb|CI177843.1|CI177843
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|88560932|gb|CI491637.1|CI491637
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|89182020|gb|CI113526.1|CI113526
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|86490550|gb|CI133183.1|CI133183
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|7273923|gb|AU083467.1|AU083467
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|88376249|gb|CI533151.1|CI533151
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGGTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|86435122|gb|CI106355.1|CI106355
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|88546014|gb|CI475621.1|CI475621
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|88546122|gb|CI475731.1|CI475731
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|89177348|gb|CI250797.1|CI250797
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|86499082|gb|CI141715.1|CI141715
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|88990011|gb|CI018861.1|CI018861
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|88469643|gb|CI406914.1|CI406914
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|14714124|gb|AU198063.1|AU198063
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|88525866|gb|CI452900.1|CI452900
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|86834178|gb|CI340689.1|CI340689
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|88554604|gb|CI484795.1|CI484795
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|86539123|gb|CI179329.1|CI179329
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGAT-CAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|88558974|gb|CI489509.1|CI489509
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|88480660|gb|CI417931.1|CI417931
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|88276546|gb|CI397348.1|CI397348
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|88549393|gb|CI479279.1|CI479279
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|88540598|gb|CI468656.1|CI468656
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|86413783|gb|CI067990.1|CI067990
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttggtagtgagtgatgtgaaacgtaaaagtgacgctgctttgttcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGCGCTGGAGCTGGCAATGATACCACTGCAGCTGGAGTTCTTGCTGACATAC
                                       ctttgttctt  CT-rich tract
                         taaaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgttttgagaggattaaagaatgtttgatatgtgattttttactgttggtagtgagtgatgtgaaacgtaaaagtgacgctgctttgttcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGCGCTGGAGCTGGCAATGATACCACTGCAGCTGGAGTTCTTGCTGACATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- tgttttg
- - - - - - - - - - - -tgtttga
- - - - - - - - - - - - - - - - tgtgatt
- - - - - - - - - - - - - - - - - - - - - - ctgttgg