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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA

Basic information

species Oryza sativa
transcript LOC_Os01g48910.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 15
-ttttcatatcaaaagagact-gacctgttaacagaa-tgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
 | || | |   |    || |  || ||  | ||||| ||| ||   | ||  |||   |  || | || ||   || | |  |  || |||| |||||| ||||||||||||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||||||||| || ||||| || || || || |||||
gtcttgaaagagatcctgatttaacttgccatcagaaatgcctttgaaattttcccaagtctaacgtttgtt--cactgccaaatattaatat-ttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA

upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA05G36910.1 (Glycine max), 3'ss of exon 15
ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccc-tgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
  ||||| |   |    |      ||   |    ||||||  || |      | ||||   ||  |  |  | |  ||   | ||  | |          || || ||||| |||||||   |  |||||| |||||| || |||||||| |||||||| || || ||||| || |||||||||||||| ||||| || ||
-gttcatttttcagtttat--gtttgaataagatatgcttctacgtggattgcatgatcatattttattcatgaatggtctatttaaaca----------gGGGATATTGGAGAGTGGCTACCCAATGGAACCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAA

upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA01G43470.2 (Glycine max), 3'ss of exon 15
-------ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
         || || |      | | |||  | |||      |   ||  |  ||      | |   |   ||| | | |    |  |   |||||| || |   ||| || ||||| ||||||||  || ||||||||||||| || |||||||| |||||||| || || ||||| || |||||||||||||| ||||| || ||
gttatttcatttatgttttccaaaattgaggt-ttatattcttatattagctgttgggttgggtcacaattttccttttattcacaaa---tgatatatt-caacagGGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA

upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 15
-ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgctt--cttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
 || |   ||  |      |  |  | | |     ||  | | | |||  |   ||  | |  | ||  ||| | |    |  |   |||||| || |   ||| || ||||| ||||||||  || | ||||||||||| || |||||||| |||||||| || || ||||| || |||||||||||||| ||||| || ||
gttatttcatttatgttttccaaatt-tgaggtttatattcttatattagctgttgggtcacagttttcctttttattaacaaa---tgatatatt-caacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA

upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 15
---ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatct-tactgt-agGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
   |||   | ||  ||       ||   |    |||||   |||   |||         ||| | ||| |   |     | |||| || |   | |||| | ||| ||  |||||||||||||  | ||||||||||||||||| |||||  | |||||||| ||||| || ||||| |||||||| ||||| || ||||||||
gtatttctttctctgaacttgtatacaattagttagaata--ttggtttttgtagtccggtgagttcttttc--agttctcacactctgcttcttatactctcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA

upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: AT4G11030.1 (Arabidopsis thaliana), 3'ss of exon 15
ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgc---ttcttgt--aaccggctcactttga-------tatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
      ||  ||||    |    || | | ||   ||||||   || |    |   || |||     ||||| |  | |    | | ||| |       ||||||||   ||| ||  |||||||||||||  |  |||||||||||||||| ||||| || || |||||||||||||| ||| | |||||||| ||||||||||| |||||
----gttactaaaaacctcaacactttgatcattttgctttcctatatatagcattttaaatatcagttcttatttaccttatttaatttaactatgtgtatcttacc--agGTGATGTTGGTGAGTGGCAACCAAATGGAAGCATGAAGATAATTGACCGGAAAAAGAACATCTTCAAACTCGCGCAAGGAGAGTATGTCGCTGTTGAGAA

upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 15
ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgc-ttcttgtaaccggctcactt-tga--tatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
  ||    ||| |   |  |  | | || | |  | | |||||  |   |   |   || || | ||  | ||||   ||  ||  |||  ||||||     ||| ||  |||||||||||||  ||||||| |||||||| || || || |||||||||||||| |||||||| || ||||||||||| || || || |||||
-gtttgc-tcatattggcatttcttcttga-attaagttttgaggtcctctattttgtggattcgtttctttaacaaccttgctgatgacttatcttttcacagGGGATGTTGGTGAGTGGCAACCTGATGGGAGCATGAAAATTATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAA

upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: EDO96800 (Chlamydomonas reinhardtii), 3'ss of exon 12
-----------------------ttttcatatcaaaagagactgacctgttaaca-gaatgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
                           || |   | | | ||  ||      ||| | | ||    ||     | |   |   ||  | |      || | | |     | |   |       || ||| | || |||  |  | | || |||| | | |||||||| || ||||||||||||||||||||||||  |||                        
tgttttccttgtgctctttaacacacacacacacacacacacacacacacacacacgcacgcacgcacgcacgcacacaaacaaacacgtacacacacagACGCGGACGGCTTCTTCCACACGGGCGACGTGGGCGAGCTGGTGACGGACGGAACCCTCAAGATCATCGACCGCAAGAAGAACATCTTCAAGCTCAGCCA------------------------

upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: PP1S47_161V6.1 (Physcomitrella patens), 3'ss of exon 15
----ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
       |  | |  ||| |   |||   | | |   |   |||||   |       | | | |||| |       ||  | ||  | |||| | |      ||| || ||||| ||||||||    |||||     ||||||| ||||||||||||||||||||||||||||| || ||||||||||| || || || || ||
caggggctgttcttgaaatatgttgaaaggattatccat--ctttgg-gtcgatgaataagtcaatgatgacatagacaagttctttgtgatgtgt-gtatcagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAA

upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 15
ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgc-ttcttgtaaccggctcactttgatat-cttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
 |  |  ||  |    ||   | |  |   |||  |   |  ||   |    |||   ||  ||  |  ||||  | | |   |||   || | |     ||| || ||||| ||||||||| | ||||| ||||||||||| ||||| || |||||||| || |||||||| || || ||||||||| | || || || ||
gtcaccaatatacgtggaaaaaacgat--gcagtttatgtaaacgaatggtgctggaggagagcgctgatgtattctgattcttttataatgcatgaatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA

upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: EFJ23443 (Selaginella moellendorffii), 3'ss of exon 15
ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
                                             |     |   |  |||  |||  |        || |||     |  ||  | ||||||| || || |||||||   |  | |||  | |||| ||||| ||  | ||||||||||| ||||| ||||| ||||| ||||| |||||||| |||||
--------------------------------------------gtagggactcaaaagaa-acttgctacgtggttcttactgaacgaggtttttatagGAGATATCGGAGAGTGGCTACCAAACGGAGCCTTGAAAATCATAGACAGGAAGAAGAACATTTTCAAACTCTCGCAAGGCGAATACGTCGCTGTAGAGAA

upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: EFJ25426 (Selaginella moellendorffii), 3'ss of exon 15
ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgcttcttgtaac-cggctcactttgat--atcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
                                                        |  || |   ||||  ||  || ||    |||   |  ||  |  |||||| || || |||||||   |  | |||  | |||| ||||| ||  | ||||||||||| ||||| ||||| ||||| ||||| |||||||| |||||
------------------------------------------------gtagggactcaaaagaaacttgctacgtggttcgtactgaacgaggtttttacagGAGATATCGGAGAGTGGCTACCAAACGGAGCCTTGAAAATCATAGACAGGAAGAAGAACATTTTCAAACTCTCGCAAGGCGAATACGTCGCTGTAGAGAA

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|86910803|gb|CI294794.1|CI294794
EST:     ACGAGAAGACCTCACCAAGGAAGTTTTAGTCGATGGATGGTTTCACACAG                         GAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCA
genomic: ACGAGAAGACCTCACCAAGGAAGTTTTAGTCGATGGATGGTTTCACACAGgtatgccaac ... cttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccccctgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
                                            tcttact  CT-rich tract
                                     tttgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA