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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctaagaaaaacagctaaatcaaacatagaaagttgatagtatgattctatgagatattcgtttgcaatatttcacaatgcattttgtttgtctcttagGATGGGTGGTTAGCACAACCCTGGCTGGTGCGACAGCAGGTTCTTTTACTGGAGGTGCTTTAGCTGACAAATTTGGACGAACACGGACGTTCATCCTGGA

Basic information

species Oryza sativa
transcript LOC_Os01g04190.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G153704_T07 (Zea mays), 3'ss of exon 2
gtctaagaaaaacagctaaatcaaacatagaaagttgatagtatgattctatgagatattcgtttgcaatat--ttcacaatgcattttgtttgtctcttagGATGGGTGGTTAGCACAACCCTGGCTGGTGCGACAGCAGGTTCTTTTACTGGAGGTGCTTTAGCTGACAAATTTGGACGAACACGGACGTTCATCCTGGA---------------------------------
                         ||   || | | | ||| || |||| ||          |||| ||||  ||||| |  ||| | ||||||  || ||| ||||||||||||||| || |||||||||| |||  ||||||||||||||| ||| |||| || || |||||||| || ||| | || |||||||||||                                 
------------------------tcactcaatgataacagt-tgcttctgtg---------cttgccatatggttcactagacatgt-gtttgttactcagggtgggtggttagcacatccttggctggtgcaaCACTAGGTTCTTTTACTGGGGGTTCTTTGGCAGATAAATTTGGGCGGACAAGAACATTCATCCTGGATGCAGTCCCACTTGCTCTAGGTGCATTCTTGAG

upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G098011_T01 (Zea mays), 3'ss of exon 4
gtctaagaaaaacagctaaatcaaacatagaaagt-tgatagta-tgattctatgagatattcgtttgcaatatttcacaatgcat-tttgtttgtctcttagGATGGGTGGTTAGCACAACCCTGGCTGGTGCGACAGCAGGTTCTTTTACTGGAGGTGCTTTAGCTGACAAATTTGGACGAACACGGACGTTCATCCTGGA
 ||||| || |  || || ||  |  |||   | | ||||| || |   | | ||||||||   ||| | ||||    || || |  | || || |  || ||||||||||||||||||| |||| |||||||| |||  |||||| ||||| || ||  |||| || || |||||||| || ||| | || |||||||||||
-tctaa-aatagtagatagat-gagtatattcactctgataatagttgctttgtgagatatcttttttccatatgcttcagtggacatctgcttattgctcagGATGGGTGGTTAGCACATCCCTAGCTGGTGCAACACTAGGTTCCTTTACCGGGGGATCTTTGGCAGATAAATTTGGGCGGACAAGAACATTCATCCTGGA

upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G153704_T03 (Zea mays), 3'ss of exon 4
----gtctaagaaaaacagctaaatcaaacatagaaagttgatagtatgattctatgagatattcgtttgcaatat--ttcacaatgcattttgtttgtctcttagGATGGGTGGTTAGCACAACCCTGGCTGGTGCGACAGCAGGTTCTTTTACTGGAGGTGCTTTAGCTGACAAATTTGGACGAACACGGACGTTCATCCTGGA
     |   | |  |  || || ||     |||   | |  ||  ||  | |   |    | |  | |||| ||||  ||||| |  ||| | ||||||  || ||| ||||||||||||||| || |||||||||| |||  ||||||||||||||| ||| |||| || || |||||||| || ||| | || |||||||||||
atgttttctatagtagaagatagat-gtctataatcactcaatgataacagttgct----tctgtgcttgccatatggttcactagacatgt-gtttgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTGGGGGTTCTTTGGCAGATAAATTTGGGCGGACAAGAACATTCATCCTGGA

upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G098011_T02 (Zea mays), 3'ss of exon 4
--------------------gtctaagaaaaacagctaaatcaaacatagaaagt-tgatagta-tgattctatgagatattcgtttgcaatatttcacaatgcat-tttgtttgtctcttagGATGGGTGGTTAGCACAACCCTGGCTGGTGCGACAGCAGGTTCTTTTACTGGAGGTGCTTTAGCTGACAAATTTGGACGAACACGGACGTTCATCCTGGA
                     |   | || |  || || ||  |  |||   | | ||||| || |   | | ||||||||   ||| | ||||    || || |  | || || |  || ||||||||||||||||||| |||| |||||||| |||  |||||| ||||| || ||  |||| || || |||||||| |                      
aaggcatacaataggcatgttttctaaaatagtagatagat-gagtatattcactctgataatagttgctttgtgagatatcttttttccatatgcttcagTGGACATCTGCTTATTGCTCAGGATGGGTGGTTAGCACATCCCTAGCTGGTGCAACACTAGGTTCCTTTACCGGGGGATCTTTGGCAGATAAATTTGGGC----------------------

upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G16150.1 (Arabidopsis thaliana), 3'ss of exon 4
----gtctaagaaaaacagctaaatcaaacatagaaa-gttgatagtatgattctatgagatattcgtttgcaatatttcacaat--gcattttgtttgtctctt-------agGATGGGTGGTTAGCACAACCCTGGCTGGTGCGACAGCAGGTTCTTTTACTGGAGGTGCTTTAGCTGACAAATTTGGACGAACACGGACGTTCATCCTGGA
    || || ||  | |  ||   | |  | |         | ||  |||||||  ||   |  |   | || | | | || |||  | ||| | | ||  |  |       ||||||| | |||||  |    || |||||||| || | |||||| || ||||||||||| |||||||||||||||||||||||| | || ||     ||||
gcaagtatatgatgatccacttctttactcctcctgtcaacggtaaaatgattc-gtgttttgattagtagccaaact-cataattggtattctctatgattggtgttgagcagGATGGATTGTTAGTTCTCTGCTTGCTGGTGCTACGGTAGGTTCATTCACTGGAGGTGCATTAGCTGACAAATTTGGACGAACAAGAACTTTTCAATTGGA

upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 4
----gtctaagaaaaacagctaaatcaaacatagaaagttgatagtatgattctatgagatattcgtttgcaatatttcacaatgcattttgtttgtctcttagGATGGGTGGTTAGCACAACCCTGGCTGGTGCGACAGCAGGTTCTTTTACTGGAGGTGCTTTAGCTGACAAATTTGGACGAACACGGACGTTCATCCTGGA
     |   |      ||  ||  | |           ||  |  ||| |       | || |   ||| ||| |||| |||||| |   | ||   |    ||||||||| |||||||||  |||||||||||| ||    ||||| |||||||| ||||| || ||||| ||||||||  ||||| |||| ||    || ||
atatattctatgttttcatttattttattttatttttattttttttatcaccaatgaatatctagctttacaagatttgacaatggagcattttgagc----agGATGGGTTGTTAGCACACTCCTGGCTGGTGCCACTCTTGGTTCATTTACTGGTGGTGCATTGGCTGATAAATTTGGCAGAACAAGGACTTTTCAACTAGA

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|88738909|gb|CI762417.1|CI762417
EST:     TGAATATCTTGCAAAGGACCTTGGAATTTCTGAGAATGCTGTGTTACAAG                         GATGGGTGGTTAGCACAACCCTGGCTGG
genomic: TGAATATCTTGCAAAGGACCTTGGAATTTCTGAGAATGCTGTGTTACAAGgtgggacatc ... tgtctcttagGATGGGTGGTTAGCACAACCCTGGCTGG
EST: gi|88385512|gb|CI564172.1|CI564172
EST:     TGAATATCTTGCAAAGGACCTTGGAATTTCTGAGAATGCTGTGTTACAAG                         GATGGGTGGTTAGCACAACCCTGGCTGGTGCGACAGCAGGTTCTTTTACTG
genomic: TGAATATCTTGCAAAGGACCTTGGAATTTCTGAGAATGCTGTGTTACAAGgtgggacatc ... tgtctcttagGATGGGTGGTTAGCACAACCCTGGCTGGTGCGACAGCAGGTTCTTTTACTG
EST: gi|88368202|gb|CI575084.1|CI575084
EST:     TGAATATCTTGCAAAGGACCTTGGAATTTCTGAGAATGCTGTGTTACAAG                         GATGGGTGGTTAGCACAACCCTGGC
genomic: TGAATATCTTGCAAAGGACCTTGGAATTTCTGAGAATGCTGTGTTACAAGgtgggacatc ... tgtctcttagGATGGGTGGTTAGCACAACCCTGGC
EST: gi|300215629|gb|HO088255.1|HO088255
EST:     TGAATATCTTGCAAAGGACCTTGGAATTGCTGAGAATGCTGTGTTACAAG                         GATGGGTGGTTAGCACAACCCTGGCTGGTGCGACAGCAGGTTCTTTTACTG
genomic: TGAATATCTTGCAAAGGACCTTGGAATTTCTGAGAATGCTGTGTTACAAGgtgggacatc ... tgtctcttagGATGGGTGGTTAGCACAACCCTGGCTGGTGCGACAGCAGGTTCTTTTACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctatgagatattcgtttgcaatatttcacaatgcattttgtttgtctcttagGATGGGTGGTTAGCACAACCCTGGCTGGTGCGACAGCAGGTTCTTTTACTGGAGGTGCTTTAGCTGACAAATTTGGACGAACACGGACGTTCATCCTGGA
                                      ttttgtttgtctctt  CT-rich tract
                      aatatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctaagaaaaacagctaaatcaaacatagaaagttgatagtatgattctatgagatattcgtttgcaatatttcacaatgcattttgtttgtctcttagGATGGGTGGTTAGCACAACCCTGGCTGGTGCGACAGCAGGTTCTTTTACTGGAGGTGCTTTAGCTGACAAATTTGGACGAACACGGACGTTCATCCTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - aagaaaa
- - - - - - - - -aaatcaa
- - - - - - - - - - - - -catagaaa
- - - - - - - - - - - - - - - - - - - - - -tgattct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgca