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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacaacttaaattataataccctggtattgttatcaggatgtgaattttttatctaatatttgttgaacctgtggattgatggtatttttcatgctatagAGGATGGAAGAAATGGCACATTTATGATTGGGAATGAAAGCTTTCCTGCATCACTCTTGGATCTCCCAACTGTTGTGGAGTCATACAAGACATATGATGA

Basic information

species Oryza sativa
transcript LOC_Os05g28010.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g28010.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G147614_T05 (Zea mays), 3'ss of exon 2
------cacaacttaaattataa--taccctggtattgttatcaggatgtgaattttttatctaatatttgttgaacctgtggattgatggtatttttcatgctatagAGGATGGAAGAAATGGCACATTTATGATTGGGAATGAAAGCTTTCCTGCATCACTCTTGGATCTCCCAACTGTTGTGGAGTCATACAAGACATATGATGA
       | ||||| || | ||   ||  || |   |||  | | ||  |||| |||| | ||  |   |        ||||  ||||||  || |||  |  || |||||||||||||||||||||||||||||| || ||||| |||||||||||||| ||||||||||| ||  |||| |||||||||||||| |||||||||||
tgagcatataacttgaactctacgctagactagatatgtatttaagaattgaaattttgaactgttccct--------tgtgcgttgatgagatatttgttcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGA

upper sequence: LOC_Os05g28010.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G029038_T01 (Zea mays), 3'ss of exon 1
----cacaacttaaattataa--taccctggtattgttatcaggatgtgaattttttatctaatatttgttgaacctgtggattgatggtatttttcatgctatagAGGATGGAAGAAATGGCACATTTATGATTGGGAATGAAAGCTTTCCTGCATCACTCTTGGATCTCCCAACTGTTGTGGAGTCATACAAGACATATGATGA
     | ||||| || | ||   ||  || |   ||| || | ||   ||| |||| | ||  |   |      | ||||  ||||||  || |||  | ||| ||||||||||| |||||||||||||||||| || ||||| |||||||||||||| ||||||||||| ||  |||| |||||||||||||| |||||||||||
agcatataacttgaactctacgctagactagatatgt-attaagaatcgaaattttgaactgttccctt-----cttgtgcgttgatgagatatttgttcctacagAGGATGGAACAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGA

upper sequence: LOC_Os05g28010.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G454830_T01 (Zea mays), 3'ss of exon 2
----cacaacttaaattataa--taccctggtattgttatcaggatgtgaattttttatctaatatttgttgaacctgtggattgatggtatttttcatgctatagAGGATGGAAGAAATGGCACATTTATGATTGGGAATGAAAGCTTTCCTGCATCACTCTTGGATCTCCCAACTGTTGTGGAGTCATACAAGACATATGATGA
     | ||||| || | ||   ||  || |   ||| || | ||   ||| |||| | ||  |   |  |     ||||  ||||||  || |||  | ||| |||||||||||||||||||||||||||||| || ||||| ||||||||| |||| ||||||||||| ||  |||| |||||||||||||| |||||||||||
agcatataacttgaactctacgctagactagatatgt-attaagaatcgaaattttgaactgttcccttat-----tgtgcgttgatgcgatatttgttcctacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTTCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGA

upper sequence: LOC_Os05g28010.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G143935_T01 (Zea mays), 3'ss of exon 1
----cacaacttaaattataa--taccctggtattgttatcaggatgtgaattttttatctaatatttgttgaacctgtggattgatggtatttttcatgctatagAGGATGGAAGAAATGGCACATTTATGATTGGGAATGAAAGCTTTCCTGCATCACTCTTGGATCTCCCAACTGTTGTGGAGTCATACAAGACATATGATGA
     | ||||| || | ||   ||  || |   ||| || | ||   ||| |||| | ||  |   |      | ||||  ||||||  || |||  | ||| ||||||||||||||||| |||||||||||| || ||||| |||||||||||||| ||||||||||| ||  |||| |||||||||||||| | |||||||| 
agcatataacttgaactctacgctagactagatatgt-attaagaatcgaaattttgaactgttccctt-----cttgtgcgttgatgagatatttgttcctacagAGGATGGAAGAAATGACACATTTATGATCGGTAATGAGAGCTTTCCTGCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAATATATGATGC

upper sequence: LOC_Os05g28010.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA17G29810.1 (Glycine max), 3'ss of exon 2
cacaacttaaattataataccctggtattgttatcaggatgtgaattttttatctaatatttgttgaacctgtgg--attgatggtatttttcatgctatagAGGATGGAAGAAATGGCACATTTATGATTGGGAATGAAAGCTTTCCTGCATCACTCTTGGATCTCCCAACTGTTGTGGAGTCATACAAGACATATGATGA
                                              | |  |   |||  || || | |    |   | | |    |||| ||||  ||  ||||||||||||| ||| |||||||||||||||||||||  ||| || || || || |||||||| ||    ||||| || || ||               
---------------------------------------------gtatgaaaacaatgcttcttcatcagaagacaagtcactagATTTGTCAT-TTAGTGAGGATGGAAGAAGTGGTACATTTATGATTGGGAATGAACACTTCCCAGCTTCTCTATTGGATCTTCCTTGCGTTGTTGAATCCTA---------------

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|95101122|gb|CI692854.1|CI692854
EST:     CTCCTCCTCTTCCAACCCCGAAGACGCGTCCCTCGANCTCTCCTTCTCAG                         AGGATGGAAGAAATGG
genomic: CTCCTCCTCTTCCAACCCCGAAGACGCGTCCCTCGACCTCTCCTTCTCAGgtgctccccg ... catgctatagAGGATGGAAGAAATGG
EST: gi|88587949|gb|CI705733.1|CI705733
EST:     CTCCTCCTCTTCCAACCCCGAAGACGCGTCCCTCGACCTCTCCTTCTCAG                         AGGATGGAAGAAATGGCACATNTATGATTGGGAATGAAAGCTT
genomic: CTCCTCCTCTTCCAACCCCGAAGACGCGTCCCTCGACCTCTCCTTCTCAGgtgctccccg ... catgctatagAGGATGGAAGAAATGGCACATTTATGATTGGGAATGAAAGCTT
EST: gi|86906396|gb|CI294519.1|CI294519
EST:     CTCCTCCTCTTCCAACCCCGAAGACGCGTCCCTCGACCTCTCCTTCTCAG                         AGGATGGAAGAAATGGCACATTTATGATTGGGAATGAAAGCTTTCCTGCAT
genomic: CTCCTCCTCTTCCAACCCCGAAGACGCGTCCCTCGACCTCTCCTTCTCAGgtgctccccg ... catgctatagAGGATGGAAGAAATGGCACATTTATGATTGGGAATGAAAGCTTTCCTGCAT
EST: gi|88732456|gb|CI755633.1|CI755633
EST:     CTCCTCCTCTTCCAACCCCGAAGACGCGTCCCTCGACCTCTCCTTCTCAG                         AGGATGGAAGAAATGGCACATTTATGATTGGGAATGAAAGCTTTCCTGCAT
genomic: CTCCTCCTCTTCCAACCCCGAAGACGCGTCCCTCGACCTCTCCTTCTCAGgtgctccccg ... catgctatagAGGATGGAAGAAATGGCACATTTATGATTGGGAATGAAAGCTTTCCTGCAT
EST: gi|88373012|gb|CI640463.1|CI640463
EST:     CTCCTCCTCTTCCAACCCCGAAGACGCGTCCCTCGACCTCTCCTTCTCAG                         AGGATGGAAGAAATGGCACATTTATGATTGGGAATGAAAGCTTTCCTGCAT
genomic: CTCCTCCTCTTCCAACCCCGAAGACGCGTCCCTCGACCTCTCCTTCTCAGgtgctccccg ... catgctatagAGGATGGAAGAAATGGCACATTTATGATTGGGAATGAAAGCTTTCCTGCAT
EST: gi|88573677|gb|CI665446.1|CI665446
EST:     CTCCTCCTCTTCCAACCCCGAAGACGCGTCCCTCGACCTCTCCTTCTCAG                         AGGATGGAAGAAATGGCCCATTTATGATTGGGAATGAAAGCTTTCCTGCAT
genomic: CTCCTCCTCTTCCAACCCCGAAGACGCGTCCCTCGACCTCTCCTTCTCAGgtgctccccg ... catgctatagAGGATGGAAGAAATGGCACATTTATGATTGGGAATGAAAGCTTTCCTGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttatctaatatttgttgaacctgtggattgatggtatttttcatgctatagAGGATGGAAGAAATGGCACATTTATGATTGGGAATGAAAGCTTTCCTGCATCACTCTTGGATCTCCCAACTGTTGTGGAGTCATACAAGACATATGATGA
                                      tatttttc  CT-rich tract
     tatctaatatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacaacttaaattataataccctggtattgttatcaggatgtgaattttttatctaatatttgttgaacctgtggattgatggtatttttcatgctatagAGGATGGAAGAAATGGCACATTTATGATTGGGAATGAAAGCTTTCCTGCATCACTCTTGGATCTCCCAACTGTTGTGGAGTCATACAAGACATATGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - -taccctg
- - - - - - - - - - - - - - - - - - ggatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgatgg