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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattgaagaaattcactagctatcattttaaacaacaaattccccactattcaacgaagtacaatgatcaaattactcaaatcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATCTGATGCAGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGT

Basic information

species Oryza sativa
transcript LOC_Os01g59340.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G020002_T02 (Zea mays), 3'ss of exon 11
------------------------------gtatattgaagaaattcactagctatcattttaaacaacaa-attc--cccactattcaacgaagtacaatgat-caaattactcaaatcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATCTGATGCAGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGT
                              || || |  |||| |   |    | |||| | |||   ||   |||  |   | |   ||  ||  |||||| | ||||||||||||   ||||||| |||||||  |||||||||| |||||||||||||||||| |||||||||||||| |||||||| || |||||||| || || ||||||||||| ||||||
gtactatacattaaatctgctcaaaccagggtttagtttagaagtaaccagattgtcatatcaaaatgcattgttcaactagcaaaaaaaaaaaaaacaatggtacaaattactcaaccattttcagCGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATCTGACGCAGATATCATAATCCTGAACCCTGAAAGGAGCTTTGTGATGGGT

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 11
------------------------------------------------------gtatattgaagaaattcactagctatcattttaaac-aacaaattccccactat------tcaacgaagtacaatgatcaaattactca-------aatcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATCTGATGCAGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGT
                                                      |   ||| |    ||| | |   | | |||||||    |  ||   |    |||        || | | |||     |  | ||| | |       |||| ||| ||||| |  || ||||| ||||| ||  |||||||||| |||||   ||||||||||||||||||||||||||| |||||  |    | |||||  ||   |
gtatattttctgttaatcaaagtaaaattagcatccagttcttatagtaataaggagaattcagagtatttaattatttttattttaatttgatgaagctctttgtatagatgccaaaagtattactgatttttatttatttatttctacaatcattttagTGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATCTGATGCAGATATTATCATCCTCAATCCAAATTCAACCTTTGAGATAACT

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA14G04030.1 (Glycine max), 3'ss of exon 11
-----------gtatattgaag---aaattcact---agctatcattttaaacaacaaattccccacta------ttcaacgaagtac-aatgatcaa-attactcaaatcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATCTGATGCAGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGT
           ||  ||  |||   |||||  ||   || | | ||   ||  || ||  |      ||         || | | |||  ||| |    ||| ||  |||| ||||||||| || || ||||| ||||| ||  ||||||||||  ||||   |||||||||||||||||||||||||||||||||  |   ||||||||  ||| ||
gtatatattcagttaatcaaagtgcaaattagcttctagttcttatggaaataaaaaagctttttggtaaagatgccaaaagtattactgatgttttttatttctacaatcatttcagTGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTGTTCTCCCAGGATCTGATGCAGATATTATCATCCTGAATCCAAATTCGAGCTTTGAGATGAGT

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA02G44690.1 (Glycine max), 3'ss of exon 11
----------------------------------------------gtatattgaagaaattcactagctatc-attttaaacaacaaattccccactattcaacgaagtacaatgatcaaattactcaaatcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATCTGATGCAGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGT
                                              |  |||  | ||||     | | ||   ||   ||| | ||||      ||| |  |||  | | |     |    || ||  |||| ||||||||| || || ||||| ||||| ||  |||||||||| |||||   ||||||||||||||||||||||||||| |||||  |   ||||||||  ||| ||
gtatattttcagttaatcaaagtgaaaattatctttcagttcttatgactataaaggaaaactgtttggtaaagatgccaaaaaccaaaagtataactgtataactga-tgct----ttttgtttctacaatcatttcagTGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTCCCAGGATCTGATGCAGATATTATCATCCTTAATCCAAATTCGAGCTTTGAGATGAGT

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 14
lower sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 11
-------------------gtatattgaagaaattcactagctatcattttaaacaacaaattccccactattcaacgaagtacaatgatcaaattactcaaatcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATCTGATGCAGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGT
                   |  | ||    |  || |  |  |    |||  ||  |    || |     | | |      | || |  | |||| |||  ||  || ||||||| |  |||||||||||||| || ||||||||||| || || |  || || |||||||||||||||||  |||||||  |    ||||  |  ||  | 
gtatatatgctctttcgaagcttctttttaatgttgaaaatttgctttttccaatgagcttttacttgaaagttatgtgtttgcatt--tgaaatgactttaagtttgtcagTGCTAGAATTTTCAACATATATCCACGGAAAGGAGCTATCCTTGCTGGCTCGGATGCAGATATTATCATATTGAATCCAAACTCAAGCTACGAGATTAGC

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|86873138|gb|CI328518.1|CI328518
EST:     GTCAGTGATTATGTGAGAGTGACAAGCACAGAATG                         TGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTGCTGGAAGGAT
genomic: GTCAGTGATTATGTGAGAGTGACAAGCACAGAATGgtatattgaa ... atcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATT-CTGGAAGGAT
EST: gi|86431074|gb|CI083497.1|CI083497
EST:     TATGTGAGAGTGACAAGCACAGAATG                         TGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATC
genomic: TATGTGAGAGTGACAAGCACAGAATGgtatattgaa ... atcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATC
EST: gi|87026885|gb|CI259538.1|CI259538
EST:     ACTGGCCGAATTTCTGTCAGTGATTATGTGAGAGTGACAAGCACAGAATG                         TGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATC
genomic: ACTGGCCGAATTTCTGTCAGTGATTATGTGAGAGTGACAAGCACAGAATGgtatattgaa ... atcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaattccccactattcaacgaagtacaatgatcaaattactcaaatcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATCTGATGCAGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGT
                                              tcttttc  CT-rich tract
                               atcaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattgaagaaattcactagctatcattttaaacaacaaattccccactattcaacgaagtacaatgatcaaattactcaaatcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATCTGATGCAGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT