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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGCTATGATTGGAGCAAGGGTGCCGAGAAGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAGgttggttctcttatagtaattattatgtgatgtataacatttttagtttgtttgatcaatttgaagtggttacatagacataaaaaagacctggggcaat...

Basic information

species Oryza sativa
transcript LOC_Os01g44394.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g44394.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G180815_T01 (Zea mays), 5'ss of exon 10
GTATGCTATGATTGGAGCAAGGGTGCCGAGAAGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAGgttggttctcttatagtaattattatgtgatgtataacatttttagtttgtttgatcaatttgaagtggttacatagacataaaaaagacctggggcaat--
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GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCAAAGACAAATATATTTCTACATAGTGCACAGgtttgattttactaaatgcc--ctgtatagcattatacgttttatattcatttgattttgtttagatagtgcttttgaatggttagaggttttcgttggcca
















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|86427756|gb|CI072853.1|CI072853
EST:     AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAG                         GAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
genomic: AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAGgttggttctc ... tcgtgtgtagGAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
EST: gi|88559425|gb|CI489997.1|CI489997
EST:     ATCTTTCTCCATAGTGTCCAG                         GAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
genomic: ATCTTTCTCCATAGTGTCCAGgttggttctc ... tcgtgtgtagGAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
EST: gi|86501979|gb|CI144612.1|CI144612
EST:     AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAG                         GAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
genomic: AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAGgttggttctc ... tcgtgtgtagGAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
EST: gi|88538285|gb|CI467300.1|CI467300
EST:     AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAG                         GAATCTGAGGTCAAAGGAAAGCCCCGTGGTAATAAGAAGTAGACCTGACAA
genomic: AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAGgttggttctc ... tcgtgtgtagGAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
EST: gi|9865435|gb|AU101185.1|AU101185
EST:     AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAG                         GAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
genomic: AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAGgttggttctc ... tcgtgtgtagGAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
EST: gi|88522457|gb|CI450218.1|CI450218
EST:     AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAG                         GAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
genomic: AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAGgttggttctc ... tcgtgtgtagGAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
EST: gi|88466073|gb|CI519946.1|CI519946
EST:     AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAG                         GAATCTGAGTTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACCA
genomic: AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAGgttggttctc ... tcgtgtgtagGAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
EST: gi|88534425|gb|CI463146.1|CI463146
EST:     AGCACAATCCTTCTACTGCCAAAACAAATATCTTTCTCCATAGTGTCCAG                         GAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
genomic: AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAGgttggttctc ... tcgtgtgtagGAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
EST: gi|88526359|gb|CI452415.1|CI452415
EST:     AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAG                         GAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
genomic: AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAGgttggttctc ... tcgtgtgtagGAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
EST: gi|88550588|gb|CI480575.1|CI480575
EST:     AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAG                         GAATCTGAGGTCAAAGGGAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
genomic: AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAGgttggttctc ... tcgtgtgtagGAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
EST: gi|86251611|gb|CI016900.1|CI016900
EST:     AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAG                         GAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
genomic: AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAGgttggttctc ... tcgtgtgtagGAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
EST: gi|88529721|gb|CI458061.1|CI458061
EST:     AGCACAATCCTTTTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAG                         GAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
genomic: AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAGgttggttctc ... tcgtgtgtagGAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
EST: gi|88523881|gb|CI451746.1|CI451746
EST:     AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAG                         GAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
genomic: AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAGgttggttctc ... tcgtgtgtagGAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
EST: gi|88960382|gb|CI382260.1|CI382260
EST:     AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAG                         GAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
genomic: AGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAGgttggttctc ... tcgtgtgtagGAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
EST: gi|88553781|gb|CI483915.1|CI483915
EST:     CTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAG                         GAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA
genomic: CTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAGgttggttctc ... tcgtgtgtagGAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 66 (upstream exon), 49 (downstream exon)
Score: 21

GTATGCTATGATTGGAGCAAGGGTGCCGAGAAGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAGgttggttctc ... tcgtgtgtagGAATCTGAGGTCAAAGGAAAGCCCCGTGTTAATAAGAAGTAGACCTGACAACAAGAAGTTGAGGATTGGTTATCATAATCATAACATCATCTCGCTGATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGCTATGATTGGAGCAAGGGTGCCGAGAAGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAGgttggttctcttatagtaattattatgtgatgtataacatttttagtttgtttgatcaatttgaagtggttacatagacataaaaaagacctggggcaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaaaaa