Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATGCACTACCTCTGCCGCCGCTGCGCCGGCCTGCCCATCGCCGTCCCCATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccgtcgtcctcggtcttcttgcagcagcagtagcagccgtgaaccaatttcctgtgcggccgtgacgatggcgagctaatcgatcgattgctaactctctgtgtgcag

Basic information

species Zea mays
transcript GRMZM2G014653_T03
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014653_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g66120.1 (Oryza sativa), 5'ss of exon 1
GTGATGCACTACCTCTGCCGCCGCTGCGCCGGCCTGCCCATCGCCGTCCCCATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccgtcgtcctcggtcttcttgcagcagcagtagcagccgtgaaccaatttcctgtgcggccgtgacgatggcgagctaatcgatcgattgctaactctctgt-gtgcag
||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||  |||||     || |||||   | || | |  ||    |  |  || | |||           || | |||||   ||      | ||   | | ||| |   |   ||| ||| ||
GTGATGCACTACCTCTGCCGCCGCTGCGCCGGCCTCCCCATCGCCGTCCCCATCATCGCCGAGATCGACCTCTACAAGTTCGATCCATGGCAGCTTCCCCgtacgata-atcctcctcctccatcctcc--caatcatcaccaccatcaac-----------gccgtcgtga-attgattgattgatt--tggtttgatttgttggtgttgtgtag

upper sequence: GRMZM2G014653_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA06G11970.1 (Glycine max), 5'ss of exon 1
GTGATGCACTACCTCTGCCGCCGCTGCGCCGGCCTGCCCATCGCCGTCCCCATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccgtcgtcctcggtcttcttgcagcagcagtagcagccgtgaaccaatttcctgtgcggccgtgacgatggcgagctaatcgatcgattgctaactctctgtgtgcag
||| ||||||| |||||||||   |||||    | ||| |||||||| |||||||||||||| |||||||||||||| | |||||| ||| |  | ||  |||     | |  || |   |    |              ||  | |    | |||||   |     | | |   |       |||| | |    || ||  |  | |       
GTGTTGCACTATCTCTGCCGCAAATGCGCGTCGCAGCCAATCGCCGTTCCCATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCGgta----acataatcattcattcatt--------------cattcattcttcgatttctgat----tcttaatttttatttattaattgttactgtgttactttacag-------

upper sequence: GRMZM2G014653_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA04G42800.1 (Glycine max), 5'ss of exon 1
GTGATGCACTACCTCTGCCGCCGCTGCGCCGGCCTGCCCATCGCCGTCCCCATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccgtcgtcctcggtcttct-tgcagcagcagtagcagccgtgaaccaatttcctgtgcggccgtgacgatggcgagctaatcgatcgattgctaactctctgtgtgcag
||| ||||||| ||||||||    |||||    | ||| |||||||| |||||||||||||| |||||||||||||| | |||||| ||| | || ||  |||     | |  || ||    |    |  |     | |   |    | ||   |||   | |  |    ||    ||   ||                                 
GTGTTGCACTATCTCTGCCGTAAATGCGCATCGCAGCCTATCGCCGTTCCCATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCGgta----acattatcttcaacttctgatatattcttattcttaattcttaattcattcattttttgaat-tgttattgtacag---------------------------------

upper sequence: GRMZM2G014653_T03 (Zea mays), 5'ss of exon 1
lower sequence: PP1S15_200V6.1 (Physcomitrella patens), 5'ss of exon 1
GTGATGCACTACCTCTGCCGCCGCTGCGCCGGCCTGCCCATCGCCGTCCCCATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccgtcgtcctcggtcttcttgcagcagcagtagcagccgtgaaccaatttcctgtgcggccgtgacgatggcgagctaatcgatcgattgctaactctctgtgtgcag
||| ||||||||||| | ||      || |       || ||    ||||| |||| |||||| || ||||||||||||||||||| ||| | ||||| |||| | |   ||   ||   |  |     | || ||  | ||    ||    |  || ||        |   |  ||   |    |    |  ||  | |||             
GTGCTGCACTACCTCCGTCGGAAGGCCGACTCTGACGCCTTCAAAATCCCCGTCATAGCCGAGGTCAACCTCTACAAGTTCGACCCTTGGGATCTCCCTAgtaag-cttttctctctgactgattcgaaaacaacatcaccaaa-atgggtgatgtttctcaataataggtgct-tgagaaatcgaatacttaatgtccaacc------------

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|211445989|gb|FL293402.1|FL293402
EST:     CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAA                         GGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
genomic: CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccg ... ctgtgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
EST: gi|211445988|gb|FL293401.1|FL293401
EST:     CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAA                         GGATGGCGCTGTACGGCGAGAAAGAGTGGTACTTCTTCTCCCCGCGGGACC
genomic: CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccg ... ctgtgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
EST: gi|211443877|gb|FL293395.1|FL293395
EST:     CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAA                         GGATGGCGCTGTACGGCGAGAAAGAGTGGTACTTCTTCTCCCCGCGGGACC
genomic: CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccg ... ctgtgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
EST: gi|211443871|gb|FL293389.1|FL293389
EST:     CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAA                         GGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
genomic: CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccg ... ctgtgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
EST: gi|211443875|gb|FL293393.1|FL293393
EST:     CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAA                         GGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
genomic: CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccg ... ctgtgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
EST: gi|86471869|gb|DY238239.1|DY238239
EST:     CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCGTGGCAGCTCCCAG                         GGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
genomic: CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccg ... ctgtgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
EST: gi|149097014|gb|EE182818.2|EE182818
EST:     CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAA                         GGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
genomic: CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccg ... ctgtgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
EST: gi|211443873|gb|FL293391.1|FL293391
EST:     ATCATCGCCGAGATCGACCTCTANCA-GTTCGACCCATGGCAGCTCCCAA                         GGATGGCGCTGTACGGCGAGAAAGAGTGGTACTTCTTCTCCCCGCGGGACC
genomic: ATCATCGCCGAGATCGACCTCTA-CAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccg ... ctgtgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
EST: gi|37419784|gb|CF647577.1|CF647577
EST:     CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAA                         GGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
genomic: CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccg ... ctgtgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
EST: gi|211443879|gb|FL293397.1|FL293397
EST:     CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAA                         GGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
genomic: CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccg ... ctgtgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
EST: gi|211446001|gb|FL293414.1|FL293414
EST:     CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAA                         GGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
genomic: CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccg ... ctgtgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
EST: gi|211448113|gb|FL293415.1|FL293415
EST:     CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAA                         GGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
genomic: CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccg ... ctgtgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
EST: gi|211443882|gb|FL293400.1|FL293400
EST:     CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAA                         GGATGGCGCTGTACGGCGAGAAAGAGTGGTACTTCTTCTCCCCGCGGGACC
genomic: CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccg ... ctgtgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
EST: gi|211446000|gb|FL293413.1|FL293413
EST:     CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAA                         GGATGGCGCTGTACGGCGAGAAAGAGTGGTACTTCTTCTCCCCGCGGGACC
genomic: CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccg ... ctgtgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
EST: gi|211443878|gb|FL293396.1|FL293396
EST:     CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAA                         GGATGGCGCTGTACGGCGAGAAAGAGTGGTACTTCTTCTCCCCGCGGGACC
genomic: CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccg ... ctgtgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
EST: gi|149078960|gb|EE167805.2|EE167805
EST:     CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAA                         GGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
genomic: CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccg ... ctgtgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC
EST: gi|93281602|gb|EB673866.1|EB673866
EST:     CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAA                         GGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGAGC
genomic: CATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccg ... ctgtgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATGCACTACCTCTGCCGCCGCTGCGCCGGCCTGCCCATCGCCGTCCCCATCATCGCCGAGATCGACCTCTACAAGTTCGACCCATGGCAGCTCCCAAgtacgtcccgtcgtcctcggtcttcttgcagcagcagtagcagccgtgaaccaatttcctgtgcggccgtgacgatggcgagctaatcgatcgattgctaactctctgtgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC