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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaggattgtttttctagtttgagttgcaaggatgaacttattgtaaaaaggatagaggctgtgaggtaattttctatgtgatatagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGATAAACCTACCTATGCACCACATGTAGAAAATGGAGACATGTGCATTGTAC

Basic information

species Zea mays
transcript GRMZM2G044584_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044584_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g15370.1 (Oryza sativa), 3'ss of exon 2
gttaggattgtttttctagtttgagttgcaaggatgaacttattgtaaaaaggatagaggctgtgaggtaattttctatgtgatatagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGATAAACCTACCTATGCACCACATGTAGAAAATGGAGACATGTGCATTGTAC
||||  ||| || | || |||  | | |  | | | |  ||  ||  ||| |  | ||       | |  | ||| | ||||  |||||| || || || ||||| ||||||||||||||||||||||| || |||||||| || || |||||||||||||| |||||||||||||||||| |||| |
gttaccattcttctgctggttccaatggttaagctaatgttcatgggaaatgttttga-----ccaagctactttgtttgtgcgatagGTCCTTGGACGGTTGGCATCCCAAATAGCTGTTGTGCTTCAGGGAAAGGATAAGCCAACTTATGCACCACATGTGGAAAATGGAGACATGTGCGTTGTGC

upper sequence: GRMZM2G044584_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g15360.7 (Oryza sativa), 3'ss of exon 2
gttaggattgtttttctagtttgagttgcaaggatgaacttattgtaaaaaggatagaggctgtgaggtaattttctatgtgatatagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGATAAACCTACCTATGCACCACATGTAGAAAATGGAGACATGTGCATTGTAC
||||  ||| || |  | |||  |||||  | |   |  ||  ||   || || |      |   | |   || | | |||||||  ||| || || || ||||| ||||||||||||||||||||||| |||||||| || || || |||||||||||||| |||||  ||||||||||| |||| |
gttaccatttttctagtggttccagttgttaagcaaatattcatgggtaatggtttt---ttaccaagcctttgtttgtgtgata--gGTCCTTGGACGGTTGGCGTCCCAAATAGCTGTTGTGCTTCAGGGCAAGGACAAGCCAACTTATGCACCACATGTGGAAAACAGAGACATGTGCGTTGTGC

upper sequence: GRMZM2G044584_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g15360.5 (Oryza sativa), 3'ss of exon 1
-----------------gttaggattgtttttctagtttgagttgcaaggatgaacttattgtaaaaaggatagaggctgtgaggtaattttctatgtgatatagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGATAAACCTACCTATGCACCACATGTAGAAAATGGAGACATGTGCATTGTAC
                 ||||  ||| || |  | |||  |||||  | |   |  ||  ||   || || |      |   | |   || | | |||||||  ||| || || || ||||| ||||||||||||||||||||||| |||||||| || || || |||||||||||||| |||||  ||||||||||| |||| |
ttgacgcaaagggccaggttaccatttttctagtggttccagttgttaagcaaatattcatgggtaatggtttt---ttaccaagcctttgtttgtgtgata--gGTCCTTGGACGGTTGGCGTCCCAAATAGCTGTTGTGCTTCAGGGCAAGGACAAGCCAACTTATGCACCACATGTGGAAAACAGAGACATGTGCGTTGTGC

upper sequence: GRMZM2G044584_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g06474.1 (Oryza sativa), 3'ss of exon 2
gttaggattgttt----ttctagtttgagttgca-aggatgaacttattgtaaa---aaggatag--aggctgtgaggtaattttcta--tgtgat-atagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGATAAACCTACCTATGCACCACATGTAGAAAATGGAGACATGTGCATTGTAC
||||| | |  ||    || |  ||  | || |  | |||| | ||||    ||   | | || |  | || || || || ||| ||   | || | ||||||||| || || ||||| |||||||| ||||||||||||||||| ||||| || || || |||||||||||||| ||||| || ||||||||  | ||||
gttagcaatccttctgattttgcttcaatttacggaagatgtatttatgtggaatgcaggaatggttatgcagtaagctactttgctgtttatgttgatagGTGCTTGGACGGTTGGCATCCCAAATTGCTGTTGTGCTTCAAGGGAAGGACAAGCCAACTTATGCACCACATGTGGAAAACGGGGACATGTGTGTCGTAC

upper sequence: GRMZM2G044584_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g15360.2 (Oryza sativa), 3'ss of exon 2
gttaggattgtttttctagtttgagttgcaaggatgaacttattgtaaaaaggatagaggctgtgaggtaattttctatgtgatatagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGATAAACCTACCTATGCACCACATGTAGAAAATGGAGACATGTGCATTGTAC
||||  ||| || |  | |||  |||||  | |   |  ||  ||   || || |      |   | |   || | | |||||||  ||| || || || ||||| ||||||||||||||||||||||| |||||||| || || || |||||||||||||| |||||  |||||||           
gttaccatttttctagtggttccagttgttaagcaaatattcatgggtaatggtttt---ttaccaagcctttgtttgtgtgata--gGTCCTTGGACGGTTGGCGTCCCAAATAGCTGTTGTGCTTCAGGGCAAGGACAAGCCAACTTATGCACCACATGTGGAAAACAGAGACAT-----------

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|16378867|gb|BI992643.1|BI992643
EST:     TTTGATGCTAAGGGTCAG                         GTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGAT
genomic: TTTGATGCTAAGGGTCAGgttaggattg ... tgtgatatagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGAT
EST: gi|18385121|gb|BM418320.1|BM418320
EST:     GAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAG                         GTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGAT
genomic: GAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattg ... tgtgatatagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGAT
EST: gi|13315880|gb|BG410228.1|BG410228
EST:     GAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAG                         GTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGAT
genomic: GAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattg ... tgtgatatagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGAT
EST: gi|211282462|gb|FL053249.1|FL053249
EST:     GAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAG                         GTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGAT
genomic: GAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattg ... tgtgatatagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGAT
EST: gi|87153153|gb|DY397942.1|DY397942
EST:     GAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAG                         GTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGAT
genomic: GAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattg ... tgtgatatagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGAT
EST: gi|211445695|gb|FL278216.1|FL278216
EST:     GAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAG                         GTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGAT
genomic: GAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattg ... tgtgatatagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaacttattgtaaaaaggatagaggctgtgaggtaattttctatgtgatatagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGATAAACCTACCTATGCACCACATGTAGAAAATGGAGACATGTGCATTGTAC
                                      ttttctat  CT-rich tract
      ttattgtaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaggattgtttttctagtttgagttgcaaggatgaacttattgtaaaaaggatagaggctgtgaggtaattttctatgtgatatagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAGGCAAGGATAAACCTACCTATGCACCACATGTAGAAAATGGAGACATGTGCATTGTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA