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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgctgagcatgacattcttcactttgctttgtacttggcactaattgcatttcaacgttatgtaaagtgagattaatcttaacaaccttcatactgtagCTTTGCAAGATCGACTCTGAGGGCAAGGCGAGGAAGGTTGTAGGCTGCTCCTGTGTTGTTGTCAAGGTGAGTATATCATTTCCTACGGTACTACTACAAG

Basic information

species Zea mays
transcript GRMZM2G132929_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132929_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g12650.4 (Oryza sativa), 3'ss of exon 3
ttgctgagcatgacattcttcactttgct--ttgtacttggcactaattgcatttcaacgttatgtaaagtgagattaatcttaacaaccttcatactgtagCTTTGCAAGATCGACTCTGAGGGCAAGGCGAGGAAGGTTGTAGGCTGCTCCTGTGTTGTTGTCAAGGTGAGTATATCATTTCCTACGGTACTACTACAAG
|  || |   | |  ||| |    ||| |  |     |  |||    |    | |  |  |  | | |  | | | || ||  ||||| | |  |  || ||||||||||||| || ||||||||||||||||||||||| |||||||||||||| || |||||||||||   ||  | ||| || ||  ||||||| ||| 
tatctaaattttaatttcattttgttgttgatatcgttctgcatctctcctttctgcatatcttctgatttaacaata-tcacaacaaacgttgt-ttgcagCTTTGCAAGATTGATTCTGAGGGCAAGGCGAGGAAGGTCGTAGGCTGCTCCTGCGTCGTTGTCAAGGTAGATAATTGATTACCCACCATACTACTTCAAA

upper sequence: GRMZM2G132929_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g12650.2 (Oryza sativa), 3'ss of exon 3
ttgctgagcatgacattcttcactttgct--ttgtacttggcactaattgcatttcaacgttatgtaaagtgagattaatcttaacaaccttcatactgtagCTTTGCAAGATCGACTCTGAGGGCAAGGCGAGGAAGGTTGTAGGCTGCTCCTGTGTTGTTGTCAAGGTGAGTATATCATTTCCTACGGTACTACTACAAG
|  || |   | |  ||| |    ||| |  |     |  |||    |    | |  |  |  | | |  | | | || ||  ||||| | |  |  || ||||||||||||| || ||||||||||||||||||||||| |||||||||||||| || |||||||||                                  
tatctaaattttaatttcattttgttgttgatatcgttctgcatctctcctttctgcatatcttctgatttaacaata-tcacaacaaacgttgt-ttgcagCTTTGCAAGATTGATTCTGAGGGCAAGGCGAGGAAGGTCGTAGGCTGCTCCTGCGTCGTTGTCAAG----------------------------------

upper sequence: GRMZM2G132929_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT2G32060.1 (Arabidopsis thaliana), 3'ss of exon 3
ttgctgagcatgacattcttcactttgctttgtacttggcactaattgcatttcaacgttatgtaaagtga-gattaatcttaacaaccttcatactgtagCTTTGCAAGATCGACTCTGAGGGCAAGGCGAGGAAGGTTGTAGGCTGCTCCTGTGTTGTTGTCAAGGTGAGTATATCATTTCCTACGGTACTACTACAAG
           |  | |  ||    |  ||| | ||||   ||   |    |  || |     |    ||   | ||||  |    |  ||  |  || ||||||||||||| || ||||||||||| || ||||||||||| || ||||| ||| | ||  |||||                                  
-----------gtaagttgtcttccttttttatccttgaagctttctctcctctaaggaagactttgatggtaactaataatcttcaatttggt--tgcagCTTTGCAAGATTGATTCTGAGGGCAATGCAAGGAAGGTTGTTGGATGCTCATGTCTCGTGATCAAG----------------------------------

upper sequence: GRMZM2G132929_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G15930.2 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------ttgctgagcatgacattcttcact-ttgctttgtacttggcactaattgcatttcaacgttatgtaaagtgagattaatcttaacaaccttcatactgtagCTTTGCAAGATCGACTCTGAGGGCAAGGCGAGGAAGGTTGTAGGCTGCTCCTGTGTTGTTGTCAAGGTGAGTATATCATTTCCTACGGTACTACTACAAG
                           |  ||   ||| | || | | | | | |||  ||   |    |||| || || |    |||||  |  |  |  | ||||||    |  ||     || |||| |||||||| || |||||||| || || ||||||||||| || ||||| ||| |||||||||||                                  
gtaagtctatgttttcctctttaatactgactcttcat-atataccttattgtcgctcagtttatcctcctaaatgaatgtttg-gttatcaatggcaaattgaatctt--tgatgtt---gttgcagCTCTGCAAGATTGATTCTGAGGGTAATGCCAGGAAGGTTGTTGGATGCTCATGTCTTGTTGTCAAG----------------------------------

upper sequence: GRMZM2G132929_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ26130 (Selaginella moellendorffii), 3'ss of exon 2
ttgctgagcatgacattcttcactttgctttgtacttggcactaattgcatttcaacgttatgtaaagtgagattaatcttaacaaccttcatactgtagCTTTGCAAGATCGACTCTGAGGGCAAGGCGAGGAAGGTTGTAGGCTGCTCCTGTGTTGTTGTCAAGGTGAGTATATCATTTCCTACGGTACTACTACAAG
                                          |||       |   | || |  || ||    | || |||  |  | || ||  || ||||||||||||||||||| || ||||||||  | ||||| || ||||||||||| || ||  ||  |                                  
-----------------------------------------gtaagcttcccttttccttctccaa-gttctctcaaacttttcg-ctttgatcttgcagCTTTGCAAGATCGACTCCGAAGGCAAGGCTCGAAAGGTCGTCGGCTGCTCCTGCGTGGTGATCCGG----------------------------------

upper sequence: GRMZM2G132929_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ10812 (Selaginella moellendorffii), 3'ss of exon 2
ttgctgagcatgacattcttcactttgctttgtacttggcactaattgcatttcaacgttatgtaaagtgagattaatcttaacaaccttcatactgtagCTTTGCAAGATCGACTCTGAGGGCAAGGCGAGGAAGGTTGTAGGCTGCTCCTGTGTTGTTGTCAAGGTGAGTATATCATTTCCTACGGTACTACTACAAG
                                          |||       |   | || |  || ||    | || |||  |  | ||  |  || ||||||||||||||||||| || ||||||||  | ||||| || ||||||||||| || ||  ||  |                                  
-----------------------------------------gtaagcttcccttttccttctccaa-gttctctcaaacttttcg-ctttgttcttgcagCTTTGCAAGATCGACTCCGAAGGCAAGGCTCGAAAGGTCGTCGGCTGCTCCTGCGTGGTGATCCGG----------------------------------

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|9952896|gb|BE639479.1|BE639479
EST:     TCCACCTGGTTACTGTGCCTAGCGCCAAAACTCTTGGAGAGTGGGCTGGG                         CTTTGCAAGATCGACTCTGAGGGCAAGGCGAGGAAGGTTGTAGGCTGCTCC
genomic: TCCACCTGGTTACTGTGCCTAGCGCCAAAACTCTTGGAGAGTGGGCTGGGgtgagttgaa ... catactgtagCTTTGCAAGATCGACTCTGAGGGCAAGGCGAGGAAGGTTGTAGGCTGCTCC
EST: gi|211457159|gb|FL092943.1|FL092943
EST:     TCCACCTGGTTACTGTGCCTAGCGCCAAAACTCTTGGAGAGTGGGCTGGG                         CTTTGCAAGATCGACTCTGAGGGCAAGGCGAGGAAGGTTGTAGGCTG
genomic: TCCACCTGGTTACTGTGCCTAGCGCCAAAACTCTTGGAGAGTGGGCTGGGgtgagttgaa ... catactgtagCTTTGCAAGATCGACTCTGAGGGCAAGGCGAGGAAGGTTGTAGGCTG
EST: gi|9254186|gb|BE344654.1|BE344654
EST:     TCCACCTGGTTACTGTGCCTAGCGCCAAAACTCTTGGAGAGTGGGCTGGG                         CTTTGCAAGATCGACTCTGAGGGCAAGGCGAGGAAGGTTGTAGGCTGCTCC
genomic: TCCACCTGGTTACTGTGCCTAGCGCCAAAACTCTTGGAGAGTGGGCTGGGgtgagttgaa ... catactgtagCTTTGCAAGATCGACTCTGAGGGCAAGGCGAGGAAGGTTGTAGGCTGCTCC
EST: gi|4647289|gb|AI622364.1|AI622364
EST:     TCCCCCTGGTTNTTGTGCCTAGCGCCAAAACTCTTGGAGAGTGGGCTGGG                         CTTTGCAAGATCGACTCTGAGGGCAAGGCGAGGAAGGTTGTAGGCTGCTCC
genomic: TCCACCTGGTTACTGTGCCTAGCGCCAAAACTCTTGGAGAGTGGGCTGGGgtgagttgaa ... catactgtagCTTTGCAAGATCGACTCTGAGGGCAAGGCGAGGAAGGTTGTAGGCTGCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatttcaacgttatgtaaagtgagattaatcttaacaaccttcatactgtagCTTTGCAAGATCGACTCTGAGGGCAAGGCGAGGAAGGTTGTAGGCTGCTCCTGTGTTGTTGTCAAGGTGAGTATATCATTTCCTACGGTACTACTACAAG
                                tcttaac  putative branch site (score: 2)
                                         ccttcat  putative PPT
                           attaatcttaacaa  TA-rich tract