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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttaattgcttgcaacctgctagctactgttttttttgccatgtgaccatgtccttgggtttgacttatcttctgctcatggtactcatccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG

Basic information

species Zea mays
transcript GRMZM2G064023_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
-ctttaattgcttgcaacct--gctagctactgttttttttgccatgtgaccatgtccttgggtttgacttatcttctgctcatggtactcatccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG
  | || ||  ||   || |  | | || | ||  | | |   ||||    ||| ||   |   |   ||  || ||   |  | ||  | || ||  | |||||||||||||||||||||||||||||||||||||| ||||| || || ||||| |||||||| ||| | || ||||| || ||||||
gatatactttttttttacttttgttggccattgcctatctc-tcatg-actcatctctgggcactaacctcttcatcccatacttgtgat-attcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 13
----ctttaattgcttgcaacctgctagcta-ctgttttttttgccatgtgaccatgtccttgggtttgacttatcttctgctcatggtactcatccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG
     ||   ||||| ||||    ||  ||  || | | | |    |     | |||  |   |   |   | ||    |||||||| || |||   |||    ||||||||||||||||||||| |||||||||||||| ||||| || || ||||| |||||||| ||  | || ||||| || ||||||
ttattttcttttgctggcaattgcctctctctctctctctctcatgactcatctatgggcactgacctc-ttcattccgtgctcatgatattcaattaca----gGTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCGTTGCACGGCCTGGCTAATCAG

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA15G42300.2 (Glycine max), 3'ss of exon 13
------------------------------------------------------------------------ctttaattgcttgcaacctgctagctactgttttttttgc-catgtgaccatgtccttgggtttg-------acttatcttctgct-catggtact---catccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG
                                                                         ||||||   |       |    ||   ||||||| ||    || |    || |   |   | |        |  ||| |  |  |  || |||||     | | | | |||||||  ||| | || ||||||||||||||| | || ||||| ||| | ||||||||||||||||| || |||||  | || ||||||
gtaagttacttcctttaatcaagccctttccattctgtcataatttagaattgtaaaacattaaaaaggattttttaatatatattgtggtaaaggcctgtgtttttattatatatatatatatatatatatatatatatatatatatatatattaatgtattgtactgtgtgttcccgt-cagGTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAATGGGTTAGCTGGGCCCCTGCATGGTTTGGCCAATCAG

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 14
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 13
ctttaattgcttgcaacctgctagctac-tgttttttttgccatgtgaccatgtccttgggtttgacttat-cttctgctcatggtactcatccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG
        |  || |   | ||  | |  |||   ||||      |   | |  |    | ||  | |  | ||| |||| |   | ||  | ||  || ||||||| ||||| || ||||| || ||||| || || ||||| ||  ||||||| |||||||||||||| |||||  | || ||||||
--------gtatgta-tatactctccatgtgtcaattttaaaggattgacctacctgaagtttctaatggttcttttgctaaaaattcttgttca--tgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG

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|6020672|gb|AW065480.1|AW065480
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttt ... ccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
EST: gi|31361054|gb|CD445411.1|CD445411
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttt ... ccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
EST: gi|6952534|gb|AW424602.1|AW424602
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttt ... ccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
EST: gi|5915419|gb|AW053060.1|AW053060
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttt ... ccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccatgtccttgggtttgacttatcttctgctcatggtactcatccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG
              gtttgac  putative branch site (score: 4)
                                        ctcatcc  putative PPT
                     ttatctt  TA-rich tract