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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgtctattttgtgctgttcatgattctctatccccaggccttcgattttaattattttccttgaatattctaattattattctgtctattttgtacagGCGAAAATGCTTGAAGCTCTGCAGGATATTGAAATTGCTTCAAAGATAGTTGGCTTCGATAGCGACAGTGATGAATCTCTTGATGATAAATATATGAAAC

Basic information

species Zea mays
transcript GRMZM5G831712_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G831712_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os07g23110.1 (Oryza sativa), 3'ss of exon 14
--tctgtctattttgtgctgttcatgattctctatccccaggccttcgattttaattattttccttgaatattctaattattattctgtctattttgtacagGCGAAAATGCTTGAAGCTCTGCAGGATATTGAAATTGCTTCAAAGATAGTTGGCTTCGATAGCGACAGTGATGAATCTCTTGATGATAAATATATGAAAC
    |   |||||| |     | || |       | |  |      | ||| ||| | | |||   ||      | | | | | | ||      | || |||| ||||||||||||||||||||| ||||||||||||||||| ||  | |||||||||||||| |||| |||||| ||||||||||| || || | |||||
ttcattcttattttctttgactgatcagatgtatttctta--ttgccaattgtaactttattcagagacccaattgactgtaactttggtgcaatggtgcagGTGAAAATGCTTGAAGCTCTGCAAGATATTGAAATTGCTTCTAAACTTGTTGGCTTCGATAGTGACAATGATGAGTCTCTTGATGACAAGTACAAGAAAC

upper sequence: GRMZM5G831712_T02 (Zea mays), 3'ss of exon 14
lower sequence: AT2G31320.1 (Arabidopsis thaliana), 3'ss of exon 13
tctgtctattttgtgctgttcatgattctctatccccaggccttcgattttaattattttccttgaatattctaattattattctgtctattttgtacagGCGAAAATGCTTGAAGCTCTGCAGGATATTGAAATTGCTTCAAAGATAGTTGGCTTCGATAGCGACAGTGATGAATCTCTTGATGATAAATATATGAAAC
      || ||      |  |||||  |    |     |   ||  |||   |   | ||  |      | | ||    |||| | ||| | |   ||||| ||||||||| || |||||||||||||| ||||| |||||||  ||||||||||| |||   || ||    ||||||||||||||||| |||| ||| |
-----gtacttgccatagaacatgaaccatggtgtt--gttttttaattcctagcctctttttctgtgttacaaagaggtattgtatctgtgtgtcacagGTGAAAATGCTCGAGGCTCTGCAGGATATCGAAATAGCTTCAAGAATAGTTGGCTTTGATGTTGATAGCACCGAATCTCTTGATGATAAGTATAAGAAGC
















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|94475980|gb|EB704938.1|EB704938
EST:     GGATGATTTGATGATCAAA                         GCGAAAATGCTTGAAGCTCTGCAGGATATTGAAATTGCTTCAAAGATAGTT
genomic: GGATGATTTGATGATCAAAgtatgtgctc ... ttttgtacagGCGAAAATGCTTGAAGCTCTGCAGGATATTGAAATTGCTTCAAAGATAGTT
EST: gi|60345790|gb|DN212763.1|DN212763
EST:     CTTCTATTCATCCTCATATTATACGGGATGAGGATGATTTGATGATCAAA                         GCGAAAATGCTTGAAGCTCTGCAGGATATTGAAATTGCTTCAAAGATAGTT
genomic: CTTCTATTCATCCTCATATTATACGGGATGAGGATGATTTGATGATCAAAgtatgtgctc ... ttttgtacagGCGAAAATGCTTGAAGCTCTGCAGGATATTGAAATTGCTTCAAAGATAGTT
EST: gi|6021377|gb|AW066305.1|AW066305
EST:     CTTCTATT-ATNCTCATATTATACGGGATGAGGATGATTTGATGATCAAA                         GCGAAAATGCTTGAAGCTCTGCAGGATATTGAAATTGCTTCAAAGA
genomic: CTTCTATTCATCCTCATATTATACGGGATGAGGATGATTTGATGATCAAAgtatgtgctc ... ttttgtacagGCGAAAATGCTTGAAGCTCTGCAGGATATTGAAATTGCTTCAAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttaattattttccttgaatattctaattattattctgtctattttgtacagGCGAAAATGCTTGAAGCTCTGCAGGATATTGAAATTGCTTCAAAGATAGTTGGCTTCGATAGCGACAGTGATGAATCTCTTGATGATAAATATATGAAAC
                        ttctaat  putative branch site (score: 2)
                                         tctatttt  putative PPT
     taattattttccttga  TA-rich tract