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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactacggttcctcagatcctctaaacaaattattcaaatctgacaagttataaaaactttattggtcatgtcatcatatgtaatgtactacgtggttgactccttgtacacacgacgccaattcgaaaatctctgcagGCAAAGGCTCCGAGCAAGCTGTCATCTGCATTCTCTGGAACTCAAGACAAATGCGCAGCCTGCCAGAAGACCGTGTATCCATTGGAGAAG

Basic information

species Zea mays
transcript GRMZM2G134752_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134752_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g42820.1 (Oryza sativa), 3'ss of exon 3
gtactacggttcctcagatcctctaaacaaattattcaaatctgacaagttataaaa-actttattggtcatgtcatcatatgtaatgtactac-gtggttgactccttgtacacacgacgccaattcgaaaatctctgcagGCAAAGGCTCCGAGCAAGCTGTCATCTGCATTCTCTGGAACTCAAGACAAATGCGCAGCCTGCCAGAAGACCGTGTATCCATTGGAGAAG
                          |||||     || | |||     |||||    | || |    | |||   | ||  || || ||  ||     ||||      | | ||    | |       ||| | | | |||| ||  ||||| |||||||| || || |||||||||||||||||||| ||||| ||||||||||| || || ||||| ||||||||||||
------------------------gtacaaaccccacagacctgt----ttatagcccaattcacacattatgcatttattagttatatatcaccaaatttgataatccgcaaactattcactctgcaaaaactttttccagGGAAGAGCTCCTAGCAAGCTATCTTCAGCATTCTCTGGAACTCAAGATAAATGTGCAGCCTGCCAAAAAACTGTGTACCCATTGGAGAAG
















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|21330224|gb|BQ485605.1|BQ485605
EST:     GTGGAGGTGGAGCATCTTCAAACAAGAACGACCCG                         GCAAAGGCTCCGAGCAAGCTGTCATCTGCATTCTCTGGAACTCAAGACAAA
genomic: GTGGAGGTGGAGCATCTTCAAACAAGAACGACCCGgtactacggt ... atctctgcagGCAAAGGCTCCGAGCAAGCTGTCATCTGCATTCTCTGGAACTCAAGACAAA
EST: gi|26455015|gb|CA826598.1|CA826598
EST:     GTGGAGGTGGAGCATCTTCAAACAAGAACGACCCG                         GCAAAGGCTCCGAGCAAGCTGTCATCTGCATTCTCTGGAACTCAAGACAAA
genomic: GTGGAGGTGGAGCATCTTCAAACAAGAACGACCCGgtactacggt ... atctctgcagGCAAAGGCTCCGAGCAAGCTGTCATCTGCATTCTCTGGAACTCAAGACAAA
EST: gi|21329770|gb|BQ485151.1|BQ485151
EST:     GTGGAGGTGGAGCATCTTCAAACAAGAACGACCCG                         GCAAAGGCTCCGAGCAAGCTGTCATCTGCATTCTCTGGAACTCAAGACAAA
genomic: GTGGAGGTGGAGCATCTTCAAACAAGAACGACCCGgtactacggt ... atctctgcagGCAAAGGCTCCGAGCAAGCTGTCATCTGCATTCTCTGGAACTCAAGACAAA
EST: gi|87154920|gb|DY399709.1|DY399709
EST:     GTGGAGGTGGAGCATCTTCAAACAAGAACGACCCG                         GCAAAGGCTCCGAGCAAGCTGTCATCTGCATTCTCTGGAACTCAAGACAAA
genomic: GTGGAGGTGGAGCATCTTCAAACAAGAACGACCCGgtactacggt ... atctctgcagGCAAAGGCTCCGAGCAAGCTGTCATCTGCATTCTCTGGAACTCAAGACAAA
EST: gi|89106608|gb|DY576825.1|DY576825
EST:     GTGGAGGTGGAGCATCTTCAAACAAGAACGACCCG                         GCAAAGGCTCCGAGCAAGCTGTCATCTGCATTCTCTGGAACTCAAGACAAA
genomic: GTGGAGGTGGAGCATCTTCAAACAAGAACGACCCGgtactacggt ... atctctgcagGCAAAGGCTCCGAGCAAGCTGTCATCTGCATTCTCTGGAACTCAAGACAAA
EST: gi|26455135|gb|CA826718.1|CA826718
EST:     GTGGAGGTGGAGCATCTTCAAACAAGAACGACCCG                         GCAAAGGCTCCGAGCAAGCTGTCATCTGCATTCTCTGGAACTCAAGACAAA
genomic: GTGGAGGTGGAGCATCTTCAAACAAGAACGACCCGgtactacggt ... atctctgcagGCAAAGGCTCCGAGCAAGCTGTCATCTGCATTCTCTGGAACTCAAGACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtactacgtggttgactccttgtacacacgacgccaattcgaaaatctctgcagGCAAAGGCTCCGAGCAAGCTGTCATCTGCATTCTCTGGAACTCAAGACAAATGCGCAGCCTGCCAGAAGACCGTGTATCCATTGGAGAAG
          ggttgac  putative branch site (score: 4)
                                              tctctgc  putative PPT
                                          aaaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactacggttcctcagatcctctaaacaaattattcaaatctgacaagttataaaaactttattggtcatgtcatcatatgtaatgtactacgtggttgactccttgtacacacgacgccaattcgaaaatctctgcagGCAAAGGCTCCGAGCAAGCTGTCATCTGCATTCTCTGGAACTCAAGACAAATGCGCAGCCTGCCAGAAGACCGTGTATCCATTGGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA