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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctttattctttattataatttataaaaaacctgattccatagtcccaactaaacaagcagaacgttagcttcctgttctcattaaactttctgattccatagAGCGCCAGGCATCTGAACCACCTCTTAAATGGGAAACAAGAAGACGGATTGCACTGGGATCTGCAAGAGGTCTTTCTTACTTGCATGATCACTGCGATCC

Basic information

species Zea mays
transcript GRMZM2G150024_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G150024_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA10G36280.1 (Glycine max), 3'ss of exon 9
---gttctttattctttattataatttataaaaaacctgattccatagtcccaactaaacaagcagaacgttagcttcctgttctcattaaactttctgattccatagAGCGCCAGGCATCTGAACCACCTCTTAAATGGGAAACAAGAAGACGGATTGCACTGGGATCTGCAAGAGGTCTTTCTTACTTGCATGATCACTGCGATCC
       |||| |  |  |  |     |   | |  ||| ||  ||| || |||  |    |   |    |||   || | |  |  |  || |   | |||   ||||||| |   ||| | ||  ||| ||  | |||  |||  | | | |  | ||  ||||||||||||| |||||||| || ||||||||||| || || ||
agaaaattttacttgtattattggcccacccata--ctggtt--atattctcaatca--ttaaatgtttattattgtcttataattttgtaattgctttattt--tagAGCGTCCTCCATATCAAGAACCCCTGGATTGGCCAACCCGGAAAAGAGTAGCTTTGGGATCTGCAAGGGGTCTTTCATATTTGCATGATCATTGTGACCC

upper sequence: GRMZM2G150024_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv07s0031g01410.t01 (Vitis vinifera), 3'ss of exon 9
gttctttattctttattataatttataaaaaacctgattccatagtcccaactaaacaagcagaacgttagcttcctgttctcattaaactttctgattccatagAGCGCCAGGCATCTGAACCACCTCTTAAATGGGAAACAAGAAGACGGATTGCACTGGGATCTGCAAGAGGTCTTTCTTACTTGCATGATCACTGCGATCC
     |||||||   || |   |||    | |   | ||||| |      |||         |       | |  ||  |  | ||     |     |    |||| || |   |||| |||||||| ||| | |||   || || | | | || ||  ||||||||||||| || ||||| || ||||||||||||||||||||
----cttattctcacttgtggatta-ggtatatgagcttccaaatctagtactgtttgctttgtgtacctggtgactcatgactttgttgataaaattcttgtagAACGTCCACCATCAGAACCACCACTTGATTGGACCACTAGGAAAAGAATAGCTTTGGGATCTGCAAGGGGGCTTTCCTATTTGCATGATCACTGCGATCC

upper sequence: GRMZM2G150024_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv18s0164g00070.t01 (Vitis vinifera), 3'ss of exon 9
gttctttattctttattataatttataaaaaacctgattccatagtcccaact--aaacaagcagaacgtt--agcttcctgttctcattaaactttctg---attcc-atagAGCGCCAGGCATCTGAACCACCTCTTAAATGGGAAACAAGAAGACGGATTGCACTGGGATCTGCAAGAGGTCTTTCTTACTTGCATGATCACTGCGATCC
              |  | | |  | || ||       | | || |   |  |  |||   | |  || ||  |  ||  |   ||  |||   ||  |    ||||   |||| |||| ||||||||||||||| ||| | |||  |||||| |  || |||||  |||||||||||||||| |||||||| ||||||||||| || || ||
-------------caaaaaagtgcaaaagaatgaaagcttcttattttgagtttcaaaaggggaagaccttccaatttttttcacttgttatctttcttatgcattcttgtagAACGCCCGGCATCTGAACCACCACTTGATTGGCCAACAAGGAAGCGAATTGCGTTGGGATCTGCAAGAGGGCTTTCTTATTTGCATGATCATTGTGACCC

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|22491126|gb|BU051049.1|BU051049
EST:     GCTGGTCTACCCATACATGGCTAATGGCAGTGTGGCATCACGTTTACGAG                         AGCGCCAGGCATCTGAACCACCTCTTAAATGGGAAACAAGAAGACGGATTG
genomic: GCTGGTCTACCCATACATGGCTAATGGCAGTGTGGCATCACGTTTACGAGgttctttatt ... gattccatagAGCGCCAGGCATCTGAACCACCTCTTAAATGGGAAACAAGAAGACGGATTG
EST: gi|19351342|gb|BM895874.1|BM895874
EST:     GCTGGTCTACCCATACATGGCTAATGGCAGTGTGGCATCACGTTTACGAG                         AGCGCCAGGCATCTGAACCACCTCTTAAATGGGAAACAAGAAGACGGATTG
genomic: GCTGGTCTACCCATACATGGCTAATGGCAGTGTGGCATCACGTTTACGAGgttctttatt ... gattccatagAGCGCCAGGCATCTGAACCACCTCTTAAATGGGAAACAAGAAGACGGATTG
EST: gi|32840243|gb|CD979924.1|CD979924
EST:     GCTGGTCTACCCATACATGGCTAATGGCAGTGTGGCATCACGTTTACGAG                         AGCGCCAGGCATCTGAACCACCTCTTAAATGGGAAACAAGAAGACGGATTG
genomic: GCTGGTCTACCCATACATGGCTAATGGCAGTGTGGCATCACGTTTACGAGgttctttatt ... gattccatagAGCGCCAGGCATCTGAACCACCTCTTAAATGGGAAACAAGAAGACGGATTG
EST: gi|19272517|gb|BM888773.1|BM888773
EST:     GCTGGTCTACCCATACATGGCTAATGGCAGTGTGGCATCACGTTTACGAG                         AGCGCCAGGCATCTGAGCCGCCTCTTAAATGGGAAACAAGAAGACGGATTG
genomic: GCTGGTCTACCCATACATGGCTAATGGCAGTGTGGCATCACGTTTACGAGgttctttatt ... gattccatagAGCGCCAGGCATCTGAACCACCTCTTAAATGGGAAACAAGAAGACGGATTG
EST: gi|29130394|gb|CB381098.1|CB381098
EST:     TGGCATCACGTTTACGAG                         AGCGCCAGGCATCTGAACCACCTCTTAAATGGGAAACAAGAAGACGGATTG
genomic: TGGCATCACGTTTACGAGgttctttatt ... gattccatagAGCGCCAGGCATCTGAACCACCTCTTAAATGGGAAACAAGAAGACGGATTG
EST: gi|32840242|gb|CD979923.1|CD979923
EST:     GCTGGTCTACCCATACATGGCTAATGGCAGTGTGGCATCACGTTTACGAG                         AGCGCCAGGCATCTGAACCACCTCTTAAATGGGAAACAAGAAGACGGATTG
genomic: GCTGGTCTACCCATACATGGCTAATGGCAGTGTGGCATCACGTTTACGAGgttctttatt ... gattccatagAGCGCCAGGCATCTGAACCACCTCTTAAATGGGAAACAAGAAGACGGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actaaacaagcagaacgttagcttcctgttctcattaaactttctgattccatagAGCGCCAGGCATCTGAACCACCTCTTAAATGGGAAACAAGAAGACGGATTGCACTGGGATCTGCAAGAGGTCTTTCTTACTTGCATGATCACTGCGATCC
                                       ctttctg  CT-rich tract
                                 attaaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctttattctttattataatttataaaaaacctgattccatagtcccaactaaacaagcagaacgttagcttcctgttctcattaaactttctgattccatagAGCGCCAGGCATCTGAACCACCTCTTAAATGGGAAACAAGAAGACGGATTGCACTGGGATCTGCAAGAGGTCTTTCTTACTTGCATGATCACTGCGATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG