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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agggctaggaagctgagttgtctgataatttattattttatttatcaacattttttgaggccaatccttccatccctaatcagttgcttgataattgcagGCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAAATGTTGGTAATGAAAAGATAGCACAGCAAAAGAAGGCAAATCCAGTGGC

Basic information

species Vitis vinifera
transcript Vv03s0038g03120.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g03120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G025366_T02 (Zea mays), 3'ss of exon 3
agggctaggaagctgagttgt--ctgataatttattattttatttatcaacattttttgaggccaatccttccatccctaatcagttgcttgataattgcagGCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAAATGTTGGTAATGAAAAGATAGCACAGCAAAAGAAGGCAAATCCAGTGGC
  |    ||||  |   |||   ||  ||||| || || |    |   |  |  |||   || ||  ||  | |  |||    |  ||| | ||  ||  |||||||||||||   ||  ||||||| ||||||||||| ||||| || ||||||||||| ||||| ||  | |   |||| ||||| ||||| || || ||
gagatatggaacttcttttggcgcttttaattaataatgtcgagtcagagtaagtttgatggtcaggcccactaatcctcgata-ctgcattatg-ttctagGCAATGTGGGTCAGGACTACGCCATCTTTGAGCAAGGCGCTTCTGCAGGAAATGTTGGGAATGAGAACCTTGTGGAGCAGAAGAAAGCAAACCCTGTCGC

upper sequence: Vv03s0038g03120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S101_151V6.1 (Physcomitrella patens), 3'ss of exon 3
agggctaggaagctgagttgtctgataatttattatttta---tttatcaacattttttga--ggccaatccttccatccctaatcagttgcttgataattgcagGCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAAATGTTGGTAATGAAAAGATAGCACAGCAAAAGAAGGCAAATCCAGTGGC
     |    | || |    |  |  |  ||     |  |   |   || ||  ||||  |  |  || || |   ||   |     | |  ||  |  ||||||||||||| || ||||| ||||| ||||||||||| || ||||| || || ||||| || |||||||   | |        || |  || |||||    ||
-----ttactatctcatccttaggccaggttgcagataaaagctgcttctacggttttcaactgatcagtcttgtaatttatctaatgatcatttttgcttgcagGCAATGTCGGAGCTGACCACGCTATTTTTGAGCAGGGAGCTTCTGCCGGTAATGTGGGAAATGAAAGACTGGTTGCTGGTAAAACAGCCAATCCCACAGC
















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|110356554|gb|EC919465.1|EC919465
EST:     GGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAG                         GCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAA
genomic: GGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAGgtaccttttc ... ataattgcagGCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAA
EST: gi|110685778|gb|EE062796.1|EE062796
EST:     GGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAG                         GCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAA
genomic: GGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAGgtaccttttc ... ataattgcagGCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAA
EST: gi|161713512|gb|FC063119.1|FC063119
EST:     GGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAG                         GCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAA
genomic: GGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAGgtaccttttc ... ataattgcagGCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAA
EST: gi|110388854|gb|EC953649.1|EC953649
EST:     GGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAG                         GCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAA
genomic: GGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAGgtaccttttc ... ataattgcagGCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAA
EST: gi|71888504|gb|DT037559.1|DT037559
EST:     GGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAG                         GCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAA
genomic: GGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAGgtaccttttc ... ataattgcagGCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAA
EST: gi|110369366|gb|EC933524.1|EC933524
EST:     GGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAG                         GCAATGTGGGTGCTGATCA
genomic: GGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAGgtaccttttc ... ataattgcagGCAATGTGGGTGCTGATCA
EST: gi|110385879|gb|EC950436.1|EC950436
EST:     GGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAG                         GCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAA
genomic: GGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAGgtaccttttc ... ataattgcagGCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAA
EST: gi|110419530|gb|EC985766.1|EC985766
EST:     GGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAG                         GCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCAGGAA
genomic: GGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAGgtaccttttc ... ataattgcagGCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAA
EST: gi|33410508|gb|CF216135.1|CF216135
EST:     GGTGTCATGCCAGGAG                         GCAATGTGGGTGCTGATCACGCCACTTTTGAGCAAGGTGCTTCAGCGGGAA
genomic: GGTGTCATGCCAGGAGgtaccttttc ... ataattgcagGCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAA
EST: gi|161714849|gb|FC063000.1|FC063000
EST:     GGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAG                         GCAATGTGGGTGCTGATCACGCCATTTTTGAGCA-GGTGCTTCAGCGGGAA
genomic: GGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAGgtaccttttc ... ataattgcagGCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacattttttgaggccaatccttccatccctaatcagttgcttgataattgcagGCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAAATGTTGGTAATGAAAAGATAGCACAGCAAAAGAAGGCAAATCCAGTGGC
                                          ttgataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agggctaggaagctgagttgtctgataatttattattttatttatcaacattttttgaggccaatccttccatccctaatcagttgcttgataattgcagGCAATGTGGGTGCTGATCACGCCATTTTTGAGCAAGGTGCTTCAGCGGGAAATGTTGGTAATGAAAAGATAGCACAGCAAAAGAAGGCAAATCCAGTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
-gggctag
- - - - - - - - - tgtctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gaggcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagttgc