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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtctcactccaaattacgtatagaatttgtaattgtagagcttatacgtttgaattgttgaggttttttttttaattgtttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAGGAAGCTCAAGTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATT

Basic information

species Arabidopsis thaliana
transcript AT4G25370.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G25370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G32910.1 (Glycine max), 3'ss of exon 2
-----------gtgagtctcactcca-aattacgtatagaatttgtaattgtagagcttatacgtttgaattgttgag-gttttttttttaa---ttgtttgattt----tagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAGGAAGCTCAAGTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATT
           ||   | ||  |    | | | |||      ||||  |||| |   || |  |||    |||||| | || | | |||| |   |||| || |||     || ||||||||||| ||||||||||||  ||||||||| |||||||| || |||||||||||||||||||  || || ||||| ||  |||||||||| |||
gtgagttcattgtttttgtcgtttttcagtgatgtaattgggttgttgttgttgttgttgt-tgttgttgttgttgtgtgtgtgtgttttgagggttgtgtggtttggttcagGTGGTCGGCGAGGGCTATAAAGTCATATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCACTTCTCATGGGGATT

upper sequence: AT4G25370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G35060.1 (Glycine max), 3'ss of exon 2
gtgagt---ctcactccaaattacgtatagaatttgtaattgtagagcttatacgtttgaattgttgaggttttttttttaattgtttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAGGAAGCTCAAGTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATT
||||||    |   |   | | | |||      ||||  ||||      |  | || ||  |   ||   |||     ||   || ||   || || ||||||||||| ||||||||||||  |||||| || |||||||| || |||||||||||||||||||  ||  | ||  | ||  |||||||||| |||
gtgagttcattgtttttgagtgatgtaattgggttgttgttgtttgttgttgatgtgtgtgtgtgtgtattttaagggttgtgtggtttggttcagGTGGTCGGCGAGGGCTATAAAGTCATATGCAATTGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGCGAACTAATGCACTTCTCATGGGGATT

upper sequence: AT4G25370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G28050.1 (Glycine max), 3'ss of exon 2
--------------gtgagtctcactccaaattac--gtatagaatttgtaattgtagagcttatacgtttgaattgttgaggttttttttttaattgtttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAGGAAGCTCAAGTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATT
              ||   | |   |     ||    ||   | | |||  ||||| | |  | |  || ||  |  |||||| || || |      ||||| ||  || ||||||||||| |||||||| ||   ||||||||| |||||||| || |||||||||||||||||||  || || ||||| ||  |||||||||| |||
gtcagttcgttgttgttgttgttgttgtcgtttttcagtgacgtaattg-gattgttgtgtgtgtctgtgtgtgtgtttgaggattgttgt------gtttggttc-agGTGGTCGGCGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCACTTCTCATGGGGATT

upper sequence: AT4G25370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G28040.1 (Glycine max), 3'ss of exon 2
--------------gtgagtctcactccaaattacgtatag---aatttg-taattgtagagcttatacgtttgaattgttgaggttttttttttaattgtttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAGGAAGCTCAAGTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATT
              ||   | | | |     ||  |  | |   |||| | |  ||||    ||| || || ||   | |||||| || |   ||   |||||| ||  || ||||||| ||| |||||||| ||   ||||||||| |||||||| || |||||||||||||||||||  || || ||||| || ||||||||||| |||
gtgagttcattgttgttgttgttattgtcgtttttgagtggcgtaattggattgttgtgtcacttgtatgtgtg---ttttgagggttgtgccttgtgtgtttggttc-agGTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATT

upper sequence: AT4G25370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G32900.1 (Glycine max), 3'ss of exon 2
gtgagtctcactccaaattacgtatagaatttgtaattgtagagcttatacgtttgaattgttgaggttttttttttaattgtttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAGGAAGCTCAAGTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATT
|||||| ||| |     |  ||| |    |  || | | ||  |  |    || ||| |   || | |||     ||   || ||   || || ||||||| ||| | |||||| ||   ||||||||| |||||||| || |||||||||||||||||||  || || ||||| ||  |||||||||| |||
gtgagt-tcattgttgttgtcgtttt---tcagtgactttattggattgttgtgtgagtg--tgtgttttgagggttgtgtggtttggttcagGTGGTCGGAGAGGGGTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCGCTTCTCATGGGGATT

upper sequence: AT4G25370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0022g01840.t01 (Vitis vinifera), 3'ss of exon 2
gtgagtctcactccaaa-ttacgtatagaatttgtaattgtagagcttatacgtttga-attgttgaggttttttttttaattgtttgat------tttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAGGAAGCTCAAGTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATT
     |   | |  ||| |||  | |     || |  || |    |||      | || | ||||     ||  |||  |  | |  ||       |||||||||||||| || || ||||||||| || | ||||  |||||||| || |||||||| ||||| |||| ||| || ||||| ||  |||| ||||| || 
-aatataatattgaaaacttatttttctttgttctccttatttttcttggcaactagacagtgttagaacttactttaaatgtatgggaaatggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAGGAAGCTGAAGTACCCAAATACTGGAACCGAGGCTCTTCTAATGGGAATC

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|86036181|gb|DR331934.1|DR331934
EST:     GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAA                         ATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
genomic: GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAAgtgagtctca ... ttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
EST: gi|86036191|gb|DR331944.1|DR331944
EST:     GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAA                         ATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
genomic: GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAAgtgagtctca ... ttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
EST: gi|47830527|gb|CK120211.1|CK120211
EST:     GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAA                         ATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
genomic: GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAAgtgagtctca ... ttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
EST: gi|86036195|gb|DR331948.1|DR331948
EST:     GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAA                         ATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
genomic: GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAAgtgagtctca ... ttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
EST: gi|86036182|gb|DR331935.1|DR331935
EST:     GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAA                         ATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
genomic: GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAAgtgagtctca ... ttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
EST: gi|47828108|gb|CK117792.1|CK117792
EST:     GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAA                         ATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
genomic: GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAAgtgagtctca ... ttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
EST: gi|86036189|gb|DR331942.1|DR331942
EST:     GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAA                         ATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
genomic: GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAAgtgagtctca ... ttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
EST: gi|86036183|gb|DR331936.1|DR331936
EST:     GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAA                         ATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
genomic: GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAAgtgagtctca ... ttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
EST: gi|86036190|gb|DR331943.1|DR331943
EST:     GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAA                         ATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
genomic: GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAAgtgagtctca ... ttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
EST: gi|86036188|gb|DR331941.1|DR331941
EST:     GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAA                         ATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
genomic: GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAAgtgagtctca ... ttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
EST: gi|86036196|gb|DR331949.1|DR331949
EST:     GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAA                         ATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
genomic: GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAAgtgagtctca ... ttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
EST: gi|86036193|gb|DR331946.1|DR331946
EST:     GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAA                         ATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
genomic: GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAAgtgagtctca ... ttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
EST: gi|86036186|gb|DR331939.1|DR331939
EST:     GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAA                         ATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
genomic: GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAAgtgagtctca ... ttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
EST: gi|86036194|gb|DR331947.1|DR331947
EST:     GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAA                         --G-TCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTBGAGGCTAG
genomic: GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAAgtgagtctca ... ttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
EST: gi|86036192|gb|DR331945.1|DR331945
EST:     GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAA                         ATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
genomic: GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAAgtgagtctca ... ttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
EST: gi|86036197|gb|DR331950.1|DR331950
EST:     GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAA                         ATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
genomic: GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAAgtgagtctca ... ttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
EST: gi|86036185|gb|DR331938.1|DR331938
EST:     GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAA                         ATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
genomic: GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAAgtgagtctca ... ttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
EST: gi|86036198|gb|DR331951.1|DR331951
EST:     GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAA                         ATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG
genomic: GCAACCGGAGAATGGTTCTTCGGATAAGATCCCAAAgtgagtctca ... ttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagagcttatacgtttgaattgttgaggttttttttttaattgtttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAGGAAGCTCAAGTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATT
                          aggttttttttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtctcactccaaattacgtatagaatttgtaattgtagagcttatacgtttgaattgttgaggttttttttttaattgtttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAGGAAGCTCAAGTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA