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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattatttgttccttgtgttttgcttgttaccattgactcaaatcttaactgaaattgatgtgttggaattttgtttgccgggaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATGCTGTTTTGCTTGTTTAAGGTCGCATCAGGGTTCCAACTTGATTTCAGAG

Basic information

species Glycine max
transcript GLYMA02G35500.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G009876_T01 (Zea mays), 3'ss of exon 8
gtaagattatttgttccttgtgttttgcttgttaccattgactcaaatcttaactgaaattgatgtgttggaattttgtttgccgggaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATGCTGTTTTGCTTGTTTAAGGTCGCATCAGGGTTCCAACTTGATTTCAGAG--
|| |||  || ||     | |  | ||||  ||       ||  |   ||| ||     |  || |    ||||||  | ||       |||||| ||||| ||||| || ||||| ||||| || |||||||| ||||| |||||||||||||| || ||  | |  |    | ||     |||||    | |  
gtgagaa-atctgccaactcttctgtgctctttttacccaaccta--ccttgaccctgttcaat-taacagaatttcttgtgt------tgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATGCTGTTTTGCTAGTGTAGAGCCATAGTGAGATTTTG--TTGATGGTGGTGAA

upper sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 8
gtaagattatttgttccttgtgttttgcttgttaccattgactcaaatcttaactgaaattgatgtgttggaattttgtttgccgggaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATGCTGTTTTGCTTGTTTAAGGTCGCATCAGGGTTCCAACT-TGATTTCAGAG
|| |||  |||||     | | || | ||| || |       ||||  | || ||  | |   | |     ||      ||||  |   |||||| ||||| ||||| || ||||| ||||| || || ||||| ||||| |||||||||||||| || ||    |  |    | ||     | || |     | 
gtgagaa-atttgccagctttcttct-cttcttgc-------tcaa--cctaccttgagtcctttt-caataaaccaaattgcttgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAATGATGGGTGTATCAATGCTGTTTTGCTAGTGTAGAACCATAGTGAGATTTTGTTTATGGTGATGAA-

upper sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagattatttgttccttgtgttttgcttgttaccattgactcaaatcttaactgaaattgatgtgttggaattttgtttgccgg--gaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATGCTGTTTTGCTTGTTTAAGGTCGCATCAGG-GTTCCAACTTGATTTCAGAG
            ||   |     | | |     | | ||    ||||   ||| |   |||   | ||   || | | | | |     || | |||| ||||||||||| || ||||| || ||||| ||||| || ||||||||||||||||| ||||| |||       || ||   |        | |   || 
------------gtaagtgacaatatacac---aaccttagtgcaaactataattttgatttcagagtcttaactctctcttcaatttgacttcagGAAAATACGCTCAAGTGACAAACAATCCAGAGAACGACGGATGTATAAATGCTGTTTTACTTGTGTAACCAAATGTCCGGCACTGTCGTAGAAGTATGGA-

upper sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 8
gtaaga--ttatttgttccttgtgttttgcttgttaccattgactcaaatcttaactgaaattgatgtgttggaattttg----tttgccgggaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATGCTGTTTTGCTTGTTTAAGGTCGCATCAG-GGTTCCAACTTGATTTCAGAG-
||||||  || |||  |  ||||  | |  |  ||    |    |    || |        ||  | | ||  | ||||     | ||  | | ||| ||| |||||||| || || |||||||||||||| || ||||| ||||||||||||||||||||||| ||||   | || |       ||||  || |   | | 
gtaagaaattttttactatttgtactattttcattgttttgtgtttgcttcatctgcagcttttttattttttattttttgaattctgtggtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATGCTGTTTTGCTTGTGTAAGA--GGATTATCAACAGCAACAAGAATATGGTGG

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|192313831|gb|FK007647.1|FK007647
EST:     GAATGTCAGTGAACTTGGTCTTGTCACGCCGGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAG-TCACAAATAACCCAGAAA-CGATGGTTGTATA
genomic: GAATGTCAGTGAACTTGGTCTTGTCACGCCGGCTGGGAAAGTTGTGTGGGgtaagattat ... gggaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATA
EST: gi|208031232|gb|GD829816.1|GD829816
EST:     CGGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGATTGTATAAATG
genomic: CGGCTGGGAAAGTTGTGTGGGgtaagattat ... gggaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATG
EST: gi|193526130|gb|FK480655.1|FK480655
EST:     CGGCTGGGAAAGTCGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAACGA
genomic: CGGCTGGGAAAGTTGTGTGGGgtaagattat ... gggaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAACGA
EST: gi|31310190|gb|CD395393.1|CD395393
EST:     GAATGTCAGTGAACTTGGTCTTGTCACGCCGGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATG
genomic: GAATGTCAGTGAACTTGGTCTTGTCACGCCGGCTGGGAAAGTTGTGTGGGgtaagattat ... gggaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATG
EST: gi|193598354|gb|FK553288.1|FK553288
EST:     CGGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATG
genomic: CGGCTGGGAAAGTTGTGTGGGgtaagattat ... gggaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATG
EST: gi|193590509|gb|FK544987.1|FK544987
EST:     GCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATG
genomic: GCTGGGAAAGTTGTGTGGGgtaagattat ... gggaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATG
EST: gi|31312274|gb|CD397477.1|CD397477
EST:     GAATGTCAGTGAACTTGGTCTTGTCACGCCGGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATG
genomic: GAATGTCAGTGAACTTGGTCTTGTCACGCCGGCTGGGAAAGTTGTGTGGGgtaagattat ... gggaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATG
EST: gi|20811431|gb|BQ295909.1|BQ295909
EST:     GAATGTCAGTGAACTTGGTCTTGTCACGCCGGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATG
genomic: GAATGTCAGTGAACTTGGTCTTGTCACGCCGGCTGGGAAAGTTGTGTGGGgtaagattat ... gggaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATG
EST: gi|16348558|gb|BI974153.1|BI974153
EST:     GAATGTCAGTGAACTTGGTCTTGTCACGCCGGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATG
genomic: GAATGTCAGTGAACTTGGTCTTGTCACGCCGGCTGGGAAAGTTGTGTGGGgtaagattat ... gggaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATG
EST: gi|208187025|gb|GD985097.1|GD985097
EST:     CGGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATG
genomic: CGGCTGGGAAAGTTGTGTGGGgtaagattat ... gggaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactcaaatcttaactgaaattgatgtgttggaattttgtttgccgggaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATGCTGTTTTGCTTGTTTAAGGTCGCATCAGGGTTCCAACTTGATTTCAGAG
                                aattttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattatttgttccttgtgttttgcttgttaccattgactcaaatcttaactgaaattgatgtgttggaattttgtttgccgggaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATGCTGTTTTGCTTGTTTAAGGTCGCATCAGGGTTCCAACTTGATTTCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT