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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggggcggtgtaatttttttgtgctggaatttttaattcagttgattgtgcttgtagttatattacataatggttaatgccttatatttgaactgtgatagGTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAGAAGGGCCAAACTCTACTATCTGAGGGAGAGAATGAACCCACTTAAAAAT

Basic information

species Glycine max
transcript GLYMA08G34520.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G34520.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g09390.t01 (Vitis vinifera), 3'ss of exon 5
------ggggcggtgtaatttttttgtgctggaatttttaattc--agttgattgtgcttgtagttatattacataatggttaatgccttatatttgaactgtgatagGTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAGAAGGGCCAAACTCTACTATCTGAGGGAGAGAATGAACCCACTTAAAAAT
      |     |||    ||||   ||||   ||  ||  ||     ||||   ||||  ||||     | ||||||||  ||      ||   ||     ||| ||||| ||||| | |||||||||||| ||||| || |||||||||| ||||||||||||||| || || ||||| ||||| | ||||||  ||||||  || 
ttttctgattttgtgggtcttttacctgctttcatcatttgtttttgattgacaatgctcttagtctc--tgcataatggccaa------atgagtgcgtgatgacagGTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAGAAGGGCCAAGCTTTATTATCTCAGGGACAAAATGAATGCACTTAGGAAA
















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|19348978|gb|BM893510.1|BM893510
EST:     AGAATTAGGAGGCAGGTGGCTGGGGTTGGGATTGAATCTTTATTCCCTCT                         GTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAG
genomic: AGAATTAGGAGGCAGGTGGCTGGGGTTGGGATTGAATCTTTATTCCCTCTgtaagtatta ... actgtgatagGTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAG
EST: gi|120532190|gb|EH260323.1|EH260323
EST:     AGAATTAGGAGGCAGGTGGCTGGGGTTGGGATTGAATCTTTATTCCCTCT                         GTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAG
genomic: AGAATTAGGAGGCAGGTGGCTGGGGTTGGGATTGAATCTTTATTCCCTCTgtaagtatta ... actgtgatagGTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAG
EST: gi|151409621|gb|EV279429.1|EV279429
EST:     AGAATTAGGAGGCAGGTGGCTGGGGTTGGGATTGAATCTTTATTCCCTCT                         GTATTCACCTAACATAAAGGAGAT
genomic: AGAATTAGGAGGCAGGTGGCTGGGGTTGGGATTGAATCTTTATTCCCTCTgtaagtatta ... actgtgatagGTATTCACCTAACATAAAGGAGAT
EST: gi|192330084|gb|FK020900.1|FK020900
EST:     AGAATTAGGAGGCAGGTGGCTGGGGTTGGGATTGAATCTTTATTCCCTCT                         GTATTCACCTAACATAAAGGAGAT
genomic: AGAATTAGGAGGCAGGTGGCTGGGGTTGGGATTGAATCTTTATTCCCTCTgtaagtatta ... actgtgatagGTATTCACCTAACATAAAGGAGAT
EST: gi|22929866|gb|BU547005.1|BU547005
EST:     AGAATTAGGAGGCAGGTGGCTGGGGTTGGGATTGAATCTTTATTCCCTCT                         GTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAG
genomic: AGAATTAGGAGGCAGGTGGCTGGGGTTGGGATTGAATCTTTATTCCCTCTgtaagtatta ... actgtgatagGTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAG
EST: gi|120531812|gb|EH259945.1|EH259945
EST:     AGAATTAGGAGGCAGGTGGCTGGGGTTGGGATTGAATCTTTATTCCCTCT                         GTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAG
genomic: AGAATTAGGAGGCAGGTGGCTGGGGTTGGGATTGAATCTTTATTCCCTCTgtaagtatta ... actgtgatagGTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAG
EST: gi|192300410|gb|FG988827.1|FG988827
EST:     AGAATTAGGAGGCAGGTGGCTGGGGTTGGGATTGAATCTTTATTCCCTCT                         GTATTCACCTAACATAAAGGAG
genomic: AGAATTAGGAGGCAGGTGGCTGGGGTTGGGATTGAATCTTTATTCCCTCTgtaagtatta ... actgtgatagGTATTCACCTAACATAAAGGAG
EST: gi|192330085|gb|FK020901.1|FK020901
EST:     AGAATTAGGAGGCAGGTGGCTGGGGTTGGGATTGAATCTTTATTCCCTCT                         GTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAG
genomic: AGAATTAGGAGGCAGGTGGCTGGGGTTGGGATTGAATCTTTATTCCCTCTgtaagtatta ... actgtgatagGTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAG
EST: gi|208030856|gb|GD829328.1|GD829328
EST:     AGAATTAGGAGGCAGGTGGCTGGGGTTGGGATTGAATCTTTATTCCCTCT                         GTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAG
genomic: AGAATTAGGAGGCAGGTGGCTGGGGTTGGGATTGAATCTTTATTCCCTCTgtaagtatta ... actgtgatagGTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAG
EST: gi|120531982|gb|EH260115.1|EH260115
EST:     GAATTAGGAGGCAGGTGGCTGGGGTTGGGAATTGAATCTTTATTCCCTCT                         GTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAG
genomic: GAATTAGGAGGCAGGTGGCTGGGGTTGGGA-TTGAATCTTTATTCCCTCTgtaagtatta ... actgtgatagGTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAG
EST: gi|193327744|gb|FK295501.1|FK295501
EST:     GGGGTTGGGATTGAATCTTTATTCCCTCT                         GTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAG
genomic: GGGGTTGGGATTGAATCTTTATTCCCTCTgtaagtatta ... actgtgatagGTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcttgtagttatattacataatggttaatgccttatatttgaactgtgatagGTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAGAAGGGCCAAACTCTACTATCTGAGGGAGAGAATGAACCCACTTAAAAAT
                         ggttaat  putative branch site (score: 4)
           ttatattacataatgg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggggcggtgtaatttttttgtgctggaatttttaattcagttgattgtgcttgtagttatattacataatggttaatgccttatatttgaactgtgatagGTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAGAAGGGCCAAACTCTACTATCTGAGGGAGAGAATGAACCCACTTAAAAAT

- ggcggtg
- - - - - - - - - - tgctgga
- - - - - - - - - - - - - - - - - - - - - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgcct