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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtgacatcaaactattcccaaaaaaattgtttctgcattctccttttcagtaaattttcctctctgattttaactctttcccgtggcacttattttagGCAATAGAAACTGGGGTTGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG

Basic information

species Glycine max
transcript GLYMA01G36890.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G36890.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G66120.2 (Arabidopsis thaliana), 3'ss of exon 5
ctgtgacatcaaactattcccaaaaaaattgtttctgcattctccttttcagtaaattttcctctctgattttaactctttcc---cgtggcacttatttt---agGCAATAGAAACTGGGGTTGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG
                         || | ||  |     |   || ||    |  | |||   || |   |  |  |  ||    |    |||||| |||   |||| |||||||||||  |||| |||||  ||||||| |||||||| ||||||||||||||||||
-----------------------gtaagtagt--ccatgatggtctcttggacatttcttctcttcgggcctagatccactcatcacccatcacttaattttgcagGCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACG

upper sequence: GLYMA01G36890.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g03820.t01 (Vitis vinifera), 3'ss of exon 5
ctgtgacatcaaactattcccaaaaaaatt-gtttctgcattctccttttcagtaaattttcctctctgattttaactct--ttcccgtggcacttattttagGCAATAGAAACTGGGGTTGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG
   ||   | |     ||         ||    | |    || |  ||  ||   ||    | |     | |   | |||  ||  |    |  ||  || |||||||||||||||||||||| |||||||||||||| |||||||| |||||||||||||||| |
--ttggtttgaggagcttttagttgttatccagtcccatgttatatttaccaaagaaacccctttaagcaatcccattctgattatcacatc-ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCATG
















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|22932048|gb|BU549187.1|BU549187
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCAT                         GCAATAGAAACTGGGGTTGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTT
genomic: AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATgtgagtgatt ... cttattttagGCAATAGAAACTGGGGTTGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTT
EST: gi|213601684|gb|DB980913.1|DB980913
EST:     GGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCAT                         GCAATAGAAACTGGGGTTGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTT
genomic: GGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATgtgagtgatt ... cttattttagGCAATAGAAACTGGGGTTGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTT
EST: gi|213601032|gb|DB983707.1|DB983707
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCAT                         GCAATAGAAACTGGGAATT-TCTATGGTCAGTGGCTTCATGGAGAGGCTGT
genomic: AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATgtgagtgatt ... cttattttagGCAATAGAAACTGGG-GTTGGCTATGGGCAGTGGCTTCATGGAGAGGCTGT
EST: gi|209726585|gb|BW666503.1|BW666503
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCAT                         GCAATAGAAACTGGGGTTGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTT
genomic: AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATgtgagtgatt ... cttattttagGCAATAGAAACTGGGGTTGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTT
EST: gi|298196729|gb|HO041472.1|HO041472
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCAT                         GCAATAGAAACAGGGGTTGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTT
genomic: AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATgtgagtgatt ... cttattttagGCAATAGAAACTGGGGTTGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTT
EST: gi|192333520|gb|FK024049.1|FK024049
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCAT                         GCAATAGAAACTGGGGTTGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTT
genomic: AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATgtgagtgatt ... cttattttagGCAATAGAAACTGGGGTTGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcagtaaattttcctctctgattttaactctttcccgtggcacttattttagGCAATAGAAACTGGGGTTGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG
                        ttttaac  putative branch site (score: 2)
                                             cttatttt  putative PPT
     agtaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtgacatcaaactattcccaaaaaaattgtttctgcattctccttttcagtaaattttcctctctgattttaactctttcccgtggcacttattttagGCAATAGAAACTGGGGTTGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
ctgtgac
- - - - tcaaact
- - - - - - - - - cccaaaa
- - - - - - - - - - - - - - - - - - gcattct