Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catcaaatgtatttcataagcctgtgcagacataaaatttatgtctattgcctgattttatattgcaaaggctaatcttatacatgctcttttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA

Basic information

species Glycine max
transcript GLYMA18G47920.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47920.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g00820.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------------------------------------------------------------catcaaatgtatttcataagcctgtgcagacataaaatttatgtctattgcctgattttatattgcaaaggctaatct--tatacatgctcttttggt--------tttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA-
                                                                                  | ||   ||| | |  |||   | |   |    |  |||   |   |   ||| |||  | | |  ||   || || |  |  |  || | |||||||        ||||||||||||| ||||||||||| ||||||||  |||| || | ||  || |||||||||| 
gtaagttgggaccaacctttatgagttggccttgttttcaaataaatcaaatctaattaaaggaatcataactccatactctcctcgtctgtttgttgtaactttttatggtttcaccatt---gcaaagaacctaattcaacacta-aagttctcatttgctgcatgtgtttttttggtctctccattttagCCTGGAAAATGGTCTTTCAACTCACACACGATTCTGAAGAACACCGAGCAGGCACCAAG
















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|193618431|gb|FK572555.1|FK572555
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|254345763|gb|GR859410.1|GR859410
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|207751867|gb|GD724084.1|GD724084
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|193325160|gb|FK291410.1|FK291410
EST:     TCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCCT                         -CCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAAC
genomic: TCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAG-CTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAAC
EST: gi|207753550|gb|GD725976.1|GD725976
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|193333542|gb|FK299488.1|FK299488
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|208309007|gb|GE101679.1|GE101679
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|208085854|gb|GD882444.1|GD882444
EST:     CAGTTATGGTGCCCCAGGGGCTTGTCCCTTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: CAGTTATGGTGCCCCAGGGGCTTG-CCCTT-ATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|254331915|gb|GR843658.1|GR843658
EST:     GGTGCCCCAGGGGCTTGCCCTTAT-CCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|192325685|gb|FK015042.1|FK015042
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCT
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCT
EST: gi|207766656|gb|GD738284.1|GD738284
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGT
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGT
EST: gi|208290698|gb|GE082790.1|GE082790
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|208145882|gb|GD941407.1|GD941407
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGCGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|208246680|gb|GE046224.1|GE046224
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTAAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|254331914|gb|GR843657.1|GR843657
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTC
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTC
EST: gi|207734721|gb|GD710152.1|GD710152
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|193427480|gb|FK393520.1|FK393520
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|208134798|gb|GD927467.1|GD927467
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|193356816|gb|FK319564.1|FK319564
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|208124293|gb|GD920505.1|GD920505
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTGTCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|208150608|gb|GD945123.1|GD945123
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|207700941|gb|GD682830.1|GD682830
EST:     GTCGGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|208080432|gb|GD878972.1|GD878972
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACAC
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACAC
EST: gi|193325826|gb|FK290265.1|FK290265
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|254345762|gb|GR859409.1|GR859409
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|207702293|gb|GD683048.1|GD683048
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|193679248|gb|FK619710.1|FK619710
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|207740907|gb|GD715853.1|GD715853
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAA-GCAGTGAAC
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAA-GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAAC
EST: gi|208035516|gb|GD837680.1|GD837680
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|208218438|gb|GE017506.1|GE017506
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|207790915|gb|GD760484.1|GD760484
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
EST: gi|192299870|gb|FG987828.1|FG987828
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAAC
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGG-AAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAAC
EST: gi|207727158|gb|GD704328.1|GD704328
EST:     GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCT                         TCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA
genomic: GTCAGTTATGGTGCCCCAGGGGCTTGCCCTTATCCCCGACAACTGAAGCTtgtaagtcac ... tttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgcctgattttatattgcaaaggctaatcttatacatgctcttttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA
                        ggctaat  putative branch site (score: 3)
                                       tgctctttt  putative PPT
         attttatattgcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catcaaatgtatttcataagcctgtgcagacataaaatttatgtctattgcctgattttatattgcaaaggctaatcttatacatgctcttttggttttaGCCTGGAAAGTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA

- - - - - - - - - - - - tgcagac
- - - - - - - - - - - - - - - - - - - - - - -tattgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgctc