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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagacaattaaaccaaatgaagataacatttcttgttcttgcttagcttacttatagttatcattgaagtgcattcatgtacttctcttgctttttgcagGTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATCAGAAAGCGGTTTTACTCTTTAAATCTGGCTAGCCTTATTGTGGTAGCAA

Basic information

species Glycine max
transcript GLYMA15G16060.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G16060.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G146012_T01 (Zea mays), 3'ss of exon 2
cagacaattaaaccaaatgaagataacatttc--ttgttcttgcttagcttacttatagttatca---ttgaagtgcattcatgtacttctcttgctttttgcagGTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATCAGAAAGCGGTTTTACTCTTTAAATCTGGCTAGC--CTTATTGTGGTAGCAA
     | | |||     | |  |   |||| |  || ||| || |   | || | |  || | ||   |||    |||||  | || || |    |||  |||||||||||| ||||| || || |||||| ||||||| ||||||||| | ||    ||||| || || || || || ||||| |     ||    |  |  ||  
--aggattaaaattcccttacaaacccattccgtttattcatgatatacatattgaatgtcaacaattttgctaagcatttttttatttgtt---cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACTCTAAAGCTGTCTTGCTATTCAAGTCTGGGTGATTGCTCGCAGCCGACGC--

upper sequence: GLYMA15G16060.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0077g02110.t01 (Vitis vinifera), 3'ss of exon 2
------cagacaattaaaccaaatgaagataacatttcttgttcttgcttagcttacttatagttatcattgaagtgcattcatgtacttctcttgctttttgcagGTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATCAGAAAGCGGTTTTACTCTTTAAATCTGGCT-AGCCTTATTGTGGTAGCAA
      |     |||     |||  || ||   ||| |   || ||    | |||    |||   ||   | ||   ||||  | |  | ||  |  ||| | ||||||||||||||||||||||||||||||| |||||||| ||||| ||||| || || || || || || || |||||||| | ||  |  |  || |     
attcttctagtcatttggtgaaa--aatatgggattgca-attgttttaaaacttttaaataaagatgccttaac--cattt-tattttcctggttttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACCAAAAGGCAGTCTTGCTGTTCAAATCTGGTTGAGAGTGGTGATGATGTTG-
















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|208049309|gb|GD845720.1|GD845720
EST:     CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         GTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC
genomic: CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaactccct ... ctttttgcagGTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC
EST: gi|193716433|gb|FK653697.1|FK653697
EST:     CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         GTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC
genomic: CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaactccct ... ctttttgcagGTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC
EST: gi|24136401|gb|BU926911.1|BU926911
EST:     CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         GTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC
genomic: CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaactccct ... ctttttgcagGTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC
EST: gi|193618662|gb|FK567942.1|FK567942
EST:     CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         GTTCATATGTGACTCATGAAAACAAACCACTTTGTTTAT
genomic: CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaactccct ... ctttttgcagGTTCATATGTGACTCATGAAA-CAAACCACTTTGTTTAT
EST: gi|207775556|gb|GD747323.1|GD747323
EST:     CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         GTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC
genomic: CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaactccct ... ctttttgcagGTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC
EST: gi|193518425|gb|FK476682.1|FK476682
EST:     CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         GTTCATATGTGACTCATGAAACAAACCNCTTTGTTTATTTCTACTTGGATC
genomic: CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaactccct ... ctttttgcagGTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC
EST: gi|208196324|gb|GD988627.1|GD988627
EST:     CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         GTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC
genomic: CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaactccct ... ctttttgcagGTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC
EST: gi|193617201|gb|FK571227.1|FK571227
EST:     CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         GTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC
genomic: CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaactccct ... ctttttgcagGTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC
EST: gi|207766817|gb|GD735617.1|GD735617
EST:     CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         GTTCATATGTGACTCATGAAACAAACCNCTTTGTTTATTTCTACTTGGATC
genomic: CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaactccct ... ctttttgcagGTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC
EST: gi|208047034|gb|GD846035.1|GD846035
EST:     CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         GTTCATATGTGACTCATGAAACAAACCACTTTGTT
genomic: CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaactccct ... ctttttgcagGTTCATATGTGACTCATGAAACAAACCACTTTGTT
EST: gi|208237838|gb|GE030792.1|GE030792
EST:     CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         GTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC
genomic: CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaactccct ... ctttttgcagGTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC
EST: gi|193616068|gb|FK568680.1|FK568680
EST:     CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         GTTCATATGTGACTCATGAAACAA
genomic: CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaactccct ... ctttttgcagGTTCATATGTGACTCATGAAACAA
EST: gi|193622739|gb|FK571051.1|FK571051
EST:     CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         GTTCATATGTGACTCATGAAACAAACCACTTTGTTTAT
genomic: CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaactccct ... ctttttgcagGTTCATATGTGACTCATGAAACAAACCACTTTGTTTAT
EST: gi|207680422|gb|GD661824.1|GD661824
EST:     CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         GTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC
genomic: CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaactccct ... ctttttgcagGTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC
EST: gi|208156673|gb|GD957235.1|GD957235
EST:     CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         GTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC
genomic: CGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaactccct ... ctttttgcagGTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttacttatagttatcattgaagtgcattcatgtacttctcttgctttttgcagGTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATCAGAAAGCGGTTTTACTCTTTAAATCTGGCTAGCCTTATTGTGGTAGCAA
 agcttac  putative branch site (score: 3)
                                  tacttctcttgctttt  putative PPT
      ttatagttatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagacaattaaaccaaatgaagataacatttcttgttcttgcttagcttacttatagttatcattgaagtgcattcatgtacttctcttgctttttgcagGTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATCAGAAAGCGGTTTTACTCTTTAAATCTGGCTAGCCTTATTGTGGTAGCAA

- - - - - aaccaaa
- - - - - - - - - - - - - - - - - -ttcttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcattca