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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcattgaaatttcacttatcttacattataatgataatgaagttatgcggcactaaatttgtcatttccctgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGTCCCCCAGGAACTGGGAAAA

Basic information

species Glycine max
transcript GLYMA16G01810.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 6
---------------------------------------------gtaagtcattgaaatttcacttatcttacattataatgataatgaagttatgcggcactaaatttgtcatttccctgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGTCCCCCAGGAACTGGGAAAA
                                             |    || |||    |     ||  |    ||  | | ||  ||   || | | |      | || |  |||      | ||||||||| |||||||||||||| |||||||| |||||||||||||| ||||||||||||||||| || ||||| ||||| || || |||||||| ||||
gtatactaatcttttttcagttcatatcccttgtcgtgcaaacttgctcatccttgtgcatcaggctagttagttttggacttattttgctatt-tactgtttgctaattattgtttgttcata-gGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 6
-------------gtaagtcattgaaatttcacttatcttacattataat-gataatga----agttatgcggcactaaatttgtcatttccctgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGTCCCCCAGGAACTGGGAAAA
              |   |  |||  |  |  |  ||  | ||| ||| |   | | |     ||||  |   | ||    ||||   ||   |||| ||||||||||||||| |||||||| ||||| || |||||||||||||| |||||||||||||| || || ||||| ||||| || || || ||||| || |
gtatgtgatccttttttcttcttgtgagctggcacatactgcatcatagttagttacgggactagtttggttactctgtgcttgtaccttttttgca-gGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAAGGCGTCCTTTGCTATGGCCCACCTGGCACTGGCAAGA

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G110185_T04 (Zea mays), 3'ss of exon 5
----------gtaagtcattgaaatttcacttatcttacattataat-gataatgaagttatgcggcactaaatttgtcat--ttccctgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGTCCCCCAGGAACTGGGAAAA
           |   || |||  |  |     ||  | ||| | | |   | ||| |  |||   |      |||||   |  |    |   |||||||||||||||| |||||||| ||||| || |||||||||||||| ||||| ||||| || ||||| ||||| ||||| || || || ||||| || |
gtatgtggtccttcttccttgtgagctgggaaatactgcatcacagttagtgatggatctattttgtttactatttgctgtactatttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATTGACCCTCCGAAAGGTGTCCTTTGCTATGGCCCACCTGGTACTGGCAAGA

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------------------gtaagtcattgaaatttcacttatcttacattataatga--taatgaagttatgcggc--actaa-atttgtcatttccctgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGTCCCCCAGGAACTGGGAAAA
                                                      ||   |   |  | |  ||  ||  ||    |    |||  |  ||   || |   |    || | |||| | | ||     | |||| ||||| || || ||||| || || ||||| ||||| |||||||| ||||||||||| ||||||||||| || |||||||| || ||||| || ||||
gtgtgtatattctttttacatttttttttgtcagatcatatatgcatttacaccgtgtctttcttgattaacagctagtttttgatcctgtgaacttctgtccttctcttgtttgctgatatttataactttggctctagGTGGTTGAGCTCCCTATGCTCCACCCTGAGAAGTTTGTGAAGCTTGGAATTGATCCTCCTAAGGGTGTTCTCTGCTATGGTCCTCCTGGAACCGGTAAAA

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ13722 (Selaginella moellendorffii), 3'ss of exon 6
gtaagtcattgaaatttcacttatcttacattataatgataatgaagttatgcggcactaaatttgtcatttccctgca-agGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGTCCCCCAGGAACTGGGAAAA
          | || | |||  || |||||||    || |       ||   || |    |  ||  | ||| |    | ||||||| || ||||| ||||| ||||| ||||| ||| |||||||||| || |||||||| || || |||||||| || || || || |||||||||||||
----------gtaactacacc-attttacatt----tggt-------ttcctcgtcgacgatcttaacttttacgcatatagGTTGTAGAGCTTCCTATGCTCCATCCTGAGAAGTTTATCAAGCTTGGAATCGATCCTCCCAAAGGAGTTCTTTGCTACGGCCCTCCGGGAACTGGGAAAA

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 6
gtaagtcattgaaatttcacttatcttacattataatgataatgaagttatgcggcactaaatttgtcatttccctgca-agGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGTCCCCCAGGAACTGGGAAAA
          | || | |||  || |||||||    || |       ||   || |    |  ||  | ||| |    | ||||||| || ||||| ||||| || || || || ||| |||||||||| || |||||||| || || |||||||| || || || || |||||||||||||
----------gtaactacacc-attttacatt----tggt-------tttctcgtcgacgatcttaacttttacgcatatagGTTGTAGAGCTTCCTATGCTCCACCCTGAAAAGTTTATCAAGCTTGGAATCGATCCTCCCAAAGGAGTTCTTTGCTACGGCCCTCCGGGAACTGGGAAAA

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|208245634|gb|GE048888.1|GE048888
EST:     GCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
genomic: GCGGTTGTAAGGAGCAGATTGAGAAGATGCGTGAAgtaagtcatt ... tccctgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
EST: gi|16281984|gb|BI944774.1|BI944774
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAGAAGATGCGTGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAGAAGATGCGTGAAgtaagtcatt ... tccctgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
EST: gi|192297093|gb|FG988189.1|FG988189
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAGAAGATGCGTGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAGAAGATGCGTGAAgtaagtcatt ... tccctgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
EST: gi|208172296|gb|GD968913.1|GD968913
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAGAAGATGCGTGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAGAAGATGCGTGAAgtaagtcatt ... tccctgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
EST: gi|24205597|gb|BU964850.1|BU964850
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAGAAGATGCGTGAA                         GTTGTTGAACTTCCCATG
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAGAAGATGCGTGAAgtaagtcatt ... tccctgcaagGTTGTTGAACTTCCCATG
EST: gi|254319386|gb|GR829006.1|GR829006
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAGAAGATGCGTGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAGAAGATGCGTGAAgtaagtcatt ... tccctgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacattataatgataatgaagttatgcggcactaaatttgtcatttccctgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGTCCCCCAGGAACTGGGAAAA
                             cactaaa  putative branch site (score: 2)
                                    tttgtcatttccct  CT-rich tract
     tataatgataatgaa  TA-rich tract