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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaatatgatcaactgatcaagtatgctgttggtatttttgctatctcatgattttgtatttggtgtttctgaattctctttatttgatgcttttgaaagGTAATGGTTTCTGCAAAAGAAGAGCCAGATTGTCCCATACCACCTGCTGTTGATGGTTTGTTAAGGGTTCATAAGCAAGTTATCAATGTTGATCGTGACC

Basic information

species Glycine max
transcript GLYMA19G34470.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G34470.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0141g00800.t01 (Vitis vinifera), 3'ss of exon 2
------gaaatatgatcaactgatcaagtatgctgttggtatttttgctatct-catgat-tttgtatttggtgtttctgaattctctttatttgatgcttttgaaagGTAATGGTTTCTGCAAAAGAAGAGCCAGATTGTCCCATACCACCTGCTGTTGATGGTTTGTTAAGGGTTCATAAGCAAGTTATCAATGTTGATCGTGACC
      | || |  |||| || | |   | || | |  ||||      |  || ||| ||     |   | |  ||| |||  | | |||  |     |||||||||||||||||||||||| || |||||||| |||   || ||  | |||||| ||||||||||| | |||||||| ||     ||||  |||| ||  ||||  
tttttaggaagagaatcagct-acctgctgtgttttaagtatgaaaaatggcttcataatgcccctgactagactttttga--tgtttttgct-----cttttgaaagGTAATGGTTTCTGCGAAGGAAGAGCCTGATGCCCCAATTGCTCCTGCTATTGATGGTTTGCTGAGGGTTCACAAATGTATTATGGATGTAGAGAGTGATG
















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|207694645|gb|GD676504.1|GD676504
EST:     AGGCGCGAATTAAAATTCTTGACGGTCCACCTGGAATCTCAGAAAGAGCA                         GTAATGGTTTCTGCAAAAGAAGAGCCAGATTGTCCCATACC
genomic: AGGCGCGAATTAAAATTCTTGACGGTCCACCTGGAATCTCAGAAAGAGCAgtgagtttcg ... cttttgaaagGTAATGGTTTCTGCAAAAGAAGAGCCAGATTGTCCCATACC
EST: gi|193425504|gb|FK389981.1|FK389981
EST:     AGGCGCGAATTAAAATTCTTGACGGTCCACCTGGAATCTCAGAAAGAGCA                         GTAATGGTTTCTGCAAAAGAAGAGCCAGATTGTCCCATACCACCTGCTGTT
genomic: AGGCGCGAATTAAAATTCTTGACGGTCCACCTGGAATCTCAGAAAGAGCAgtgagtttcg ... cttttgaaagGTAATGGTTTCTGCAAAAGAAGAGCCAGATTGTCCCATACCACCTGCTGTT
EST: gi|193348789|gb|FK316913.1|FK316913
EST:     AGGCGCGAATTAAAATTCTTGACGGTCCACCTGGAATCTCAGAAAGAGCA                         GTAATGGTTTCTGCAAAAGAAGAGCCAGATTGTCCCATACCACCTGCTGTT
genomic: AGGCGCGAATTAAAATTCTTGACGGTCCACCTGGAATCTCAGAAAGAGCAgtgagtttcg ... cttttgaaagGTAATGGTTTCTGCAAAAGAAGAGCCAGATTGTCCCATACCACCTGCTGTT
EST: gi|193340089|gb|FK305414.1|FK305414
EST:     AGGCGCGAATTAAAATTCTTGACGGTCCACCTGGAATCTCAGAAAGAGCA                         GTAATGGTTTCTGCAAAAGAAGAGCCAGATTGTCCCATACCACCTGCTGTT
genomic: AGGCGCGAATTAAAATTCTTGACGGTCCACCTGGAATCTCAGAAAGAGCAgtgagtttcg ... cttttgaaagGTAATGGTTTCTGCAAAAGAAGAGCCAGATTGTCCCATACCACCTGCTGTT
EST: gi|193437978|gb|FK399211.1|FK399211
EST:     AGGCGCGAATTAAAATTCTTGACGGTCCACCTGGAATCTCAGAAAGAGCA                         GTAATGGTTTCTGCAAAAGAAGAGCCAGATTGTCCCATACCACCTGCTGTT
genomic: AGGCGCGAATTAAAATTCTTGACGGTCCACCTGGAATCTCAGAAAGAGCAgtgagtttcg ... cttttgaaagGTAATGGTTTCTGCAAAAGAAGAGCCAGATTGTCCCATACCACCTGCTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcatgattttgtatttggtgtttctgaattctctttatttgatgcttttgaaagGTAATGGTTTCTGCAAAAGAAGAGCCAGATTGTCCCATACCACCTGCTGTTGATGGTTTGTTAAGGGTTCATAAGCAAGTTATCAATGTTGATCGTGACC
                                     atttgat  putative branch site (score: 5)
                                           tgctttt  CT-rich tract
                           aattctctttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaatatgatcaactgatcaagtatgctgttggtatttttgctatctcatgattttgtatttggtgtttctgaattctctttatttgatgcttttgaaagGTAATGGTTTCTGCAAAAGAAGAGCCAGATTGTCCCATACCACCTGCTGTTGATGGTTTGTTAAGGGTTCATAAGCAAGTTATCAATGTTGATCGTGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - caactga
- - - - - - - - - - -gtatgct
- - - - - - - - - - - - - - gttggta
- - - - - - - - - - - - - - - - - - - -tgctatc
- - - - - - - - - - - - - - - - - - - - - - - -catgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttctg