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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattttatggctgttgttttaaactgtgatatagaatattcttagttcttcatcccaaaacctaatcataaatttctttgacgttattgagTTATGATGCACTACATGGGGTTGGTGGAGCATATGCAAAGAGTATATTTGTGGATGAGCTTGGGGCACAAGAAAGCTCTTTACTGAACTGTACACCAAAG

Basic information

species Glycine max
transcript GLYMA05G34790.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 9
-------gtatattttatggctgttgttttaaactgtgatatagaatattctt---agttcttcatcccaaaacctaat------cataaatttc-tttgacgttatt----gagTTATGATGCACTACATGGGGTTGGTGGAGCATATGCAAAGAGTATATTTGTGGATGAGCTTGGGGCACAAGAAAGCTCTTTACTGAACTGTACACCAAAG
       |||    |  | | || |  ||||        |||| | | || ||    |    |  |     || ||  |      | ||| |||  ||  | ||||||     |||||||||||||| ||||| ||||||||||| ||||||||| | |||||||| || |||||||| |||||||||||||| || ||||||||    || |||
gtatatagtaggcctcttagttggttctttattgctgagtatatatttttttttttggaatatttttttggaatctggtggataccttaacttttgttcaatgttatttttaaagTTATGATGCACTGCATGGAGTTGGTGGAGCTTATGCAAAGCGAATATTTGTTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAG
















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|254347113|gb|GR856783.1|GR856783
EST:     GATTTTGAATCTATCAGGAAACTGCTGTCATCTCCTAAATTCACATTCTG                         TTATGATGCACTACATGGGGTTGGTGGAGCAT--GCAAAGAGTATATTTGT
genomic: GATTTTGAATCTATCAGGAAACTGCTGTCATCTCCTAAATTCACATTCTGgtatatttta ... cgttattgagTTATGATGCACTACATGGGGTTGGTGGAGCATATGCAAAGAGTATATTTGT
EST: gi|193582060|gb|FK536943.1|FK536943
EST:     GA-TTTGAATCTATCAGGAAACTGCTGTCATCTCCTAAATTCACATTCTG                         TTATGATGCACTACATGGGGTT
genomic: GATTTTGAATCTATCAGGAAACTGCTGTCATCTCCTAAATTCACATTCTGgtatatttta ... cgttattgagTTATGATGCACTACATGGGGTT
EST: gi|6567342|gb|AW234953.1|AW234953
EST:     GATTTTGAATCTATCAGGAAACTGCTGTCATCTCCTAAATTCACATTCTG                         TTATGATGCACTACATGGGGTTGGTGGAGCATATGCAAAGAGTATATTTGT
genomic: GATTTTGAATCTATCAGGAAACTGCTGTCATCTCCTAAATTCACATTCTGgtatatttta ... cgttattgagTTATGATGCACTACATGGGGTTGGTGGAGCATATGCAAAGAGTATATTTGT
EST: gi|193696490|gb|FK639774.1|FK639774
EST:     GATTTTGAATCTATCAGGAAACTGCTGTCATCTCCTAAATTCACATTCTG                         TTATGATGCACTACATGGGGTT
genomic: GATTTTGAATCTATCAGGAAACTGCTGTCATCTCCTAAATTCACATTCTGgtatatttta ... cgttattgagTTATGATGCACTACATGGGGTT
EST: gi|208318113|gb|GE110636.1|GE110636
EST:     GATTTTGAATCTATCAGGAAACTGCTGTCATCTCCTAAATTCACATTCTG                         TTATGATGCACTACATGGGGTTGGTGGAGCATATGCAAAGAGTATATTTGT
genomic: GATTTTGAATCTATCAGGAAACTGCTGTCATCTCCTAAATTCACATTCTGgtatatttta ... cgttattgagTTATGATGCACTACATGGGGTTGGTGGAGCATATGCAAAGAGTATATTTGT
EST: gi|10845957|gb|BF068962.1|BF068962
EST:     GATTTTGAATCTATCAGGAAACTGCTGTCATCTCCTAAATTCACATTCTG                         TTATGATGCACTACATGGGGTTGGTGGAGCATATGCAAAGAGTATATTTGT
genomic: GATTTTGAATCTATCAGGAAACTGCTGTCATCTCCTAAATTCACATTCTGgtatatttta ... cgttattgagTTATGATGCACTACATGGGGTTGGTGGAGCATATGCAAAGAGTATATTTGT
EST: gi|193710091|gb|FK645155.1|FK645155
EST:     CATCTCCTAAATTCACATTCTG                         TTATGATGCACTACATGGGGTT
genomic: CATCTCCTAAATTCACATTCTGgtatatttta ... cgttattgagTTATGATGCACTACATGGGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcttagttcttcatcccaaaacctaatcataaatttctttgacgttattgagTTATGATGCACTACATGGGGTTGGTGGAGCATATGCAAAGAGTATATTTGTGGATGAGCTTGGGGCACAAGAAAGCTCTTTACTGAACTGTACACCAAAG
                          taatcataaatttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattttatggctgttgttttaaactgtgatatagaatattcttagttcttcatcccaaaacctaatcataaatttctttgacgttattgagTTATGATGCACTACATGGGGTTGGTGGAGCATATGCAAAGAGTATATTTGTGGATGAGCTTGGGGCACAAGAAAGCTCTTTACTGAACTGTACACCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA