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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttcttgttagtgcatgctttgttattattttggcctggactagaaattaaacgacttgttgaacttgttgattttggttttgttactttttggtcagGACAAAAAACGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGATACAAGAAAGATCTAATTAAGTTTGCCATCATTACATGTCGAAAACCTGA

Basic information

species Glycine max
transcript GLYMA12G01690.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G01690.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0039g01410.t01 (Vitis vinifera), 3'ss of exon 5
aatttcttgttagtgcatgctttgttattattttggcctggactagaa------attaaacgacttgttgaacttgttgattttggttttgttactttttggtcagGACAAAAAACGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGATACAAGAAAGATCTAATTAAGTTTGCCATCATTACATGTCGAAAACCTGA
  ||| ||| || || |    || | |||   |    |||  |   |        ||| || | ||  | |  ||  | |||    ||  ||   || ||  ||||||   ||||| |||| |||||| ||||  ||||||||||||||    || |||||||  |  || ||||||||||| ||||||||||||||||| || ||
--ttttttggta-tgaaattattttcattgcatcaaactgagcattagcttttcgttacaccattttcttagttt-ctaattc--attaagtgttttctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGTACAAGATGGGCCTGATTAAGTTTGCTATCATTACATGTCGAAAGCCCGA
















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|58023022|gb|CX709763.1|CX709763
EST:     GATACGCTCAGCCTTCACATGGAAGGGTCTAACTTCACTCTTGAGCAGTG                         GACAAAAAACGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGAT
genomic: GATACGCTCAGCCTTCACATGGAAGGGTCTAACTTCACTCTTGAGCAGTGgtaagcttgg ... ttttggtcagGACAAAAAACGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGAT
EST: gi|17023756|gb|BM094790.1|BM094790
EST:     GATACGCTCAGCCTTCACATGGAAGGGTCTAACTTCACTCTTGAGCAGTG                         GACNNNNNNNCGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGA
genomic: GATACGCTCAGCCTTCACATGGAAGGGTCTAACTTCACTCTTGAGCAGTGgtaagcttgg ... ttttggtcagGACAAAAAA-CGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGA
EST: gi|21994774|gb|BQ786302.1|BQ786302
EST:     GATACGCTCAGCCTTCACATGGAAGGGTCTAACTTCACTCTTGAGCAGTG                         GACAAAAAACGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGAT
genomic: GATACGCTCAGCCTTCACATGGAAGGGTCTAACTTCACTCTTGAGCAGTGgtaagcttgg ... ttttggtcagGACAAAAAACGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGAT
EST: gi|57574459|gb|CX547434.1|CX547434
EST:     GATACGCTCAGCCTTCACATGGAAGGGTCTAACTTCACTCTTGAGCAGTG                         GACAAAAAACGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGAT
genomic: GATACGCTCAGCCTTCACATGGAAGGGTCTAACTTCACTCTTGAGCAGTGgtaagcttgg ... ttttggtcagGACAAAAAACGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGAT
EST: gi|21889261|gb|BQ742474.1|BQ742474
EST:     GATACGCTCAACCTTCACATGGAAGGGTCTAACTTCACTTTTGAGCAGTG                         GACAAAAAACGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGAT
genomic: GATACGCTCAGCCTTCACATGGAAGGGTCTAACTTCACTCTTGAGCAGTGgtaagcttgg ... ttttggtcagGACAAAAAACGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGAT
EST: gi|120493216|gb|EH221383.1|EH221383
EST:     GATACGCTCAGCCTTCACATGGAAGGGTCTAACTTCACTCTTGAGCAGTG                         GACAAAAAACGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGAT
genomic: GATACGCTCAGCCTTCACATGGAAGGGTCTAACTTCACTCTTGAGCAGTGgtaagcttgg ... ttttggtcagGACAAAAAACGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGAT
EST: gi|120494419|gb|EH222586.1|EH222586
EST:     GATACGCTCAGCCTTCACATGGAAGGGTCTAACTTCACTCTTGAGCAGTG                         GACAAAAAACGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGAT
genomic: GATACGCTCAGCCTTCACATGGAAGGGTCTAACTTCACTCTTGAGCAGTGgtaagcttgg ... ttttggtcagGACAAAAAACGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGAT
EST: gi|15000769|gb|BI321583.1|BI321583
EST:     GATACGCTCAGCCTTCACATGGAAGGGTCTAACTTCACTCTTGAGCAGTG                         GACAAAAAACGATAAAAG
genomic: GATACGCTCAGCCTTCACATGGAAGGGTCTAACTTCACTCTTGAGCAGTGgtaagcttgg ... ttttggtcagGACAAAAAACGATAAAAG
EST: gi|120495732|gb|EH223899.1|EH223899
EST:     GATACGCTCAGCCTTCACATGGAAGGGTCTAACTTCACTCTTGAGCAGTG                         GACAAAAAACGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGAT
genomic: GATACGCTCAGCCTTCACATGGAAGGGTCTAACTTCACTCTTGAGCAGTGgtaagcttgg ... ttttggtcagGACAAAAAACGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaattaaacgacttgttgaacttgttgattttggttttgttactttttggtcagGACAAAAAACGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGATACAAGAAAGATCTAATTAAGTTTGCCATCATTACATGTCGAAAACCTGA
                       tgttgat  putative branch site (score: 4)
                                   ttttgttacttttt  putative PPT
                                   ttttgttacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatttcttgttagtgcatgctttgttattattttggcctggactagaaattaaacgacttgttgaacttgttgattttggttttgttactttttggtcagGACAAAAAACGATAAAAGGAGCTTTGGCTATGCCATTGATGATAGAGGGATACAAGAAAGATCTAATTAAGTTTGCCATCATTACATGTCGAAAACCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - gcatgct
- - - - - - - - - - - - - - - - - - cctggac
- - - - - - - - - - - - - - - - - - - - - - - aaattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgttg