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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaattttgatcgtcacggcttaatcaattactagttcggttgactctatgtatatctctatttgattcttattaccttacctttgttgttatctctagAACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCAAAATTGGAGCCTGATGTTG

Basic information

species Glycine max
transcript GLYMA03G34300.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G34300.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 2
tgaaattttgatcgtcacggcttaatcaattactagttcggttgactctatgtatatc--tctatttgattcttattacc--ttacctttgttgttatctctagAACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCAAAATTGGAGCCTGATGTTG
     || || |    || ||  |||    |||   |    ||  | || || || ||  | || ||  || | |||  |  ||  | || |||||   | ||||| || ||||||||||| ||||| ||||||||| |||||||||||| ||||||||||||| ||||||| |
---ttttctgcttaaaactgca-aatgctgtacagatattttttgccctttgcatgtcgttttagtttgttataattgacatttttcatttttgtttcatttagAATGGGACAAAAGACTCCATCAGTAAGCTTGTTTCTGACTTGAACAGTGCAAAATTGGAGGCTGATGTCG
















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|151395984|gb|EV265861.1|EV265861
EST:     TTCTTTGTTGGTGGCAACTGGAAGTGT                         AACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
genomic: TTCTTTGTTGGTGGCAACTGGAAGTGTgtaagtatct ... ttatctctagAACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
EST: gi|209724178|gb|BW659712.1|BW659712
EST:     TTCTTTGTTGGTGGCAACTGGAAGTGT                         AACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
genomic: TTCTTTGTTGGTGGCAACTGGAAGTGTgtaagtatct ... ttatctctagAACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
EST: gi|20813031|gb|BQ297509.1|BQ297509
EST:     TTCTTTGTTGGTGGCAACTGGAAGTGT                         AACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
genomic: TTCTTTGTTGGTGGCAACTGGAAGTGTgtaagtatct ... ttatctctagAACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
EST: gi|4314103|gb|AI461222.1|AI461222
EST:     TTCTTTGTTGGTGGCAACTGGAAGTGT                         AACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
genomic: TTCTTTGTTGGTGGCAACTGGAAGTGTgtaagtatct ... ttatctctagAACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
EST: gi|20449041|gb|BQ253165.1|BQ253165
EST:     TTCTTTGTTGGTGGCAACTGGAAGTGT                         AACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
genomic: TTCTTTGTTGGTGGCAACTGGAAGTGTgtaagtatct ... ttatctctagAACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
EST: gi|15204096|gb|BI426864.1|BI426864
EST:     TTCTTTGTTGGTGGCAACTGGAAGTGT                         AACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
genomic: TTCTTTGTTGGTGGCAACTGGAAGTGTgtaagtatct ... ttatctctagAACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
EST: gi|10233567|gb|BE802455.1|BE802455
EST:     TTCTTTGTTGGTGGCAACTGGAAGTGT                         AACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
genomic: TTCTTTGTTGGTGGCAACTGGAAGTGTgtaagtatct ... ttatctctagAACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
EST: gi|20449080|gb|BQ253204.1|BQ253204
EST:     TTCTTTGTTGGTGGCAACTGGAAGTGT                         AACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
genomic: TTCTTTGTTGGTGGCAACTGGAAGTGTgtaagtatct ... ttatctctagAACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
EST: gi|9204176|gb|BE330400.1|BE330400
EST:     TTCTTTGTTGGTGGCAACTGGAAGTGT                         AACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
genomic: TTCTTTGTTGGTGGCAACTGGAAGTGTgtaagtatct ... ttatctctagAACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
EST: gi|120530487|gb|EH258620.1|EH258620
EST:     TTCTTTGTTGGTGGCAACTGGAAGTGT                         AACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
genomic: TTCTTTGTTGGTGGCAACTGGAAGTGTgtaagtatct ... ttatctctagAACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
EST: gi|9563997|gb|BE473506.1|BE473506
EST:     TTCTTTGTTGGTGGCAACTGGAAGTGT                         AACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
genomic: TTCTTTGTTGGTGGCAACTGGAAGTGTgtaagtatct ... ttatctctagAACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
EST: gi|209715618|gb|BW657385.1|BW657385
EST:     TTCTTTGTTGGTGGCAACTGGAAGTGT                         AACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
genomic: TTCTTTGTTGGTGGCAACTGGAAGTGTgtaagtatct ... ttatctctagAACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
EST: gi|17964485|gb|BM271219.1|BM271219
EST:     TTCTTTGTTGGTGGCAACTGGAAGTGT                         AACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA
genomic: TTCTTTGTTGGTGGCAACTGGAAGTGTgtaagtatct ... ttatctctagAACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctatgtatatctctatttgattcttattaccttacctttgttgttatctctagAACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCAAAATTGGAGCCTGATGTTG
                              accttac  putative branch site (score: 3)
                                             ttatctct  putative PPT
               tatttgattcttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaaattttgatcgtcacggcttaatcaattactagttcggttgactctatgtatatctctatttgattcttattaccttacctttgttgttatctctagAACGGAACAAAAGACTCAATCAGCAAGCTTGTTGCTGACTTGAACAATGCAAAATTGGAGCCTGATGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - -ctatgta