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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacgaagatgatcaaaataaaatgttaaggaacctgtttataggatttggcccattctgtcccaaatataaaagttgttcgcatttgtgttctttgtcagGCTAAGATAGTAGGAAAAACAAGCTATGCCAGCAACTTGTCTGGGTATGATGAATATGTTCCAATGGTAGACATACCTGTTGATGCTGGTTGGAAGAAGC

Basic information

species Glycine max
transcript GLYMA04G01220.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G01220.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 3'ss of exon 11
cacgaagatgatcaaaataaaatgttaaggaacctgttta---taggatttggcccattctgtcccaaatataaaagttgttcgcatttgtgttctttgt-----cagGCTAAGATAGTAGGAAAAACAAGCTATGCCAGCAACTTGTCTGGGTATGATGAATATGTTCCAATGGTAGACATACCTGTTGATGCTGGTTGGAAGAAGC
          ||  |    |  | || ||     ||| ||   | | |    || ||   |||     |  ||    || |||  || | | ||   ||      ||||||||| |||| |||||   |||||||||  | | |||    |||||||||||||||||||| ||||| |||| | |||||||||| |||||||||||||
--------gtattgagggcatttcttgagtgcaatgtctaagattgaaagaagctcacattgtatagtagttacttattcttcaaatatttctttggtggaaatgcagGCTAAGGTAGTTGGAAAGGTAAGCTATGCTGGTAGCTTCGGGGGGTATGATGAATATGTTCCCATGGTCGACAAAGCTGTTGATGCAGGTTGGAAGAAGC
















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|254337686|gb|GR845256.1|GR845256
EST:     AAGCGATGAAGAGTTATTCACACCTTACGCTGACCCCTGTTCATGAGGAA                         GCTAAGATAGTAGGAAAAACAAGCTATGCCAGCAACTTGTCTGGGTATGAT
genomic: AAGCGATGAAGAGTTATTCACACCTTACGTTGACCCCTGTTCATGAGGAAgtgagtttta ... tctttgtcagGCTAAGATAGTAGGAAAAACAAGCTATGCCAGCAACTTGTCTGGGTATGAT
EST: gi|209728327|gb|BW658539.1|BW658539
EST:     AAGCGATGAAGAGTTATTCACACCTTACGTTGACCCCTGTTCATGAGGAA                         GCTAAGATAGTAGGAAAAACAAGCTATGCCAGCAACTTGTCTGGGTATGAT
genomic: AAGCGATGAAGAGTTATTCACACCTTACGTTGACCCCTGTTCATGAGGAAgtgagtttta ... tctttgtcagGCTAAGATAGTAGGAAAAACAAGCTATGCCAGCAACTTGTCTGGGTATGAT
EST: gi|192306575|gb|FG996237.1|FG996237
EST:     AAGCGATGAAGAGTTATTCACACCTTACGTTGACCCCTGTTCATGAGGAA                         GCTAAGATAGTAG-AAAAACAAGCTATGCCAGCAACTTGTCTGGGTATGAT
genomic: AAGCGATGAAGAGTTATTCACACCTTACGTTGACCCCTGTTCATGAGGAAgtgagtttta ... tctttgtcagGCTAAGATAGTAGGAAAAACAAGCTATGCCAGCAACTTGTCTGGGTATGAT
EST: gi|193644833|gb|FK588723.1|FK588723
EST:     AAGCGATGAAGAGTTATTCACACCTTACGTTGACCCCTGTTCATGAGGAA                         GCTAAGATAGTAGGAAAAACAAGCTATGCCAGCAACTTGTCTGGGTATGAT
genomic: AAGCGATGAAGAGTTATTCACACCTTACGTTGACCCCTGTTCATGAGGAAgtgagtttta ... tctttgtcagGCTAAGATAGTAGGAAAAACAAGCTATGCCAGCAACTTGTCTGGGTATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggcccattctgtcccaaatataaaagttgttcgcatttgtgttctttgtcagGCTAAGATAGTAGGAAAAACAAGCTATGCCAGCAACTTGTCTGGGTATGATGAATATGTTCCAATGGTAGACATACCTGTTGATGCTGGTTGGAAGAAGC
                                            ttctttgtc  CT-rich tract
                  aaatataaaagttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacgaagatgatcaaaataaaatgttaaggaacctgtttataggatttggcccattctgtcccaaatataaaagttgttcgcatttgtgttctttgtcagGCTAAGATAGTAGGAAAAACAAGCTATGCCAGCAACTTGTCTGGGTATGATGAATATGTTCCAATGGTAGACATACCTGTTGATGCTGGTTGGAAGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - -aaaataa
- - - - - - - - - - - - - - - - cctgttt
- - - - - - - - - - - - - - - - - - - - - ggatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatttg