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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatttgttgaaactttaatgtcatacgcctcattgcacatatattgcctgtttactgtgtgttccatcttaattcttttgtataatacatgtcatgcagGTCATAGACTTGGATTCACGCTACAAGCTATCTGAGTCAAAAGATTACGAGGTAAAGGTGTCATTTCTCCAAAGGGCTATTTCATGTGGATGCAAAACTT

Basic information

species Glycine max
transcript GLYMA20G38780.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38780.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0067g03300.t01 (Vitis vinifera), 3'ss of exon 3
-------acatttgt--tgaaactttaatgtcatacgcctcattgcacatatattgcctgtttactgtgtgttccatcttaattcttttgtataatacatgtcatgcagGTCATAGACTTGGATTCACGCTACAAGCTATCTGAGTCAAAAGATTACGAGGTAAAGGTGTCATTTCTCCAAAGGGCTATTTCATGTGGATGCAAAACTT
       |  ||     ||   | | | | | |   |   | || || | ||| |   | ||||    ||||   ||  | |  | ||||  |       || |||||| || ||| ||| |||  |||||||| |||||| |||||||| ||||| ||||| |||||| |||||||||||  ||| || | |  ||| ||||||  ||
cctgcacaagttgaccatgggtcataagtattacttggtgccttccaaa-ataataaatatttaactggtgtcttat--tgaagcatttggttg------gttatgcagATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAGGTGAAGGTGGCATTTCTCCAACTGGCCATCTTAGCTGGGTGCAAAGATT
















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|208308362|gb|GE103658.1|GE103658
EST:     AGTGGGAGCTCTACTTGGACAACTTGCCAAAATCCATTGAAGCTTCTCAG                         GTCATAGACTTGGATTCACGCTACAAGCTATCTGAGTACAAAAGATTAC
genomic: AGTGGGAGCTCTACTTGGACAACTTGCCAAAATCCATTGAAGCTTCTCAGgttaatactg ... tgtcatgcagGTCATAGACTTGGATTCACGCTACAAGCTATCTGAGT-CAAAAGATTAC
EST: gi|151411306|gb|EV281117.1|EV281117
EST:     AGTGGGAGCTCTACTTGGACAACTTGCCAAAATCCATTGAAGCTTCTCAG                         GTCATAGACTTGGATTCACGCTACAAGCTATCTGAGTCAAAAGATTACGAG
genomic: AGTGGGAGCTCTACTTGGACAACTTGCCAAAATCCATTGAAGCTTCTCAGgttaatactg ... tgtcatgcagGTCATAGACTTGGATTCACGCTACAAGCTATCTGAGTCAAAAGATTACGAG
EST: gi|207733300|gb|GD710508.1|GD710508
EST:     GTGGGAGCTCTACCTTGGACAACTTGCCAAAATCCATTGAAGCTTCTCAG                         GTCATAGACTTGGATTCACGCTACAAGCTATCTGAGTCAAAAGATTAC
genomic: GTGGGAGCTCTAC-TTGGACAACTTGCCAAAATCCATTGAAGCTTCTCAGgttaatactg ... tgtcatgcagGTCATAGACTTGGATTCACGCTACAAGCTATCTGAGTCAAAAGATTAC
EST: gi|298175857|gb|HO015262.1|HO015262
EST:     AGTGGGAGCTCTACTTGGACAACTTGCCAAAATCCATTGAAGCTTCTCAG                         GTCATAGACTTGGATTCACGCTACAAGCTATCTGAGTCGAAAGATTACGAG
genomic: AGTGGGAGCTCTACTTGGACAACTTGCCAAAATCCATTGAAGCTTCTCAGgttaatactg ... tgtcatgcagGTCATAGACTTGGATTCACGCTACAAGCTATCTGAGTCAAAAGATTACGAG
EST: gi|208036690|gb|GD837349.1|GD837349
EST:     AGTGGGAGCTCTACTTGGACAACTTGCCAAAATCCATTGAAGCTTCTCAG                         GTCATAGACTTGGATTCACGCTACAAGCTATCTGAGTCAAAAGATTAC
genomic: AGTGGGAGCTCTACTTGGACAACTTGCCAAAATCCATTGAAGCTTCTCAGgttaatactg ... tgtcatgcagGTCATAGACTTGGATTCACGCTACAAGCTATCTGAGTCAAAAGATTAC
EST: gi|193602261|gb|FK558342.1|FK558342
EST:     AGTGGGAGCTCTACTTGGACAACTTGCCAAAATCCATTGAAGCTTCTCAG                         GTCATAGACTTGGATTCACGCTACAAGCTATCTGAGTCAAAAGATTACGAG
genomic: AGTGGGAGCTCTACTTGGACAACTTGCCAAAATCCATTGAAGCTTCTCAGgttaatactg ... tgtcatgcagGTCATAGACTTGGATTCACGCTACAAGCTATCTGAGTCAAAAGATTACGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctgtttactgtgtgttccatcttaattcttttgtataatacatgtcatgcagGTCATAGACTTGGATTCACGCTACAAGCTATCTGAGTCAAAAGATTACGAGGTAAAGGTGTCATTTCTCCAAAGGGCTATTTCATGTGGATGCAAAACTT
                      tcttaat  putative branch site (score: 3)
                     atcttaattcttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatttgttgaaactttaatgtcatacgcctcattgcacatatattgcctgtttactgtgtgttccatcttaattcttttgtataatacatgtcatgcagGTCATAGACTTGGATTCACGCTACAAGCTATCTGAGTCAAAAGATTACGAGGTAAAGGTGTCATTTCTCCAAAGGGCTATTTCATGTGGATGCAAAACTT

- - -tgttgaa
- - - - - - - - - - - - - cgcctca
- - - - - - - - - - - - - - - - - tgcacat
- - - - - - - - - - - - - - - - - - - - - tattgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtgtg