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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctctctctctctctcccctgggtgtgtgtgcgtgttacctgttcattgttattctactgagtttcgaacaatgggtaagatacagccacttgtctgcagTTGTTCGGCTTATGGGACGTGCAGCTTCACACATTACACTGGAATGTGCTTTGCAAACTCATCCGAACATTACTATTATTGGAGAAGAG

Basic information

species Glycine max
transcript GLYMA17G01360.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 7
tctctctctctctctcccctgggtgt----gtgtgcgtgttacctgttcattgttattctactgagtttcga-acaatg--ggtaagatacagccacttgtctgcagTTGTTCGGCTTATGGGACGTGCAGCTTCACACATTACACTGGAATGTGCTTTGCAAACTCATCCGAACATTACTATTATTGGAGAAGAG
        | |     || || ||||     | |||   |      || |   ||||| |    | ||  || |||||     ||||     |  |  |   || ||||||  |||||||||||||||| ||||| ||||||||| |||| |||||| ||||||| ||||| ||  || |  | ||||||||||||
-------atataaaatccttgagtgtcaacttctgcagatggttaatttaacattattttgtctatttctgacacaatactaataagtatttgttatgttcatgtagTTGTGAGGCTTATGGGACGTGCTGCTTCTCACATTACATTGGAGTGTGCTCTGCAAACACATCCTAATGTTGCACTCATTGGAGAAGAG

upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 7
--tctctctctctctctcccctgggtgt-gtgtgcgtgttacctgttcattgttattctactgagtttcgaacaatgggtaagatacagccacttgtctgcagTTGTTCGGCTTATGGGACGTGCAGCTTCACACATTACACTGGAATGTGCTTTGCAAACTCATCCGAACATTACTATTATTGGAGAAGAG
    |       | |   || ||  | | |   |  | | ||    | |  | |     | |  ||    || |||   ||| |  ||    ||    |||||||||  |||||||||| ||||| ||||| |||||||| |||||||| ||||||||||| || || ||   | |  | ||||| ||||||
gcagtgctaacgtgtagtccatgaatattggaagtatataacagaattacagatcggacattttgtcaataaaaattc-taacaagcacttgctc--ttgcagTTGTGAGGCTTATGGGTCGTGCTGCTTCTCACATTACGCTGGAATGCGCTTTGCAAACACACCCCAATGCTGCACTCATTGGGGAAGAG

upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 7
tctctctctctctctcccctgggtgtgtgtgcgtgttacctgttcattgttattctactgagtttcgaacaatgggtaagatacagccacttgtctgcagTTGTTCGGCTTATGGGACGTGCAGCTTCACACATTACACTGGAATGTGCTTTGCAAACTCATCCGAACATTACTATTATTGGAGAAGAG
                   |  || ||| | |   |  |    | | | || ||      | |||   | |     | |  |   |     | |||  |||||| || |||||||| ||||| ||||| ||||||||||| ||||| ||||||||||| ||||| |||||||| |||||||||||||||
------------------gtaagtttgttttctcttagcaaaatgaattttcttgatacaaatttactatatcatttcatctgttgat-tatctctatagTTGTGCGTCTTATGGGTCGTGCTGCTTCTCACATTACACTTGAATGCGCTTTGCAAACCCATCCAAACATTACCATTATTGGAGAAGAG

upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 7
tctctctctctctctcccctgggtgtgtgtgcgtgttacctgttcattgttattctactgagtttcgaacaatgggtaagatacagccacttgtctgcagTTGTTCGGCTTATGGGACGTGCAGCTTCACACATTACACTGGAATGTGCTTTGCAAACTCATCCGAACATTACTATTATTGGAGAAGAG
        |   |      |         | | ||        |||||  |||| | |    |||       |   |    ||   |   ||   |||||||||  | |||||||| ||||| ||||| |||||||| || || |||||||| |||||||| || ||||| || |||||||||||||||
-------gtaagtaaatgtttaacaaaatttcttgaagttgcatcatttctattgtgccctatttg----tttacatgctgtatcacattttcattgcagTTGTAAGACTTATGGGTCGTGCTGCTTCCCACATTACGCTTGAGTGTGCTTTACAAACTCACCCAAACATAACCATTATTGGAGAAGAG

upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 7
tctctctctctctctcccctgggtgtgtgtgcgtgttacctgttcattgttattctactgagtttcg-aacaatgggtaagatacagccacttgtctgca---gTTGTTCGGCTTATGGGACGTGCAGCTTCACACATTACACTGGAATGTGCTTTGCAAACTCATCCGAACATTACTATTATTGGAGAAGAG
      |    ||||    ||      | | | | || | | ||  || |  |||   |   ||     |   |  ||   ||        |||| ||||   ||||| || |||||||| |||||||| |||||||||||| |||| |||||||||||||||||||| |||||||| |||||||| ||||||
---gatttcaactcttttatgctccaatttacat-ttccttatttgttttatttcctttcttttatatgattgtaagtggtatttgtatgtttgtgtgcatcagTTGTACGACTTATGGGGCGTGCAGCCTCACACATTACATTGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAG

upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ13842 (Selaginella moellendorffii), 3'ss of exon 7
tctctctctctctctcccctgggtgtgtgtgcgtgttacctgttcattgttattctactgagtttcgaacaatgggtaagatacagccacttgtctgcagTTGTTCGGCTTATGGGACGTGCAGCTTCACACATTACACTGGAATGTGCTTTGCAAACTCATCCGAACATTACTATTATTGGAGAAGAG
                                  || |   |||  |||    | ||    ||||  ||    | |      ||   | || |   |||||||| || ||||||||||||||||| |||||||| ||  | || |||||| |||| || || || ||  |  || |||| || ||||||
----------------------------------gtaagaagtttgttgc--ctttagcttgttttaaagtccgtgacgaggactttctctcga--gcagTTGTCCGCCTTATGGGACGTGCAGCCTCACACATAACTTTAGAGTGTGCTCTGCAGACGCACCCAAATGTCGCTCTTATCGGTGAAGAG

upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ12684 (Selaginella moellendorffii), 3'ss of exon 7
tctctctctctctctcccctgggtgtgtgtgcgtgttacctgttcattgttattctactgagtttcgaacaatgggtaagatacagccacttgtctgcagTTGTTCGGCTTATGGGACGTGCAGCTTCACACATTACACTGGAATGTGCTTTGCAAACTCATCCGAACATTACTATTATTGGAGAAGAG
                                  || |   |||  |||    | ||     |||  ||    | |      ||   | || |   |||||||| || ||||||||||||||||| |||||||| ||  | || |||||| |||| || || || ||  |  || |||| || ||||||
----------------------------------gtaagaagtttgttgc--ctttagcttcttttaaagtccgtgacgaggactttctctcga--gcagTTGTCCGCCTTATGGGACGTGCAGCCTCACACATAACTTTAGAGTGTGCTCTGCAGACGCACCCAAATGTCGCTCTTATCGGTGAAGAG

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|13181599|gb|BG352939.1|BG352939
EST:     GATTGGCAATGTTATGATAGATGCTCGATCAACTGGAAAATATTACCATT                         TTGTTCGGCTTATGGGACGTGCAGCTTCACACATTACACTGGAATGTGCTT
genomic: GATTGGCAATGTTATGATAGATGCTCGATCAACTGGAAAATATTACCATTgtaagttctg ... ttgtctgcagTTGTTCGGCTTATGGGACGTGCAGCTTCACACATTACACTGGAATGTGCTT
EST: gi|208051397|gb|GD847236.1|GD847236
EST:     GATTGGCAATGTTATGATAGATGCTCGATCAACTGGAAAATATTACCATT                         TTGTTCGGCTTATGGGACGTGCAGCTTCACACATTACACTGGAATGTGCTT
genomic: GATTGGCAATGTTATGATAGATGCTCGATCAACTGGAAAATATTACCATTgtaagttctg ... ttgtctgcagTTGTTCGGCTTATGGGACGTGCAGCTTCACACATTACACTGGAATGTGCTT
EST: gi|254330861|gb|GR842126.1|GR842126
EST:     GATTGGCAATGTTATGATAGATGCTCGATCAACTGGAAAATATTACCATT                         TTGTTCGGCTTATGGGACGTGCAGCTTCACACATTACACTGGAATGTGCTT
genomic: GATTGGCAATGTTATGATAGATGCTCGATCAACTGGAAAATATTACCATTgtaagttctg ... ttgtctgcagTTGTTCGGCTTATGGGACGTGCAGCTTCACACATTACACTGGAATGTGCTT
EST: gi|208027932|gb|GD823124.1|GD823124
EST:     GATTGGCAATGTTATGATAGATGCTCGATCAACTGGAAAATATTACCATT                         TTGTTCGGCTTATGGGACGTGCAGCTTCGCACATTACACTGGAATGTGCTT
genomic: GATTGGCAATGTTATGATAGATGCTCGATCAACTGGAAAATATTACCATTgtaagttctg ... ttgtctgcagTTGTTCGGCTTATGGGACGTGCAGCTTCACACATTACACTGGAATGTGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttattctactgagtttcgaacaatgggtaagatacagccacttgtctgcagTTGTTCGGCTTATGGGACGTGCAGCTTCACACATTACACTGGAATGTGCTTTGCAAACTCATCCGAACATTACTATTATTGGAGAAGAG
                                            cttgtct  CT-rich tract
     tattcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctctctctctctctcccctgggtgtgtgtgcgtgttacctgttcattgttattctactgagtttcgaacaatgggtaagatacagccacttgtctgcagTTGTTCGGCTTATGGGACGTGCAGCTTCACACATTACACTGGAATGTGCTTTGCAAACTCATCCGAACATTACTATTATTGGAGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
-ctctctc
- - - - - -ctctccc
- - - - - - - - - - gggtgtg
- - - - - - - - - - - - - - - - -tgttacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgagtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagccac