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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaacatggtcatgacttcaaaattgtgtttaatttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAGGTATCAA

Basic information

species Glycine max
transcript GLYMA08G18760.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 11
-------------------gtgagtcatttatttgatatggagagaatataagtttcctggatgttgtgatat-tttttgttttgggtgctgggaa-atgctcctgac-tgttgttttcaaattcaac-tccaaacatggtcatgacttcaaaattgtgtttaatttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAGGTATCAA
                    | | |||||  |||  |  |       |||||   || |   |     | | | |||||||    | | ||  | | |||     ||  ||    | || ||||     |||   |    | |    ||  |  |  || || |  |||  ||||||||||||| ||||| |  ||||| || || |||||  | ||||| ||||| |||||||||||||| ||||| || ||||| |  ||||||       
gtttacaaccatgatctactttattcattgtttttgttcgagtgttctataaacctcatctctcaaaagttctgtttttgtgcctgctactatgtatatgggttagaaatgaccatctcgaatttgttgtcctttctaattgacttgttgtatgtattgcttgaactttttagGTTGGAGCTGAAATTGTAAGGAGAGCGCTGAGCTACCCGCTTAAATTGATTGCTAAGAATGCTGGTGTTAATGGAAGCGTTGTTACCGAGAAG-------

upper sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 10
lower sequence: AT1G55490.1 (Arabidopsis thaliana), 3'ss of exon 11
gtgagtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaacatggtca-tgacttcaaaattg-tgtttaatttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAGGTATCAA
                                                                              |    | | |   || |||| |||  |   ||   |   ||  |  ||  ||  ||| || | | |   |  |||||||||| ||||| || |||||||| || ||||||||  | ||| |||| ||||||||||||||||| ||||| ||||| || || ||||||       
------------------------------------------------------------------------------gtaaatcaatcaagtcttcagattttaactcatgaaccttcggtttctctaactttgctgatgattccctttagGTTGGAGCGGATATAGTTAAAAGAGCACTAAGTTACCCCCTAAAACTAATCGCCAAGAATGCTGGTGTTAATGGAAGTGTAGTTAGCGAGAAG-------

upper sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 10
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 11
gtgagtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaacatggtcatgacttcaaaattgtgtttaatttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAGGTATCAA
                                                                  ||| | || ||   ||  || | |||   |    | ||| |       |  |  ||  ||   || | | |   || | |  |||||||||| || ||||| |||||||| || ||||||||| ||||||| || || |||||||||||||| ||||| ||||||||||| ||||||       
------------------------------------------------------------------gtgattggcaaaa-tcaagaattttgaaattttttgcaaattgcttgctcttactgcattttcaactatttcccatctct--agGTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAG-------

upper sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 10
lower sequence: AT5G56500.1 (Arabidopsis thaliana), 3'ss of exon 11
gtgagtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgct--cctgactgttgttttcaaattcaactccaaacatggtcatgacttcaaaattgtgtttaatttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAGGTATCAA
                                               || |        |  |||       |  || | |  | ||| ||  |  ||      |  || |         |   | || | ||||    ||||  |   |||||||||||||| ||||| || | |||  | || |||||  |||| ||||| |||||||| |||||||||||||| || |||||||||||||||       
-----------------------------------------------gttagtccagaagagttgcacagcagagaaagataacatgaatgaggagtttg---ccgtctgcgggttataacgccattttacaattcatcttaacctc--cagGTTGGAGCTGACATTGTTAAGAAAGCATTGAGCTACCCACTGAAGTTAATCGCCAAGAACGCTGGTGTCAATGGCAGCGTTGTCAGTGAGAAG-------

upper sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 11
-------gtgagtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaaca-tggtcatgacttcaaaattgtgtttaattt-ttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAGGTATCAA
        || | | | | ||  ||||||      |  || |  | ||  | |||   |      |  ||||  |  ||   ||||      |    |||    | |||   |   | | | || | ||    | ||| | |  || ||||  ||||||||||||||||||||||| || |||||| | ||||||||| |||| ||||||||||| ||||||||||| ||||| ||||| ||||||||||||       
gtgatacttgtggc-tgtgttcaatatgggatttgtccaa-taccttgagttttggttttcccaatagtttgaatcatgctgaatgtgttcaaaatgtgtcaatatattggccaggatatagtgtttatcctcttaaagtggacttgaattgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATTGCCAAAAATGCTGGTGTTAATGGAAGTGTGGTCAGTGAGAAG-------

upper sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 10
lower sequence: PP1S14_298V6.1 (Physcomitrella patens), 3'ss of exon 7
gtgagtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaacatggtcatgacttcaaaat-tgtgt-ttaatttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAGGTATCAA
                              |||||       || || || ||||  |    |   ||       || | |    |         |  || | ||||      ||| |||   ||  |   | || ||    | || |||||||||| ||||| |||||||   | ||  |  |||||||||||||||| || ||||||||||||||||| || || || || ||   |||||||       
-----------------------------gtaagtgat----attttatgctattcctacaatcaagttacaatcaaggtttgacatgaagccgatacaacttaactt--gttatgttcagatctgaattgtctgggtgcctacttctgcagGTTGGCGCTGAGATTGTGAGGCGGGCCTTGTGTTACCCTTTGAAATTGATCGCCAAGAATGCTGGTGTGAACGGAAGCGTGGTGGTTGAGAAG-------

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|16284130|gb|BI945921.1|BI945921
EST:     CATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAGAA                         GTTGGAGCTGATATTGTGAANAGAGCTCTCAGTTACGCTTTGAAATTAATT
genomic: CATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatt ... atttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
EST: gi|298191386|gb|HO038865.1|HO038865
EST:     CATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAA                         GTCGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
genomic: CATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatt ... atttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
EST: gi|16279729|gb|BI943586.1|BI943586
EST:     CATCAAAGGTGGATGCAATCAATGATAGCCTTGATAATGATGAAGAAAAA                         GTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
genomic: CATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatt ... atttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
EST: gi|17964146|gb|BM270885.1|BM270885
EST:     CATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAA                         GTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
genomic: CATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatt ... atttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
EST: gi|208281737|gb|GE077693.1|GE077693
EST:     CATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAA                         GTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
genomic: CATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatt ... atttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
EST: gi|208026723|gb|GD823525.1|GD823525
EST:     CATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAA                         GTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT
genomic: CATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatt ... atttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaattcaactccaaacatggtcatgacttcaaaattgtgtttaatttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAGGTATCAA
                                        gtttaat  putative branch site (score: 4)
                                              tttttgc  CT-rich tract
                             ttcaaaattgtgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaacatggtcatgacttcaaaattgtgtttaatttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAGGTATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG