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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttatagcctgcgaacagtactttttttttctttttctttttaagccgtctggaataaatatccatgtatattatcatacttactaatttatattcatttcatactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATTATGTTAAAATAAATGCTGAGTACACAACATAGGCAAAAGGAAACCTCAC

Basic information

species Glycine max
transcript GLYMA13G19450.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G19450.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G044237_T03 (Zea mays), 3'ss of exon 15
gtaagttatagcctgcgaacagtactttttttttctttttctttttaagccgtctggaataaatatccatgtatattatcatacttactaatttatattcatttcat-actaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATTATGTTAAAATAAATGCTGAGTACACAACAT-AGGCAAAAGGAAACCTCAC
        |   |||    || ||| ||       | || ||    ||  |  |   |  | ||  | || | | |||| |         | ||||  | |||   | | | ||||| | ||||  ||||  |||| | |||||||| |||||| | |||||| | |||||| ||||||||||||| || ||||||| ||    |      ||    
--------tgctctgtctgcactaccttaccaaattcttactaaaaaaagctgccttatgagattgctatct-tgttattacg-------aattatggtgattgtgttattgacagGGAGTGGAGGAGGAAATGGAAAGGCATGGGGCTGTGATCTGAGCTACAAATATGTTGAAATAAATGCTGAATATACAACATGAGATTTATATTTGCCATG-

upper sequence: GLYMA13G19450.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv08s0040g03320.t01 (Vitis vinifera), 3'ss of exon 16
gtaagttatagcctgcgaacagtactttttttttctttttctttttaagccgtctggaataaatatccatgtatattatcatacttactaatttatattcatttcatactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATTATGTTAAAATAAATGCTGAGTACACAACATAGGCAAAAGGAAACCTCAC
                ||| |      | |||   ||||  |  |||||   ||| |  |  |   |||| |   ||    |  | | |  ||| |  || |    |   ||||||  ||||  |||| || || || |||||||||||||||||||| || || || || || |||||||| |||||||| ||||||    |      ||||  
------------agaagaagaaagggctctttgatttttcttggttaagttttctagcgtggac--ccatctgctttgctctg-tgatttttttttcctcttccatttgcaacagGTGATGGGGCAGGGCGGGGGCAGGCATGGGGATGTGATTTAAGTTATGACTACGTGAAGATAAATGCCGAGTACACGACATAGAATGATTTTTCCCTCTA

upper sequence: GLYMA13G19450.1 (Glycine max), 3'ss of exon 16
lower sequence: PP1S90_220V6.2 (Physcomitrella patens), 3'ss of exon 17
gtaagttatagcctgcgaacagtactttttttttctttttctttttaagccgtctggaataaatatccatgtatattatcatacttactaatttatattcatttcatactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATTATGTTAAAATAAATGCTGAGTACACAACATAGGCAAAAGGAAACCTCAC
              |  |    |    | |||||    |  | |||  ||    |    |  |  | | ||| ||| ||  |||| ||   |||  |   |||  ||  |   |||  |||| || ||||   | ||||||||||| |||||| | |||||||| || || ||||| |||||||| |||||||| ||  |  || |     | | 
--------------gtaaggctttacctattttttagatcatctttgtgc---ttaagctccactttcttgtgtataat-gtactgacaggtttgcaca-attggatgttg-tagGACATGGCCCTGGACAAAGCCAAGCATGGGGTTGTGATCTTAGCTACGACTACGTCAAAATTAATGCTGAATACACAACTTAATCGTAATGTGCTTTGAA

upper sequence: GLYMA13G19450.1 (Glycine max), 3'ss of exon 16
lower sequence: PP1S90_220V6.1 (Physcomitrella patens), 3'ss of exon 17
gtaagttatagcctgcgaacagtactttttttttctttttctttttaagccgtctggaataaatatccatgtatattatcatacttactaatttatattcatttcatactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATTATGTTAAAATAAATGCTGAGTACACAACATAGGCAAAAGGAAACCTCAC
              |  |    |    | |||||    |  | |||  ||    |    |  |  | | ||| ||| ||  |||| ||   |||  |   |||  ||  |   |||  |||| || ||||   | ||||||||||| |||||| | |||||||| || || ||||| |||||||| |||||||| ||                  
--------------gtaaggctttacctattttttagatcatctttgtgc---ttaagctccactttcttgtgtataat-gtactgacaggtttgcaca-attggatgttg-tagGACATGGCCCTGGACAAAGCCAAGCATGGGGTTGTGATCTTAGCTACGACTACGTCAAAATTAATGCTGAATACACAACTTAA-----------------

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|207705751|gb|GD686827.1|GD686827
EST:     GGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: GGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|193625610|gb|FK577878.1|FK577878
EST:     TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAAGCATGGGGATGTGATTTAAGCTACGAT
genomic: TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGAC-AAGCATGGGGATGTGATTTAAGCTACGAT
EST: gi|208144232|gb|GD941087.1|GD941087
EST:     TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|193367113|gb|FK330819.1|FK330819
EST:     GGCTGGGGAGACTTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTTAAGCTACGAT
genomic: GGCTGGGGAGAC-TCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGA-TTTAAGCTACGAT
EST: gi|208117555|gb|GD917797.1|GD917797
EST:     TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|193688707|gb|FK628762.1|FK628762
EST:     CGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: CGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|213590895|gb|DB975109.1|DB975109
EST:     TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|16283915|gb|BI945808.1|BI945808
EST:     TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|207711749|gb|GD693129.1|GD693129
EST:     TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|208293166|gb|GE096402.1|GE096402
EST:     TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|209709064|gb|BW658780.1|BW658780
EST:     TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|208089488|gb|GD886581.1|GD886581
EST:     TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|193378440|gb|FK343773.1|FK343773
EST:     TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|207802725|gb|GD772636.1|GD772636
EST:     GGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: GGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|208133908|gb|GD931841.1|GD931841
EST:     TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|193365907|gb|FK333296.1|FK333296
EST:     AGAAAGGCGTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: AGAAAGGC-TGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|193596822|gb|FK551350.1|FK551350
EST:     GGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: GGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|193335235|gb|FK297975.1|FK297975
EST:     AGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: AGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTC-AGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|193455505|gb|FK420910.1|FK420910
EST:     TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|207689392|gb|GD671337.1|GD671337
EST:     TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|208123539|gb|GD924119.1|GD924119
EST:     TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|207807423|gb|GD777520.1|GD777520
EST:     TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|27423687|gb|CA935207.1|CA935207
EST:     CACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: CACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|208324387|gb|GE122692.1|GE122692
EST:     GGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: GGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
EST: gi|193374652|gb|FK342894.1|FK342894
EST:     TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTG                         GCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT
genomic: TAGAAAGGCTGGGGAGACTCACGACACGGTTAAAATTCAGATATCAGTTGgtaagttata ... atactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatatccatgtatattatcatacttactaatttatattcatttcatactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATTATGTTAAAATAAATGCTGAGTACACAACATAGGCAAAAGGAAACCTCAC
                         tactaat  putative branch site (score: 1)
           tatattatcatactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttatagcctgcgaacagtactttttttttctttttctttttaagccgtctggaataaatatccatgtatattatcatacttactaatttatattcatttcatactaacagGCAATGGACCAGGACGTGGACAAGCATGGGGATGTGATTTAAGCTACGATTATGTTAAAATAAATGCTGAGTACACAACATAGGCAAAAGGAAACCTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA