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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgtggaaaggtattgtggtaggctggttgatgatttttaacgtaatttaatatttattcccatttctgtgtttataataattggtgattgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCATTATTCTACGCCAGTTGATGTTTGGTCAGTGGGATGTATATTTGCAGAGA

Basic information

species Glycine max
transcript GLYMA15G14390.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G14390.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 4
--------------------------------ttttgtggaa-aggtattgtggtaggctggttgatgatttttaacgtaa-tttaatatttatt--cccatt---tctgtgtttataataattggtgattgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCATTATTCTACGCCAGTTGATGTTTGGTCAGTGGGATGTATATTTGCAGAGA
                                 ||  |  |  |  | || |  | | |     | | |||||| |  ||  |||  |||  | |  | ||||   ||    |  ||    || ||   |  |||  |||| || || || ||||| ||||||||||| ||  | ||||||||  | || |||||||| ||||||||| | |||||||| || ||||| |||||||| |
gtactatagatttgtgttcaacattttgttttcttcataaagtacatttttttttcgtcataaagttcatttttcatttaccttttctatacactagcacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA

upper sequence: GLYMA15G14390.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g02680.1 (Oryza sativa), 3'ss of exon 3
-----------------------------ttttgtggaaaggta---ttgtggtaggctggttgatgatttttaacgtaa-tttaatatttatt--cccatt---tctgtgtttataataattggtgattgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCATTATTCTACGCCAGTTGATGTTTGGTCAGTGGGATGTATATTTGCAGAGA
                             |||  |   || |||   || |  | | |     | | |||||| |  ||  |||  |||  | |  | ||||   ||    |  ||    || ||   |  |||  |||| || || || ||||| ||||||||||| ||  | ||||||||  | || |||||||| ||||||||| | |||||||| || ||||| |||||||| |
gtactatagatttgtgttcaacattttgttttcttcataaagtacattttttttcgtcataaagttcatttttcatttaccttttctatacactagcacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA

upper sequence: GLYMA15G14390.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------------------------ttttgtggaaaggtattgtggtaggctggttgatgattttta--------acgtaa---tttaatatttattcccatttc-tgtgtttataata-at-----tggtgattgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCATTATTCTACGCCAGTTGATGTTTGGTCAGTGGGATGTATATTTGCAGAGA
                                                               || || || | |  |  ||  | |  |     |  |||||||        ||||||   |||  | | |||||   |  | |   || | | || ||     |||   |  |||  |||| |||||||||||||||||||||||||||||  |||||||| | || || ||||| || ||||||||||| ||||| ||||| ||||| ||||| || |
gtacatttgttatgctctaacttgagaaagggagtctgaattgtcctgttagggaaaaaaatattgtgagggatgccaaagttatggatt--cccacaatttttacccgaataacgtaaccttttgctgtatattctagtcacattaattcacagtacatatctatggaagtatttttcagGTAGTGACATTATGGTACAGAGCTCCAGAAATTCTGCTTGGAGCGCGGCAGTATTCCACACCAGTTGATGTGTGGTCTGTGGGCTGTATCTTTGCGGAAA

upper sequence: GLYMA15G14390.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G143213_T02 (Zea mays), 3'ss of exon 4
--------------------------------------------------------ttttgtggaaaggtattgtggtaggc-------tggttgat------gatttt---------taacgtaa---tttaatatttattcccat--ttctgtgtttata---ataattggtgattgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCATTATTCTACGCCAGTTGATGTTTGGTCAGTGGGATGTATATTTGCAGAGA
                                                         || | | |||  |||||||   ||        |  | |||      ||||||         |||| |||   |||  | | |||||   |  |      |  |||   ||   |||   |  |||  |||| |||||||||||||||||||||||||||||  | |||||| |  | || ||||| || |||||||| || ||||| |||                   
gtaaatttgctatgctgcttattgcttaacttgagaaagggagtttgaattatcctattagggaaaaaatattgtgaggggtgccaaaattatggatcccaccgattttatacccatataacataaccttttgttgtctattctagtcatatcaactcaatacatatctatggaagtatttttcagGTAGTGACATTATGGTACAGAGCTCCAGAAATCCTTCTTGGAGCGAGACAGTATTCCACACCAGTTGACGTATGGTCTGTG-------------------

upper sequence: GLYMA15G14390.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G143213_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------------------ttttgtggaaaggtattgtggtaggc-------tggttgat------gatttt---------taacgtaa---tttaatatttattcccat--ttctgtgtttata---ataattggtgattgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCATTATTCTACGCCAGTTGATGTTTGGTCAGTG-GGATGTATATTTGCAGAGA
                                                         || | | |||  |||||||   ||        |  | |||      ||||||         |||| |||   |||  | | |||||   |  |      |  |||   ||   |||   |  |||  |||| |||||||||||||||||||||||||||||  | |||||| |  | || ||||| || |||||||| || ||||| ||| || ||||| ||||| ||  
gtaaatttgctatgctgcttattgcttaacttgagaaagggagtttgaattatcctattagggaaaaaatattgtgaggggtgccaaaattatggatcccaccgattttatacccatataacataaccttttgttgtctattctagtcatatcaactcaatacatatctatggaagtatttttcagGTAGTGACATTATGGTACAGAGCTCCAGAAATCCTTCTTGGAGCGAGACAGTATTCCACACCAGTTGACGTATGGTCTGTGTGGCTGTATCTTTGCGGAA-

upper sequence: GLYMA15G14390.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 5
--ttttgtggaaaggtattgtggtaggctggttgatga--tttttaacgtaatttaatatttattcccatttctgtgtttataataattggtgattgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCATTATTCTACGCCAGTTGATGTTTGGTCAGTGGGATGTATATTTGCAGAGA
    |      |    ||    | |   || ||| |||   |||| |    || |     | |||   || |||| ||| ||||  ||||||| || |    ||||||||||  | ||||||||||| || |||||| |||||||||| || || |||||||| || |||||||| ||||| ||||| ||||||||||| ||||
tacctccacagatcacatatgaggaatttgtttggtgaaccttttgataccatct----ctcattattatgtctgggttcataaacattggtggttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCACTATTCTACTCCTGTTGATGTGTGGTCTGTGGGCTGTATATTTGCTGAGA

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|207761694|gb|GD734625.1|GD734625
EST:     GATTGGTCTTAGGGCATTTTGGCATTCCTGTCAGGACATTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: GATTGG-C-TAGGGCA-TTTGGCATTCCTGTCAGGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|8669339|gb|BE190446.1|BE190446
EST:     ATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: ATTCCTGTCAGGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|193339683|gb|FK302286.1|FK302286
EST:     ACATTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: ACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|15815178|gb|BI787453.1|BI787453
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|208184982|gb|GD984968.1|GD984968
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|192301718|gb|FG994412.1|FG994412
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|193607667|gb|FK560122.1|FK560122
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|9985866|gb|BE660093.1|BE660093
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAG                         GTGGTGACATTATGGT-CAGAGCTCCAGAAATATTGCTTGGGATCTCGTCA
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGG-ATCTCGTCA
EST: gi|193728140|gb|FK667640.1|FK667640
EST:     ACATTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: ACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|209726535|gb|BW658089.1|BW658089
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|192304398|gb|FG996720.1|FG996720
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|193395746|gb|FK364819.1|FK364819
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|207847783|gb|GD818752.1|GD818752
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|192312082|gb|FK003859.1|FK003859
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|151411049|gb|EV280860.1|EV280860
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|41145798|gb|CK606009.1|CK606009
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|193359793|gb|FK328539.1|FK328539
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|193464902|gb|FK430156.1|FK430156
EST:     ACATTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: ACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|193464022|gb|FK428324.1|FK428324
EST:     ACATTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: ACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|193378745|gb|FK344316.1|FK344316
EST:     GGACATTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: GGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|192301719|gb|FG994413.1|FG994413
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|209726536|gb|BW658090.1|BW658090
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|192302862|gb|FG998544.1|FG998544
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|192304397|gb|FG996719.1|FG996719
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACATTTACACATGAGgtttgtgtcc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttaatatttattcccatttctgtgtttataataattggtgattgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCATTATTCTACGCCAGTTGATGTTTGGTCAGTGGGATGTATATTTGCAGAGA
  atttaat  putative branch site (score: 4)
                   atttctgtgtttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgtggaaaggtattgtggtaggctggttgatgatttttaacgtaatttaatatttattcccatttctgtgtttataataattggtgattgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCATTATTCTACGCCAGTTGATGTTTGGTCAGTGGGATGTATATTTGCAGAGA

ttttgtg
- - - - - - - - - - -taggctg
- - - - - - - - - - - - - - gttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attggtg