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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattttgtgagaacttatctgtgatgaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAG

Basic information

species Glycine max
transcript GLYMA02G13860.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G13860.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g29830.2 (Oryza sativa), 3'ss of exon 2
---------gtaagattttgtgagaacttatctgtgatgaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAG
           |   || |   |       | ||   || |  ||   |   |  | ||||       |  ||   |||    ||||| |||| ||||| ||||| ||||||||||||||  ||||||| ||||| || ||||| |||||||||
gtacatatttcagtgttctagtatggacagtatgctttgcaattggcatcagtacgttgaaactgagtattttacgtttcgtgtgcagTTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAG

upper sequence: GLYMA02G13860.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g38080.1 (Oryza sativa), 3'ss of exon 2
-------------------------------------------------------------------gtaagattttgtgagaacttatctgtgatgaagatgaagttttttggatgaagaatttcaaattg-gat------tttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAG
                                                                     |  | | | |   || || |      |||  |       | |  |   || ||||  | |||| | |      ||||   |||| |||| ||||| ||||| || |||||||||||| | || ||||||||||| ||||| |||||||| 
gtataccctacatacaaaatttgaacagtttcaaatttttttaaatattttttttggggggaagagaacagtaatatttacaaatttcttcaaactgatcacctgaactatgagtcaaataattgaagattgtggtgttatgtttcttggcagCTGAGAAGGGAGAAGATCAGCGAGAGGATGAAGCTCCTGCAAGACCTTGTCCCTGGCTGCAGCAAA

upper sequence: GLYMA02G13860.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G137541_T01 (Zea mays), 3'ss of exon 2
----------------gtaagattttgtga------gaacttatctgtgatgaagatga--agttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAG
                  ||  |||||         | |    ||||  |   | ||||   ||  |    |    |  | |   |||| || ||| |||||| |||||||||| ||||| || |||||||||||| |||| || |||||||| ||||| |||||||| 
gtacggatttggtcacccaacgttttgccgcttgctggatcgctctgaaactgacatgaccggtcctgaaaaccctggctgttgcattgcatcttccctgcagTTGAGGAGGGAGAAGATTAGCGAGAGGATGAAGCTTCTGCAGGACCTTGTTCCTGGTTGCAGCAAA

upper sequence: GLYMA02G13860.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G818643_T01 (Zea mays), 3'ss of exon 2
------------------------------------gtaagattttgtgagaacttatctgtgatgaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAG
                                          |  ||||        ||||  ||  | |      | |||  |    |  |      |    ||||| |||||| |||||||||| ||||| || |||||||||||| | || || ||||| || ||||| |||||||| 
gtacggatttgatcaacgggtggcatccccgtgtttaccgtctgctgtggatcgcggtctggaattcacaccccaatgttta-accctgcttgctgcgtctttttttctctgcagTTGAGGAGGGAGAAGATTAGCGAGAGGATGAAGCTGCTGCAGGACCTCGTTCCTGGCTGCAGCAAA

upper sequence: GLYMA02G13860.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G818643_T02 (Zea mays), 3'ss of exon 2
------------------------------------gtaagattttgtgagaacttatctgtgatgaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAG----------------------------------
                                          |  ||||        ||||  ||  | |      | |||  |    |  |      |    ||||| |||||| |||||||||| ||||| || |||||||||||| | || || ||||| || ||||| ||||||||                                   
gtacggatttgatcaacgggtggcatccccgtgtttaccgtctgctgtggatcgcggtctggaattcacaccccaatgttta-accctgcttgctgcgtctttttttctctgcagTTGAGGAGGGAGAAGATTAGCGAGAGGATGAAGCTGCTGCAGGACCTCGTTCCTGGCTGCAGCAAAGTAGGTCTATCTTCCACACAGAAGAAAGAAAAGG

upper sequence: GLYMA02G13860.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G68920.2 (Arabidopsis thaliana), 3'ss of exon 3
---------gtaagatt-ttgtgagaacttatctgtgat-gaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAG
          ||| | | |  ||  |  |||  |   || |||| |     || ||| ||     || |  ||||   ||   |    |||| ||||| ||||| || ||||| |||||||||||||||||||| || ||||| || |||| ||||
gtacaatttctaaaactatcttggaagtttaagtcgaatagaagctatctcttcttgtatttttcatct--aattactttgcgatgatagGTTAGGAGAGAAAAAATTAGTGAAAGGATGAAGTTTCTTCAAGATCTAGTACCGGGTTGCAACAAG

upper sequence: GLYMA02G13860.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0010g00740.t01 (Vitis vinifera), 3'ss of exon 3
gtaagattttgtgagaac----ttatctgtgatgaagatga----agttttttggatgaagaatttcaaat--tggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAG
||||||||||    | |     |||  | ||||  |    |    | | |  | |     || ||  |  |  ||||  || |   ||||| || ||||||||||| ||||| ||||||||||||||||||||||| |||||||| |||||||||
gtaagatttttcatggatagttttagttttgatagaagcaattctattgtcctagtcttggagttaaagctggtggaccttgatgacagGTAAGAAGGGAAAAGATCAGTGAAAGGATGAAGTTTCTTCAAGACCTGGTACCTGGTTGCAGCAAG

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|193469602|gb|FK435962.1|FK435962
EST:     GCCGGGGTCAAGCAACAAATAGCCATAGCCTTGCAGAGAGA                         GTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTA
genomic: GCCGGGGTCAAGCAACAAATAGCCATAGCCTTGCAGAGAGAgtaagatttt ... ttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTA
EST: gi|193378765|gb|FK345106.1|FK345106
EST:     GTCAAGCAACAAATAGCCATAGCCTTGCAGAGAGA                         GTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTCTCTTCAAGACCTTGTA
genomic: GTCAAGCAACAAATAGCCATAGCCTTGCAGAGAGAgtaagatttt ... ttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTA
EST: gi|208266542|gb|GE062805.1|GE062805
EST:     TTGCAGAGAGA                         GTGAGGAGGG-AAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTA
genomic: TTGCAGAGAGAgtaagatttt ... ttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTA
EST: gi|208316755|gb|GE115383.1|GE115383
EST:     GTCAAGCAACAAGTAGCCATAGCCTTGCAGAGAGA                         GTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTA
genomic: GTCAAGCAACAAATAGCCATAGCCTTGCAGAGAGAgtaagatttt ... ttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTA
EST: gi|193448449|gb|FK412404.1|FK412404
EST:     GTCAAGCAACAAATAGCCATAGCCTTGCAGAGAGA                         GTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTA
genomic: GTCAAGCAACAAATAGCCATAGCCTTGCAGAGAGAgtaagatttt ... ttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatgaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAG
                                           ttttcact  CT-rich tract
                          aagaatttcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattttgtgagaacttatctgtgatgaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG