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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcggcataccaaagttatactctgttccaaatttaagtatatattttcaatgactattgctcatgtggtgttttgtttattgcacatgttcaaatacatgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGTGCAGTTGATTTTTTAGTGAAACCTATTCGGAGGAATGAACTTAAAAA

Basic information

species Glycine max
transcript GLYMA12G07860.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G07860.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g17570.4 (Oryza sativa), 3'ss of exon 5
gtaagcggcataccaa---agttatactctgttccaa-atttaagtatatattttca-atgactattgctcatgtggtgttttgtttattgcacatgttcaaatacatgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGTGCAGTTGATTTTTTAGTGAAACCTATTCGGAGGAATGAACTTAAAAA
|||||  |||| |      |   | | | |   |  | ||      | | ||||  | || ||  ||     ||      ||||  |  |||  |||| ||  | |||||||||||||| ||  |||| || ||||||| |||||||||||||||||||||||| |||||||| ||| ||||||| ||||| || | |||||||||||| ||
gtaagtagcattcttgctcaaccacatttttcacttatatactgtgacacatttctacataaccttttagtctgaatatgtttgactgatgctgatgt-cattttcatgcagTGATGTCTTCGAATGACTCAATGGGTACAGTCTTTAAGTGTTTGTCAAAAGGAGCAGTTGACTTTCTAGTGAAGCCTATACGTAAGAATGAACTTAAGAA

upper sequence: GLYMA12G07860.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g49460.3 (Oryza sativa), 3'ss of exon 5
gtaagcggcatacc--aaagttatactctgttccaaatttaagtatatattttcaatgactattgctcatgtggtgttttgtttattgcac-atgttcaaatacatgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGTGCAGTTGATTTTTTAGTGAAACCTATTCGGAGGAATGAACTTAAAAA
|||||  || | ||  ||   || | |    | |   |  ||     |    |       ||||     | |    ||||   |  | |||  |  |    ||  |||||||||||| ||  ||||| ||||||||| ||| ||||||||||||||||| || || ||||| || ||||| || || || || | |||||||||||| ||
gtaagtagctttcctcaactctacagtacaattcttgtacaaaatgttgcccttgtcatttatttactttctatgcttttagctgctacactgttgtggtttatgtgcagTGATGTCTTCAAATGATGCTATGGGTACAGTTTTTAAGTGTTTGTCAAAGGGCGCTGTTGACTTCTTAGTCAAGCCCATACGTAAGAATGAACTTAAGAA

upper sequence: GLYMA12G07860.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G005732_T02 (Zea mays), 3'ss of exon 2
----gtaagcggcataccaaagttatactctgttccaaatttaagtatatattttcaatgactattgctcatgtggtgttttgtttattgcacatgt-tcaaatacatgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGTGCAGTTGATTTTTTAGTGAAACCTATTCGGAGGAATGAACTTAAAAA
    ||||    |||  | |   | || |   |  ||   ||||     |  |||||     ||||            ||||   |  | |||   | |    |   |||||||||||| ||   |||| ||||| ||| ||||||||| ||||||||||||||||| ||||| |||||||| || ||||| || | |||||||||||| ||
gtaagtaactttcatctctacagtgtagttcatatcatgattaaaatgttgctttcatcatttatttagtcccaatgcttttagctgctacactgatgttgtttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAGGTGCTGTTGACTTTTTAGTCAAGCCTATACGTAAGAATGAACTTAAGAA

upper sequence: GLYMA12G07860.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G095727_T04 (Zea mays), 3'ss of exon 6
gtaagcggcataccaaagttatactctgttccaaatttaagtatatattttcaatgactattgctcatgtggtgttttgtttattgcacatgttcaaat-acatgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGTGCAGTTGATTTTTTAGTGAAACCTATTCGGAGGAATGAACTTAAAAA
|||||  |  | ||  |  ||  | ||  | ||  |  || | ||| || | |||   | |||    |      ||||   |  | |||   |     |  ||||||||||||||  |  ||||||||||| |||| || |||||||||||||| || || ||||||||||| || || |||||  | || | |||||| ||||| ||
gtaagtagatttcctcaacta--ccctaatgcacgtgaaattttatcttgttaat---tgttgggtttaaatacttttagctgctacactgatgtgttttgcatgcagTGATGTCTACGAATGATTCTATGAGTATGGTGTTTAAGTGTTTGTCGAAGGGAGCAGTTGATTTCTTGGTAAAACCACTACGTAAGAATGAGCTTAAGAA

upper sequence: GLYMA12G07860.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G033962_T01 (Zea mays), 3'ss of exon 2
gtaagcggcataccaaagt----tatactctgttccaaatttaagtatatattttcaatgactattgctcatgtggtg-ttttgtttattgcacatgt-tcaaatacatgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGTGCAGTTGATTTTTTAGTGAAACCTATTCGGAGGAATGAACTTAAAAA
|||||   | | ||   ||    | || |   |  ||   | ||  || |   ||   ||| |  |     |    || ||||   |  | |||   | |    |   |||||||||||| ||   ||||  |||| ||| ||||||||| ||| ||||||||||||| ||||| ||||| || || ||||| || | |||||||||||| ||
gtaagtaactttcctctgtacagtgtagttcatatcatgatcaaa-atgttgctttcttgatttatttagttccaatgcttttagctgctacaccgatgtggtttttgtgcagTGATGTCTTCGAGTGATGATATGAGTACAGTCTTTAAATGTCTGTCAAAAGGTGCTGTTGACTTTTTGGTCAAGCCTATACGTAAGAATGAACTTAAGAA

upper sequence: GLYMA12G07860.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G60100.3 (Arabidopsis thaliana), 3'ss of exon 3
gtaagcggcataccaaagttatactctgttccaaatttaagtatatattttcaatgactattgctcatgtggtgttttgtttattgcacatgttcaaatacatgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGTGCAGTTGATTTTTTAGTGAAACCTATTCGGAGGAATGAACTTAAAAA
          |||  || |    ||   ||  |  |||   |||  |  ||||||      ||||||  | ||||         ||   |||||    |   || |||||||||||| ||||||||||||| | | ||||||||||||||||| || ||||| ||||||||| | |||||||| ||| | | ||| ||||| || ||
-----gtatttactcaaatc---cttgattaaatttttgtttatccagcttcaatatgccatgctcagtttgtgtaactcaagatgtg-atgtttc--tttttgtagTGATGTCATCACATGATTCTATGGTTCTGGTCTTTAAGTGTTTGTCGAATGGTGCTGTTGATTTTCTCGTGAAACCCATTAGAAAGAACGAACTAAAGAA

upper sequence: GLYMA12G07860.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g03650.t01 (Vitis vinifera), 3'ss of exon 2
gtaagcggcataccaaagttat-actctgttccaaatttaagtatatattttcaatgactattgctcatgtggtgttttgtttattgcacatgttcaaatac--atgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGTGCAGTTGATTTTTTAGTGAAACCTATTCGGAGGAATGAACTTAAAAA
|||||   |||   |  ||| | | | |  |  |||||||||  |   ||| | || ||| ||||| || || ||  |||  | |    | ||   |  |    |||||||||||||||| |||||||||||||||||||||||||||||| |||| || ||||||||||||||||| |||||||||||||| | |||||||||||||||
gtaagtatcattttagtgttttcattttcatagaaatttaaggcttattttcctatcactcttgctgatttgatgcattgaatttccaccctgacgatctttttatgcagTGATGTCATCCCATGATTCTATGGGTATAGTCTTTAAGTGTCTGTCCAAGGGTGCAGTTGATTTTTTGGTGAAACCTATTCGAAAGAATGAACTTAAAAA

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|22522834|gb|BU081645.1|BU081645
EST:     TTTGTGCAAGATCATGAGCCACAAAACTCTGAAGAATATTCCTGTGATTA                         TGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAG
genomic: TTTGTGCAAGATCATGAGCCACAAAACTCTGAAGAATATTCCTGTGATTAgtaagcggca ... atacatgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAG
EST: gi|17518648|gb|BM187690.1|BM187690
EST:     TTTGTGCAAGATCATGAGCCACAAAACTCTGAAGAATATTCCTGTGATTA                         TGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAG
genomic: TTTGTGCAAGATCATGAGCCACAAAACTCTGAAGAATATTCCTGTGATTAgtaagcggca ... atacatgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgactattgctcatgtggtgttttgtttattgcacatgttcaaatacatgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGTGCAGTTGATTTTTTAGTGAAACCTATTCGGAGGAATGAACTTAAAAA
                      ttttgtttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcggcataccaaagttatactctgttccaaatttaagtatatattttcaatgactattgctcatgtggtgttttgtttattgcacatgttcaaatacatgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGTGCAGTTGATTTTTTAGTGAAACCTATTCGGAGGAATGAACTTAAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA