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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCCAATGACAAACTATTGCTAGTACAAGCATTGAGGAGGAAGGGTCATGTTGTGGCTGTAACTGGGGATGGAACAAATGATGCTCCTGCACTTCATGAGgtttgcatatatatatgatatttgaggcttgtgcttttattgtttgtaagtatccattacaatgatgacattgatggtaatggagcatttagtttgatta...

Basic information

species Glycine max
transcript GLYMA15G18180.1
intron # 24
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G18180.1 (Glycine max), 5'ss of exon 24
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 5'ss of exon 8
TCCCAATGACAAACTATTGCTAGTACAAGCATTGAGGAGGAAGGGTCATGTTGTGGCTGTAACTGGGGATGGAACAAATGATGCTCCTGCACTTCATGAGgtttgcatatatatatgatatttgaggcttgtgcttttatt-gtttgtaagtatccattacaatgatgacat-tgatggtaatggagcatttagtttgatta--------------------------------------
||| | |||||||||  | |||||| ||||| |||  | ||| ||  ||||||| ||||| ||||| |||||||| ||||||||||||||| | ||||||||   |||| |||  ||  | ||  |  |||  |   ||   |  |  |  ||    ||  | |     ||  ||| |  ||| || |||  |  |||||                                        
TCCAAGTGACAAACTTCTCCTAGTAAAAGCACTGAAAAAGAAAGGCAATGTTGTTGCTGTTACTGGAGATGGAACGAATGATGCTCCTGCATTGCATGAGgt--acatacataattgggaattttgttttgaacaaataaaaggataaacataatggttttatttcaatcagatgaagacaatcgatcatgcatgttgatgcacatttctaattttgatctcttattcctcctaatttag

upper sequence: GLYMA15G18180.1 (Glycine max), 5'ss of exon 24
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 25
TCCCAATGACAAACTATTGCTAGTACAAGCATTGAGGAGGAAGGGTCATGTTGTGGCTGTAACTGGGGATGGAACAAATGATGCTCCTGCACTTCATGAGgtttgcatat--atatatgatatttgaggcttgtgcttttattgtttgtaagtatccattacaatgatgacattgatggtaatggagcatttagtttgatta
 || |||||||| || || || ||  ||||||| || |  |  ||||||||||| ||||| ||||| ||||| ||||||||||| || ||  | ||||||||||   | |  |   ||| |   | | | ||        |   | |  | || || |  || || ||  || |  |  | ||| |    | |  || ||  
ACCAAATGACAAGCTTTTACTTGTTAAAGCATTAAGAAAAAGAGGTCATGTTGTTGCTGTGACTGGAGATGGCACAAATGATGCCCCAGCTTTGCATGAGgtttatctctcgactaatgttccatcatgttttgaaagaaacaatcttcatgt-tcaacaaccataatc-cagtctttcttatgcaatgctgaacttaatag

upper sequence: GLYMA15G18180.1 (Glycine max), 5'ss of exon 24
lower sequence: GRMZM2G140328_T03 (Zea mays), 5'ss of exon 25
TCCCAATGACAAACTATTGCTAGTACAAGCATTGAGGAGGAAGGGTCATGTTGTGGCTGTAACTGGGGATGGAACAAATGATGCTCCTGCACTTCATGAGgtttgcatatatatatgatatttgaggcttgtgcttttattgtttgtaagtatcc--attacaatgatgacattgatggtaatggagcatttagtttgatta------------------------------------------------------------------
 || ||||| ||||| || || ||  | ||| |||||   |  ||||||||||| ||||| ||||| ||||| ||||||||||| || ||||| |||||||||||   |    ||     | | |   || |  | || |  | || ||  | ||  |||  ||  ||||  ||    ||     |  || || |||    |                                                                  
ACCAAATGATAAACTTTTACTTGTTAAGGCACTGAGGGCAAGAGGTCATGTTGTTGCTGTTACTGGAGATGGCACAAATGATGCCCCAGCACTGCATGAGgtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaa-tatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcag

upper sequence: GLYMA15G18180.1 (Glycine max), 5'ss of exon 24
lower sequence: GRMZM5G893864_T01 (Zea mays), 5'ss of exon 4
TCCCAATGACAAACTATTGCTAGTACAAGCATTGAGGAGGAAGGGTCATGTTGTGGCTGTAACTGGGGATGGAACAAATGATGCTCCTGCACTTCATGAGgtttgcatatatatatgatatttgaggcttgtgcttttattgtttgtaagtatccattaca---atgatgacattga--------tggtaatggagcatt--tagtttgatta--------------------------------------------
||| |||||||||||  | |||||| ||||  | | ||  |  || |||||||| ||||| ||||| |||||||| ||||||||||||||| | ||||||||        | ||   || || |  | |  |  ||| | ||  |  ||| || ||  |      |||| | ||  |        |||||||  |||| |  ||   || | |                                            
TCCTAATGACAAACTTCTCCTAGTAAAAGCTCTTAAGAAAATAGGCCATGTTGTAGCTGTTACTGGTGATGGAACGAATGATGCTCCTGCATTGCATGAGgt--------acattcaat-ttgggagttcatattttaaatgaatacaagaattcaacatgcatgtgattatatgaagcactatttggtaatacagcacttctaacatgttgaggtttcttccccttctcaatcttatcattattcccacttatcag

upper sequence: GLYMA15G18180.1 (Glycine max), 5'ss of exon 24
lower sequence: GRMZM2G391042_T01 (Zea mays), 5'ss of exon 25
TCCCAATGACAAACTATTGCTAGTACAAGCATTGAGGAGGAAGGGTCATGTTGTGGCTGTAACTGGGGATGGAACAAATGATGCTCCTGCACTTCATGAGgtttgcatatatatatgatatttgaggcttgtgcttttattg-tttgtaagtatc--cattacaatgatgacattgatggtaatggagcatttagtttgatta------------------------------------------------------------------
 || ||||| ||||| || || ||  | ||| |||||   |  ||||| ||||| ||||| ||||| ||||| ||||||||||| || ||||| |||||||||||   |    | |  | | |  |  ||    ||| |||  |||| ||  | |  | ||      ||||  ||  | ||     |  || || ||| |  |                                                                  
ACCAAATGATAAACTTTTACTTGTTAAGGCACTGAGGGCAAGAGGTCACGTTGTTGCTGTTACTGGAGATGGCACAAATGATGCCCCAGCACTGCATGAGgtttgtggac---tgtagtctctatgaatt----tttaattactttgaaaccagcctcgttttggacatgaactttctagttcctaa-tatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtacttgagaaactctgaaacttgcag

upper sequence: GLYMA15G18180.1 (Glycine max), 5'ss of exon 24
lower sequence: GRMZM2G138195_T01 (Zea mays), 5'ss of exon 1
TCCCAATGACAAACTATTGCTAGTACAAGCATTGAGGAGGAAGGGTCATGTTGTGGCTGTAACTGGGGATGGAACAAATGATGCTCCTGCACTTCATGAGgtttgcatatatatatgatatttgaggcttgtgcttttattgtttgtaagtatccattacaatgatgacattgatggtaatggagcatttagtttgatta------------------------------------------------------------------
 || ||||| ||||| || || ||  | ||| |||||   |  ||||| ||||| ||||| ||||| ||||| ||||||||||| || ||||| |||||||||||   |    | |  | | |  |  || |   ||  ||       || |||  ||   |  ||||  ||  | ||     |  || || ||| |  |                                                                  
ACCAAATGATAAACTTTTACTTGTTAAGGCACTGAGGGCAAGAGGTCACGTTGTTGCTGTTACTGGAGATGGCACAAATGATGCCCCAGCACTGCATGAGgtttgtggac---tgtagtctctatgaatttttaattactttgaaaccagcatcggtttggac-atgaactttctagttcctaa-tatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtactcgacaaactctgaaacttgcag

upper sequence: GLYMA15G18180.1 (Glycine max), 5'ss of exon 24
lower sequence: AT5G57110.1 (Arabidopsis thaliana), 5'ss of exon 26
TCCCAATGACAAACTATTGCTAGTACAAGCATTGAGGAGGAAGGGTCATGTTGTGGCTGTAACTGGGGATGGAACAAATGATGCTCCTGCACTTCATGAGgtttgcatatatatatgatatttga---------ggcttgtgcttttattgtttgtaagtatccatta--caa------tgatgacattgatggtaatggagcatttagtttgatta-------------------------------
|||||||||||||||  |||| |||||| |  ||||  |  | || |||||||| ||||| || |||||||| |||||||||||||||||| | || ||||| |    || ||  ||| |||| |         | |    |||     |   || |||| ||  ||   |||      ||   || ||  |  | |  ||||   |  ||   | |                               
TCCCAATGACAAACTTCTGCTGGTACAATCTCTGAGACGACAAGGGCATGTTGTTGCTGTCACCGGGGATGGGACAAATGATGCTCCTGCATTGCACGAGgtatagtaatttac-tgaaatttaaactgataatgtcgaaagctacatctaactgaaagtttcttttggccaagtattttgcctacgtttttactcagcgagcggatcattatctcattggtgttaaattttttgagtgtatttgcag

upper sequence: GLYMA15G18180.1 (Glycine max), 5'ss of exon 24
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 5'ss of exon 26
TCCCAATGACAAACTATTGCTAGTACAAGCATTGAGGAGGAAGGGTCATGTTGTGGCTGTAACTGGGGATGGAACAAATGATGCTCCTGCACTTCATGAGgtttgcatatatatatgatatttg-aggcttgtgcttttattgtttgtaagtatccattacaatgatgacattgatggtaatggagcatttagtttgatta
 ||||||||||||||  | || || ||| |  ||| ||||| ||| || || |||||||| ||||| |||||||| ||||||||||||||||| || ||||||   ||| || ||   |  | | | |  |  ||||| |   |       |||  |  |  |   |  |  || ||       | | || ||        
ACCCAATGACAAACTTCTTCTTGTGCAATCGCTGAAGAGGAGGGGACACGTCGTGGCTGTGACTGGTGATGGAACCAATGATGCTCCTGCACTGCACGAGgttca-atacatttacattcctcgtatgtgtaagctttaaaaatacactgttattgaggatcacactttctgtgttgccccccaa-ctttcag--------

upper sequence: GLYMA15G18180.1 (Glycine max), 5'ss of exon 24
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 27
TCCCAATGACAAACTATTGCTAGTACAAGCATTGAGGAGGAAGGGTCATGTTGTGGCTGTAACTGGGGATGGAACAAATGATGCTCCTGCACTTCATGAGgtttgcata--tatatatgatatttgaggcttgtgcttttattgtttgtaagtatccattacaatgatgacattgatggtaatggagcatttagtttgatta-
||| |||||||| ||  | || || ||||||||||  | ||| || |||||||| ||||||||||| |||||||| ||||||||||||||||| || ||||||||   |  | || ||   ||   || |   || |   | | | | | | | |       | | |  | | |     || | |  || |  |||    || 
TCCAAATGACAAGCTTCTTCTTGTGCAAGCATTGAAAAAGAAAGGGCATGTTGTTGCTGTAACTGGAGATGGAACTAATGATGCTCCTGCACTACACGAGgtttggcgagctctagatagaatgatagaccgatggtagaaatctgtttgaatctttggataagtcac-atacttcaattacttggccact--gttaacctat

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|23729217|gb|BU762697.1|BU762697
EST:     TTGTGGCTGTAACTGGGGATGGAACAAATGATGCTCCTGCACTTCATGAG                         GCCGATATAGGTCTAGCAATGGGTATCCAAGGTACAGAAGTTGCCAAAGAG
genomic: TTGTGGCTGTAACTGGGGATGGAACAAATGATGCTCCTGCACTTCATGAGgtttgcatat ... tggaatatagGCCGATATAGGTCTAGCAATGGGTATCCAAGGTACAGAAGTTGCCAAAGAG




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCCAATGACAAACTATTGCTAGTACAAGCATTGAGGAGGAAGGGTCATGTTGTGGCTGTAACTGGGGATGGAACAAATGATGCTCCTGCACTTCATGAGgtttgcatatatatatgatatttgaggcttgtgcttttattgtttgtaagtatccattacaatgatgacattgatggtaatggagcatttagtttgatta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA