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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAATTCGATCATTAGAACATCTTCTACAATATGGAGAGCAGAATATTCGCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatggacttgcttccctgcatttttatcactttggcagtgctatcattgaacagtgtgaaacacattaccttgctcttaaaagatgacatagttgtagggctgcaagatgccactaacttttgctaacttttctctgaataattacag

Basic information

species Glycine max
transcript GLYMA06G44340.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 19
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 5'ss of exon 19
GGCAATTCGATCATTAGAACATCTTCTACAATATGGAGAGCAGAATATTCGCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatggacttgcttccctgcatttttatcactttggcagtgctatcattgaacagtgtgaaacacattaccttgctcttaaaagatgacatagttgtagggctgcaagatgccactaacttttgctaacttttctctgaataattacag
|||  | || ||| | || | |||| |||| ||||| |||||||||||| | || ||||||||| | || |||||  ||||||| ||||| ||||| ||||||      | |||     |   | |||| | |     | |   | |||   |   | | ||||  |   | | ||| |  | ||   | | | |    | | |                                                
GGCTGTACGGTCACTTGAGCGTCTTTTACAGTATGGCGAGCAGAATATTAGACGGGCAGTTCCTCTTGCTCTTGGCATACTCTGCATATCTAATCCGAAGgtatgcaacatttgaccaacataagttttgtta----aggatcacgatctaagttaaatttgaagtaa--tgctttgatgattaagtgtaaaaaaaactttgagag----------------------------------------------

upper sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 19
lower sequence: GRMZM5G816609_T01 (Zea mays), 5'ss of exon 5
GGCAATTCGATCATTAGAACATCTTCTACAATATGGAGAGCAGAATATTCGCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgta---aaatggacttgcttccctgcatttttatcactttggca-gtgctatcattgaacagtgtgaaacacattaccttgctcttaaaagatgacatagttgtagggctgcaagatgccactaacttttgctaacttttctctgaataattacag
|||  | || ||| | || | |||||| || ||||| |||||||||||  | |||||||||||| | || |||||| ||||||| ||||| ||||| ||||||    |||  |   |  |   ||||   | |    | ||  | |||  |||  | |    ||  | | ||| | |||      |  |   | | | |  | |                                                    
GGCTGTACGTTCACTTGAGCGTCTTCTGCAGTATGGCGAGCAGAATATAAGACGAGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtatgtgaataaatccgtctta-tgcacactaaa-gttctgatacgtgaaatc--taattcctgctagaaacaatgcctgatcaatgcagtttta-agaactttg---------------------------------------------------

upper sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 19
lower sequence: GRMZM2G155384_T03 (Zea mays), 5'ss of exon 19
GGCAATTCGATCATTAGAACATCTTCTACAATATGGAGAGCAGAATATTCGCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatggacttgcttccctgcatttttatcactttggcagtgctatcattgaacagtgtgaaacacattaccttgctcttaaaagatgacatagttgtagggctgcaagatgccactaacttttgctaacttttctctgaataattacag
|||  | || ||| | || | |||||| || ||||| |||||||||||  | || ||||||||| | || |||||| ||||||| ||||| ||||| |||||||  ||||     ||      || ||   ||||     |   || | ||        |||| |   | |   |   | ||  | ||     |||||  ||  || || | | | |                                   
GGCTGTACGTTCACTTGAGCGTCTTCTGCAGTATGGCGAGCAGAATATAAGACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaac-tggataaattt------atcttgtacact--aataaatctctgat------acgtgagatctactggatacatttttgatga--gtgtagtttaagaacttcaggtttcaa-----------------------------------

upper sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 19
lower sequence: AT2G20580.1 (Arabidopsis thaliana), 5'ss of exon 17
GGCAATTCGATCATTAGAACATCTTCTACAATATGGAGAGCAGAATATTCGCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatggacttgcttccctgcatttttatcactttggcagtgctatcattgaacagtgtgaaacacattaccttgctcttaaaagatgac--atagttgtagggctgcaagatgccactaacttttgctaacttttctctgaataattacag
||  || || ||  | || |   | |||||||| ||||| || || ||||| || || || ||||||||||||||||| || |||||||| ||||||||||||||    ||||   |   || | |||||   |    ||  | | || |||     | ||  |    | |||   | | |||| |  |  |  | | ||  ||                                                  
GGAGATCCGTTCTCTGGAGCGGATGCTACAATACGGAGAACAAAACATTCGGCGTGCTGTGCCTTTGGCCCTTGGTCTCCTTTGTATATCCAATCCAAAGgtaaat---acttttgtaaatgtagttttactgcacctgct-tacaattattagtgggcgtctagagtaatactgggtttttaatatttttcccacaattccag--------------------------------------------------

upper sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 19
lower sequence: AT4G28470.1 (Arabidopsis thaliana), 5'ss of exon 17
GGCAATTCGATCATTAGAACATCTTCTACAATATGGAGAGCAGAATATTCGCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatggacttgcttccctgcatttttatcactttggcagtgctatcattgaacagtgtgaaacacattacc-ttgctcttaaaagatgacatagttgtagggctgcaagatgccactaacttttgctaacttttctctgaataattacag
||  || || || || || |   | ||||| |||||||||||||| ||||| || ||||| |||||||| |||||||| || ||||||||||| |||||||| |    |  ||  ||      || |   |  |   ||| ||||  | | |   | |  | | | | | |    || ||||  ||   |   ||| ||  ||                                                  
GGAGATCCGTTCTTTGGAGCGCGTACTACAGTATGGAGAGCAGAACATTCGACGTGCAGTGCCTTTGGCTCTTGGTCTCCTATGTATATCAAACCCAAAGgtga----gtattatttttgcatatctagttttcggcggc-gtgcagttacttttctgcttaaga-atactgttgttactctctaacttttttataattccag--------------------------------------------------

upper sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 19
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 19
GGCAATTCGATCATTAGAACATCTTCTACAATATGGAGAGCAGAATATTCGCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaa--aatggacttgcttccctgcatttttatcactttggcagtgctatcattgaacagtgtgaaacacattaccttgctcttaaaagatgacatagttgtagggctgcaagatgccactaacttttgctaacttttctctgaataattacag
||||||||| || ||||| |||||||| || ||||||||||||||||| ||||||||||| || |||||||||||||| ||||| |||||||| || ||||||   ||||   |  | ||  ||  ||     || ||  ||||||       | ||   |||| |       || ||  |  | |||| |||  | |  ||  |  |  ||||                                        
GGCAATTCGTTCCTTAGAGCATCTTCTTCAGTATGGAGAGCAGAATATCCGCCGAGCAGTCCCATTGGCCCTTGGTCTCCTCTGCATATCAAACCCTAAGgtacctaatgctttaacatctttgggttgggtccatttgtgcagtg-------taaagcctgtgca------cactttaattcttaaaggtga-gttgaagtctgtattaaaga----------------------------------------

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|193711290|gb|FK643885.1|FK643885
EST:     TTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAG                         GTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
genomic: TTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatgga ... ataattacagGTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
EST: gi|7693027|gb|AW761125.1|AW761125
EST:     GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAG                         GTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
genomic: GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatgga ... ataattacagGTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
EST: gi|120530135|gb|EH258269.1|EH258269
EST:     GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAG                         GTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
genomic: GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatgga ... ataattacagGTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
EST: gi|193425219|gb|FK389906.1|FK389906
EST:     GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAG                         GTCAATGTTATGG
genomic: GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatgga ... ataattacagGTCAATGTTATGG
EST: gi|207763019|gb|GD731150.1|GD731150
EST:     GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAG                         GTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
genomic: GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatgga ... ataattacagGTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
EST: gi|10847592|gb|BF070244.1|BF070244
EST:     GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAG                         GTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
genomic: GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatgga ... ataattacagGTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
EST: gi|6566730|gb|AW234362.1|AW234362
EST:     GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAG                         GTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
genomic: GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatgga ... ataattacagGTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
EST: gi|10237756|gb|BE806644.1|BE806644
EST:     GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAG                         GTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
genomic: GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatgga ... ataattacagGTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
EST: gi|193458615|gb|FK423704.1|FK423704
EST:     CCGAGCAGTTCCTTTCGGCCCTTGGTCTACTCTGTATATCAAATCCAAAG                         GTCAATGTTATGGATACGTTAAGCAGAC
genomic: CCGAGCAGTTCCTTT-GGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatgga ... ataattacagGTCAATGTTATGGATACGTTAAGCAGAC
EST: gi|9440032|gb|BE440543.1|BE440543
EST:     GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAG                         GTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
genomic: GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatgga ... ataattacagGTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
EST: gi|22521874|gb|BU080685.1|BU080685
EST:     GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAG                         GTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
genomic: GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatgga ... ataattacagGTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
EST: gi|193437445|gb|FK401730.1|FK401730
EST:     GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAG                         GTCAATGTTATGG
genomic: GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatgga ... ataattacagGTCAATGTTATGG
EST: gi|120492692|gb|EH220859.1|EH220859
EST:     GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAG                         GTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
genomic: GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatgga ... ataattacagGTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
EST: gi|120530034|gb|EH258168.1|EH258168
EST:     GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAG                         GTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
genomic: GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatgga ... ataattacagGTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
EST: gi|208301986|gb|GE097466.1|GE097466
EST:     GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAG                         GTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA
genomic: GCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatgga ... ataattacagGTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAA

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCAATTCGATCATTAGAACATCTTCTACAATATGGAGAGCAGAATATTCGCCGAGCAGTTCCTTTGGCCCTTGGTCTACTCTGTATATCAAATCCAAAGgtaaaatggacttgcttccctgcatttttatcactttggcagtgctatcattgaacagtgtgaaacacattaccttgctcttaaaagatgacatagttgtagggctgcaagatgccactaacttttgctaacttttctctgaataattacag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG