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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAGgtaattattttttgttttacttggtagaatttgttccaagtgttctgtatatctgcaggaattaactatggctatttattgaacag

Basic information

species Glycine max
transcript GLYMA16G01810.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01810.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os06g09290.2 (Oryza sativa), 5'ss of exon 3
GTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAGgtaattattt---tttgttttact-------tggtagaatttgttccaagtg--ttctgt--atatctgcaggaattaactatggctatttattgaacag--------------
| || || |||||||| |||||||| ||  |||| ||||||||||| ||||| || |||||||| ||||||||||| ||||| || || ||||||||  ||    ||    | |||       ||||   |||   | ||| ||  | ||||  ||||   | |   ||    ||| || | || | |  ||              
GAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTGTATCCGATAAGCAGATGATGCAGGAGGAGCAACCCCTGCAGgtaatgcttgacgttcacctaactgactttttggttttattgcattcaaatgcatactgtcaatattccctgtgcttcctcatgcct-tctactaataagcgtccttctgcaag

upper sequence: GLYMA16G01810.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os02g54340.1 (Oryza sativa), 5'ss of exon 3
GTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAGgta-attattttttgttttacttggtagaatttgttccaagtgtt-----ctgtatatct-gcaggaattaactatggctatttattgaacag----------------------------------------------------------------
| || ||||||||||| |||||  | ||| |||| ||||| |||||||| || || |||||||| |||||||| |||||||| || || || ||| ||   ||    | || |   |   |  || ||||  || ||      | | |  || |||    | |   |||     | |      ||                                                                
GGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatcgcttaacctatttccccgcctaccttcttccttgttttaatagttttgtgcctagcatacttcatgcatgatgcctaaggacttagatttcctgctttagttttatgtcttctgtgattttactgacaagatattttcctccttttgaag

upper sequence: GLYMA16G01810.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G181359_T01 (Zea mays), 5'ss of exon 3
GTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAGgta------attatttt----ttgttttacttggtagaatttgttccaagtgttctgtatatctgcaggaattaactatggctatttattgaacag------------------------------------------------------------
|||| |||||||||||||| || || ||  |||| |||||||||||| | ||||| ||||| || |||||||| ||||| || ||  | || |||      || |   |    |||| |||||| ||||| |||  |   |  | | ||  | | || |   |  |   |||    ||  | |||                                                               
GTATAAAGGAGTCTGATACAGGGTTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAACAGATGATGCAAGAAGAACAACCGTTACAAgtatattaaatgaccctgatattgtgttacttcgtagattttacttttacagctttgagt-tatg-acctaccatgcatgatagttggtagaaatctttttggtttcaattttacatgtgctagtgcattaataacttctctttctctttctgcag

upper sequence: GLYMA16G01810.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G110185_T01 (Zea mays), 5'ss of exon 3
GTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAGgta-attattt---------tttgttttacttggtagaattt---gttccaagtgttctgtatatctgcaggaa----ttaactatggctatttattgaacag-----------------------------
| || |||||||||||||| ||  | ||  |||| |||||||||||| | ||||| |||||||| |||||||| ||||| || ||  | || ||| ||||  |          |||| | |||| || |  |||   | |   ||  |  |   ||    ||  |     ||   |   | | |  ||    |||                             
GGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgtatattaactgaacctgatattgtgtcacttagttgtttttacagctttgagcatgatagttaggcacaaaatctttttggtttcagttttacatgtgccagcgcactataacttctctctctttctgcag

upper sequence: GLYMA16G01810.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 5'ss of exon 3
GTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAGgtaattattttttgttttacttggtagaatttgtt--ccaagtgttctgtatatctgcagga--attaactatggctatttattgaacag
|||||||||| ||||||||||| ||||| |||||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||||||  || || ||  ||||  |    |  ||||  |  |  | | |  |||||||||| ||      |   | |||  | |          
GTATCAAGGAATCTGATACTGGCTTAGCTGCACCAAGTCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAGGAGCAGCCTCTTCAGgtggtttttcttgattttgttgaacaacatttactgtcttaatataatgtatatctgaagagtggctggttttggaaactag--------

upper sequence: GLYMA16G01810.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ13722 (Selaginella moellendorffii), 5'ss of exon 3
GTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAGgtaatt---attttttgttttacttggtagaatttgttccaagtgttctgtatatctgcaggaattaactatggctatttattgaacag
| ||||||||||| || |||||  ||||||| || |||||||||||||| || |||||||||||||||||||| ||||||||||| || || |||| |   |||||||  ||   |   | |  ||| ||     | |  ||| |   |   | |                          
GGATCAAGGAGTCCGACACTGGTCTAGCAGCTCCTAGCCAGTGGGATCTGGTGTCTGATAAGCAAATGATGCAAGAAGAGCAGCCACTGCAAgtaagtgagatttttttcttcgatctcttgcttttcttttttctctcatgtttggttttggtag-------------------------

upper sequence: GLYMA16G01810.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ29161 (Selaginella moellendorffii), 5'ss of exon 3
GTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAGgtaattattttttgttttacttggtagaatttgttccaagtgttctgtatatctgcaggaattaactatggctatttattgaacag
| ||||||||||| || |||||  ||||||| || |||||||||||||| || |||||||||||||||||||| ||||||||||| || || ||||      ||| ||||  | | |  | |   || |   |||| ||  | |  | ||                            
GGATCAAGGAGTCCGACACTGGTCTAGCAGCTCCTAGCCAGTGGGATCTGGTGTCTGATAAGCAAATGATGCAAGAAGAGCAGCCACTGCAAgtaagggagattt-ttttcttcgatctattgcttttctcatgttttg-gttttggtag----------------------------

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|213602597|gb|DB968879.1|DB968879
EST:     GGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAG                         GTGGCACGATGCACAAAGATCATAAATCCAAACTCTGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAGgtaattattt ... tattgaacagGTGGCACGATGCACAAAGATCATAAATCCAAACTCTGAAGATGCCAAATAT
EST: gi|16281984|gb|BI944774.1|BI944774
EST:     GGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAG                         GTGGCACGATGCACAAAGATCATAAATCCAAACTCTGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAGgtaattattt ... tattgaacagGTGGCACGATGCACAAAGATCATAAATCCAAACTCTGAAGATGCCAAATAT
EST: gi|24205597|gb|BU964850.1|BU964850
EST:     GGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAG                         GTGGCACGATGCACAAAGATCATAAATCCAAACTCTGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAGgtaattattt ... tattgaacagGTGGCACGATGCACAAAGATCATAAATCCAAACTCTGAAGATGCCAAATAT
EST: gi|193388500|gb|FK356213.1|FK356213
EST:     GGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAG                         GTGGCACGATGCACA
genomic: GGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAGgtaattattt ... tattgaacagGTGGCACGATGCACA
EST: gi|254319386|gb|GR829006.1|GR829006
EST:     GGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAG                         GTGGCACGATGCACAAAGATCATAAATCCAAACTCTGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAGgtaattattt ... tattgaacagGTGGCACGATGCACAAAGATCATAAATCCAAACTCTGAAGATGCCAAATAT
EST: gi|209717050|gb|BW668704.1|BW668704
EST:     GGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAG                         GTGGCACGATGCACAAAGATCATAAATCCAAACTCTGTAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAGgtaattattt ... tattgaacagGTGGCACGATGCACAAAGATCATAAATCCAAACTCTGAAGATGCCAAATAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAGgtaattattttttgttttacttggtagaatttgttccaagtgttctgtatatctgcaggaattaactatggctatttattgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG