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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATCACTCCGATTGTGACTTCTGGGCTAGTAATGCAACTTCTGGCTGGGTCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtatgtgcctttctttgtacttatattccttttgctgaacatatttttttttctctgtctaatattatctgattttgcatttgtggccatcaatttaact...

Basic information

species Glycine max
transcript GLYMA12G35990.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G35990.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 5'ss of exon 2
GAATCACTCCGATTGTGACTTCTGGGCTAGTAATGCAACTTCTGGCTGGGTCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtatgtgcctttctttgtac-ttatattccttttgctgaacatatttttttttctc--tgtctaatattatctgattttgcatttgtggcc-atca-atttaact---------------------------------------------------------------------------------------------
| |||||||| |||||||| |||||  | |||||||||||||| |  || ||||||||||||||||| ||||||| |||  |||||||||| || ||| |||| ||    |    |  ||  ||| ||| ||    | | |  |   ||    ||   || || || |  | || | |    ||||| ||| | || |||| |                                                                                               
GTATCACTCCAATTGTGACATCTGGCATGGTAATGCAACTTCTAGTGGGATCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtattatgagattaacactatgttctttactattacctgaaccttgaaacttagtgccttatttactatggtctgctgtttgtagcccaccatatttcagcgaatggctattgattaaatgctactacgtatctgattcatgtttaccatgtcttttgattatatttgttacgctaatgtacttttttacccag

upper sequence: GLYMA12G35990.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os09g17840.1 (Oryza sativa), 5'ss of exon 1
GAATCACTCCGATTGTGACTTCTGGGCTAGTAATGCAACTTCTGGCTGGGTCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtatgtgcctttctttgta-cttatattccttttgctgaacatatttttttttctctgtctaatat-tatctgattttg--ca--tttgtggccatcaatttaact-----------------------------------------------------------------------
| || || || |||||||| |||||  | |||||||||||||| |  || |||||||| |||||||| ||||||| |||  ||||||| || || ||  |||| ||   | |     || |  |   |||| ||  |      ||    | |||   ||||| | |  || |  |  |   ||   || |  | |    |||| ||                                                                       
GTATTACCCCAATTGTGACATCTGGAATGGTAATGCAACTTCTAGTGGGATCAAAGATTATTGAAGTTGACAACAGTGTGAGAGAGGACCGTGCACTTCTgtaagtatttatagaaataacacaatctcctatttattggtggataacatgttcagagtctagtgtgcatgtactgctagccagtcttctacctagtgttttagctaacatcagaaaattgcagagcttccttattctttttctttctcctggtggtaatcttttgatgtgacttag

upper sequence: GLYMA12G35990.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os09g17830.1 (Oryza sativa), 5'ss of exon 1
GAATCACTCCGATTGTGACTTCTGGGCTAGTAATGCAACTTCTGGCTGGGTCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtatgtgccttt--------ctttgtacttatattccttttgctgaacatatttttttttctctgtctaatattatctgattttgcatttgtggccatcaatttaact--------------------------------------------------------------
| || || || |||||||| |||||  | |||||||||||||| |  || |||||||| |||||||| ||||||| |||  ||||||| || || ||  |||| ||   | |        |    ||      ||  | |||    | |||||  |  |  | |||  |   |    ||    || | |  | |||     |  | ||                                                              
GTATTACCCCAATTGTGACATCTGGAATGGTAATGCAACTTCTAGTGGGATCAAAGATTATTGAAGTTGACAACAGTGTGAGAGAGGACCGTGCACTTCTgtaagtatttatagaaatagcgcaatatcctattttatattgtcttatatattggtggtaatgtgttcagagtctaatgtgcatgtactgctagcctgtcctgcacctagtgatttagtgaatgaaagttttttttttttgcctggtggtaatcttgtgatgtgactcag

upper sequence: GLYMA12G35990.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G073498_T02 (Zea mays), 5'ss of exon 1
GAATCACTCCGATTGTGACTTCTGGGCTAGTAATGCAACTTCTGGCTGGGTCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtatgtgcc--tttctttgtacttatatt-ccttttgctgaacatatttttttttctctgtc-taatattatctg--attttgcatttgtggccatcaatttaact----------------------------------------------------------------
| || ||||| |||||||| |||||| | |||||||||||||| | ||| || |||||||||||||| ||||||| |||  |||||||||| || ||| |||| |||     || ||   | | || |  ||||    | | || | || |   | |  ||  |  | | |||||   | || |  | |      || ||   | |                                                                
GTATTACTCCAATTGTGACATCTGGGATGGTAATGCAACTTCTTGTTGGATCGAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtgttgtcttattaaaaataatgtaaccttcaatttatcacaattctaactgttggtggttgtttcatctgcagtctttctgtagcatttctctatcatagtctgtcaaagtagattataaaccttctgatttgtattgtgatgcacattgcacttctttactcag

upper sequence: GLYMA12G35990.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G130987_T04 (Zea mays), 5'ss of exon 1
GAATCACTCCGATTGTGACTTCTGGGCTAGTAATGCAACTTCTGGCTGGGTCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtatgtgcctttctttgtacttatatt---ccttttgctgaacatatttttt---------tttctctgtctaatat----tatctgattttgcatttgtggccatcaatttaact--------------------------------------
| || ||||| |||||||| |||||  | |||||||||||||| |  || || |||||||||||||| ||||||| |||  |||||||||| || ||| |||| |||  | ||||| ||   |||||      ||   | | || | || |          ||||||| || | | |    ||   |||| |  |  |   |   |  ||||||                                        
GTATTACTCCAATTGTGACCTCTGGTATGGTAATGCAACTTCTTGTCGGATCGAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtgt-tgtctttctaaaaatattgtgatcttcaattatcacaattctaatcgtagcatttctctatcaagtctgccatagtagattataaaccttctgatctgtatttaatatatttgtattgtgatgcacattgcatttctttactcag

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|209698282|gb|BW678040.1|BW678040
EST:     TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTT                         AAACGGAGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
genomic: TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtatgtgcct ... tctttcccagAAACGGAGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
EST: gi|254316195|gb|GR827732.1|GR827732
EST:     TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTT                         AAACGGAGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
genomic: TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtatgtgcct ... tctttcccagAAACGGAGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
EST: gi|208171512|gb|GD971909.1|GD971909
EST:     TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTT                         AAACGGAGCACA
genomic: TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtatgtgcct ... tctttcccagAAACGGAGCACA
EST: gi|213614652|gb|DB972864.1|DB972864
EST:     TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTT                         AAACGGAGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAAGCAGT
genomic: TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtatgtgcct ... tctttcccagAAACGGAGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
EST: gi|207702735|gb|GD684737.1|GD684737
EST:     TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTT                         AAACGGAGCACA
genomic: TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtatgtgcct ... tctttcccagAAACGGAGCACA
EST: gi|254347543|gb|GR853792.1|GR853792
EST:     TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTT                         AAACGGAGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
genomic: TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtatgtgcct ... tctttcccagAAACGGAGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
EST: gi|254329727|gb|GR839280.1|GR839280
EST:     TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTT                         AAACGGAGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
genomic: TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtatgtgcct ... tctttcccagAAACGGAGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATCACTCCGATTGTGACTTCTGGGCTAGTAATGCAACTTCTGGCTGGGTCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtatgtgcctttctttgtacttatattccttttgctgaacatatttttttttctctgtctaatattatctgattttgcatttgtggccatcaatttaact

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT