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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATCACTCCCATTGTGACTTCTGGGCTAGTAATGCAACTTCTGGCTGGGTCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtaagtgtctttctttgtacctatattcctttctgaacatattttttttctccgtctaattttatttgcatttgtggccatcaatttaactgtgcaaaat...

Basic information

species Glycine max
transcript GLYMA13G34370.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G34370.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 5'ss of exon 2
GAATCACTCCCATTGTGACTTCTGGGCTAGTAATGCAACTTCTGGCTGGGTCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtaagtgtctttctttgtac-ctatattcctt-------tctgaacat---attttttttctccgtctaattttatttgc-atttgtggccatcaatttaactgtgcaaaat--------------------------------------------------------------------------------------
| |||||||| |||||||| |||||  | |||||||||||||| |  || ||||||||||||||||| ||||||| |||  |||||||||| || ||| ||||||| |  |    |  || |||| ||| ||        |||||| |   |  ||  | |    | || | |  | |||  ||||| |||  | || |  | | | |                                                                                          
GTATCACTCCAATTGTGACATCTGGCATGGTAATGCAACTTCTAGTGGGATCAAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtattatgagattaacactatgttctttactattacctgaaccttgaaacttagtgccttatttactatggtctgctgtttgtagcccaccatatttcagcgaatggctattgattaaatgctactacgtatctgattcatgtttaccatgtcttttgattatatttgttacgctaatgtacttttttacccag

upper sequence: GLYMA13G34370.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os09g17840.1 (Oryza sativa), 5'ss of exon 1
GAATCACTCCCATTGTGACTTCTGGGCTAGTAATGCAACTTCTGGCTGGGTCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtaagtgtctttctttgtacctatattcctttctgaacatattttttttctccgtctaattttatttgcatttgtggccatcaatttaactgtgcaaaat------------------------------------------------------------------------------
| || || || |||||||| |||||  | |||||||||||||| |  || |||||||| |||||||| ||||||| |||  ||||||| || || ||  ||||||| | | |     || | | | ||   | |  |    |   |    |      | | |  | ||||| |   || | | | |   ||    |   |                                                                              
GTATTACCCCAATTGTGACATCTGGAATGGTAATGCAACTTCTAGTGGGATCAAAGATTATTGAAGTTGACAACAGTGTGAGAGAGGACCGTGCACTTCTgtaagtatttatagaaataac-acaatctcctatttattggtggataacatgttcagagtctagtgtgcatgtactgctagccagtcttctacctagtgttttagctaacatcagaaaattgcagagcttccttattctttttctttctcctggtggtaatcttttgatgtgacttag

upper sequence: GLYMA13G34370.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os09g17830.1 (Oryza sativa), 5'ss of exon 1
GAATCACTCCCATTGTGACTTCTGGGCTAGTAATGCAACTTCTGGCTGGGTCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtaagtgtctttctttgtacctatat-tcctttctgaacatattttttttctccgtctaattttatttgcatt----tgtggccat-caatttaactgtgcaaaat----------------------------------------------------------------
| || || || |||||||| |||||  | |||||||||||||| |  || |||||||| |||||||| ||||||| |||  ||||||| || || ||  ||||||| | | |     || |   || |||| | | |   | | || | | |  ||   | | | ||   | |    ||||    | |   |   |||| |   |                                                                 
GTATTACCCCAATTGTGACATCTGGAATGGTAATGCAACTTCTAGTGGGATCAAAGATTATTGAAGTTGACAACAGTGTGAGAGAGGACCGTGCACTTCTgtaagtatttatagaaatagcgcaatatcctattttatattgtcttatatattggtggtaatgtgttcagagtctaatgtgcatgtactgctagcctgtcctgcacctagtgatttagtgaatgaaagttttttttttttgcctggtggtaatcttgtgatgtgactcag

upper sequence: GLYMA13G34370.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G073498_T02 (Zea mays), 5'ss of exon 1
GAATCACTCCCATTGTGACTTCTGGGCTAGTAATGCAACTTCTGGCTGGGTCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtaagtgtc--tttctttgtacctatattcctttctgaacatattttttttctccgtc-----taattttatttgca-----tttgtggc---catcaatttaactgtg-caaaat------------------------------------------------------
| || ||||| |||||||| |||||| | |||||||||||||| | ||| || |||||||||||||| ||||||| |||  |||||||||| || ||| |||||||||    || ||   |   || |  | |||     ||     || |  | ||      |  ||| || ||||     | ||| ||     || ||   | | || |||| |                                                      
GTATTACTCCAATTGTGACATCTGGGATGGTAATGCAACTTCTTGTTGGATCGAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtgttgtcttattaaaaataatgtaaccttcaatttatcacaattctaactgttggtggttgtttcatctgcagtctttctgtagcatttctctatcatagtctgtcaaagtagattataaaccttctgatttgtattgtgatgcacattgcacttctttactcag

upper sequence: GLYMA13G34370.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G130987_T04 (Zea mays), 5'ss of exon 1
GAATCACTCCCATTGTGACTTCTGGGCTAGTAATGCAACTTCTGGCTGGGTCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtaagtgtctttctttgtacctatattcctttctgaacatattttttttct--ccgtctaattttatttgca--tttgtggccatcaatt-taactgtgcaaaat-------------------------------------------------
| || ||||| |||||||| |||||  | |||||||||||||| |  || || |||||||||||||| ||||||| |||  |||||||||| || ||| ||||||||| | ||||| ||   |||||    |||  |  |||     ||||   |||   ||||   |  ||  | ||      |  ||| |||   | |  |                                                   
GTATTACTCCAATTGTGACCTCTGGTATGGTAATGCAACTTCTTGTCGGATCGAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtgt-tgtctttctaaaaatattgtgatcttcaattatcacaattctaatcgtagcatttctctatcaagtctgccatagtagattataaaccttctgatctgtatttaatatatttgtattgtgatgcacattgcatttctttactcag

upper sequence: GLYMA13G34370.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G307252_T01 (Zea mays), 5'ss of exon 2
GAATCACTCCCATTGTGACTTCTGGGCTAGTAATGCAACTTCTGGCTGGGTCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtaagtgtc-tttctttgtacctatattcctttctgaacatatttttt--ttctccgtctaattttatttgcatttgtggccatcaatttaactgtgcaaaat--------------------------------------------------------------
| |||||||| ||||| || |||||  | || ||||||||||| |  || |||||||| |||||||| ||||||| |||  | |||||||| || ||| |||||||||  ||   | |||   | ||    ||||  |  ||||  |   | ||  |  ||    |  ||  ||   | | |    ||| |    ||||||                                                                
GTATCACTCCAATTGTAACATCTGGAATGGTGATGCAACTTCTAGTGGGATCAAAGATTATTGAAGTTGACAACAGTGTGAGGGAGGATCGTGCTCTGCTgtaagtgttgttgggtagtatagacatcaaattctatatgtattggtggatgctttgattatccatccttttatcaattgactgacattgagaactgcaaagctttatggtttttattcttgtatctggtgttttcatgtgattcatagtgtactttttacccag

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|192302459|gb|FG994795.1|FG994795
EST:     TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTT                         AAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
genomic: TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtaagtgtct ... actttcccagAAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
EST: gi|209725183|gb|BW672656.1|BW672656
EST:     TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTT                         AAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
genomic: TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtaagtgtct ... actttcccagAAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
EST: gi|16349322|gb|BI974917.1|BI974917
EST:     TCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTT                         AAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
genomic: TCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtaagtgtct ... actttcccagAAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
EST: gi|213611043|gb|DB970970.1|DB970970
EST:     TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTT                         AAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
genomic: TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtaagtgtct ... actttcccagAAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
EST: gi|209721281|gb|BW665775.1|BW665775
EST:     TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTT                         AAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
genomic: TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtaagtgtct ... actttcccagAAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
EST: gi|213608397|gb|DB970868.1|DB970868
EST:     TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTT                         AAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
genomic: TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtaagtgtct ... actttcccagAAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
EST: gi|16348617|gb|BI974212.1|BI974212
EST:     TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTT                         AAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
genomic: TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtaagtgtct ... actttcccagAAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
EST: gi|7640034|gb|AW734344.1|AW734344
EST:     TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTT                         AAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
genomic: TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtaagtgtct ... actttcccagAAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
EST: gi|151396883|gb|EV266756.1|EV266756
EST:     TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTT                         AAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
genomic: TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtaagtgtct ... actttcccagAAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
EST: gi|209699069|gb|BW652862.1|BW652862
EST:     TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTT                         AAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
genomic: TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtaagtgtct ... actttcccagAAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
EST: gi|213612035|gb|DB958961.1|DB958961
EST:     TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTT                         AAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT
genomic: TCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtaagtgtct ... actttcccagAAACGGGGCACAGAAGCTACTTGGTATTTTGATAGCTGTTGGTGAGGCAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATCACTCCCATTGTGACTTCTGGGCTAGTAATGCAACTTCTGGCTGGGTCAAAGATCATTGAAGTGGACAACAATGTACGAGAGGATCGAGCCCTGTTgtaagtgtctttctttgtacctatattcctttctgaacatattttttttctccgtctaattttatttgcatttgtggccatcaatttaactgtgcaaaat

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