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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgtaatttacatttcttttaactgacactgacaatttttctcttatttttctttccacttgaaattggaatcacccatacatgctggtatagtttcaaaagcatcatttgtgaatcaaattgataaatcttctctgttatcag

Basic information

species Glycine max
transcript GLYMA16G28310.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G28310.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os01g64660.4 (Oryza sativa), 5'ss of exon 9
TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgtaatttacatttcttttaactgacactgac-aatttttctcttatttttctttccacttgaaattggaatcacccatacatgctggtatagtttcaaaagcatcatttgtgaatcaaattgataaatcttctctgttatcag
||| ||||||||||| ||||| ||||||||| ||||||| ||||| ||||| ||||||||||| ||||| ||||||||| ||     ||| || |  | |   |||  ||     |    || |||  |   | | | |  | || |    | |  || ||| || | | |  |||       ||||   | | ||||  ||  |              
TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGGCCAGTCTTTCACAGGCAAAGAACGGgtacttatttcttcattcatttcatcttgattaaaacagcatgcatgtttagt---attagcatcttgagtt---cttgaatcctgatacattgttcaaa------cttgttgct-acattggcaatgcag------------

upper sequence: GLYMA16G28310.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os05g36270.1 (Oryza sativa), 5'ss of exon 10
TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgtaatttacatttcttttaactgacactgacaatttttctcttatttttctttccacttgaaattggaatcacccatacatgctggtatagtttcaaaagcatcatttgtgaatcaaattgataaatcttctctgttatcag
||| ||||| ||||| ||||||||||||||||||||||| || || ||||||||  ||||||| |||||  ||||||| |  |  | |||  ||   |   | |  ||   ||  |||||   ||    | |    ||| || | || | |       |      |||      |||||                                       
TGTTCTGTACGAAGTGTTCCCAATGTCATTCTTGATGGAGCAAGCTGGAGGACAAGCTTTCACAGGCAAACAACGGgtgagctgaacttcacttcggttttagtagca-cattcatcttacgatttaaccaa---aaaaatgtactccctctgtttcacaatgcaagtcattctagcatt--------------------------------------

upper sequence: GLYMA16G28310.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os05g36270.3 (Oryza sativa), 5'ss of exon 9
------------------------TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgtaatttacatttcttttaactgacactgacaatttttctcttatttttctttccacttgaaattggaatcacccatacatgctggtatagtttcaaaagcatcatttgtgaatcaaattgataaatcttctctgttatcag
                        ||| ||||| ||||| ||||||||||||||||||||||| || || ||||||||  ||||||| |||||  ||||||| |  |  | |||  ||   |   | |  ||   ||  |||||   ||    | |    ||| || | || | |       |      |||      |||||                                       
AGTTCGCTACATGTGGCATGGCAGTGTTCTGTACGAAGTGTTCCCAATGTCATTCTTGATGGAGCAAGCTGGAGGACAAGCTTTCACAGGCAAACAACGGgtgagctgaacttcacttcggttttagtagca-cattcatcttacgatttaaccaa---aaaaatgtactccctctgtttcacaatgcaagtcattctagcatt--------------------------------------

upper sequence: GLYMA16G28310.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G322953_T03 (Zea mays), 5'ss of exon 9
TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgtaatttacatttcttttaactgacactgacaatttttctcttatttttctttccacttgaa--attggaatcacccatacatgctggtatagtttcaaaagcatcatttgtgaatcaaattgataaatcttctctgttatcag
 || ||||||||||||||||| ||||||||| |||||||||| || ||||| ||| ||||||| |||||  |||||||   || || ||    |  || | ||   ||||      || |    ||||    || ||   ||   | |  ||        | ||   | |||||| |                                           
CGTTCTGTATGAAGTCTTCCCGATGTCATTCCTGATGGAACAAGCTGGAGGCCAGGCTTTCACAGGCAAACAACGGgtgtgtttcagtttccctttctcagaccc-caatccccaactgaaaaatcttgatgctagagctatcacatttgcctgagatatcagggggaatttcaaca-------------------------------------------

upper sequence: GLYMA16G28310.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM5G836250_T03 (Zea mays), 5'ss of exon 10
TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgta--atttacatttcttt-taactgacactgacaatttttctcttatttttctttccacttgaaattggaatcacccatacatgctggtatagtttcaaaagcatcatttgtgaatcaaattgataaatcttctctgttatcag
| ||||||| ||||| ||||| ||||| ||| | ||||| ||||||||||| ||||| ||||| ||||| |||||||||   |||||   |||   |  |  | ||  | ||     | ||| |  | | |     | |||  | |||   |   | ||     |  | ||||     | | | ||  || ||         |                  
TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGGCCAGTCCTTCACAGGCAAAGAACGGgtagggtttacgcctctccatttcctatacaaaaaaaaaagcacttctgctccctcgtcatagaa--tagaactgcttgttcacttctgcttggttt---gggtacctttgatgcattggcactgcatgcag-------------

upper sequence: GLYMA16G28310.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv18s0072g00770.t01 (Vitis vinifera), 5'ss of exon 11
TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgtaatttacatttcttttaactgacactgacaatttttctcttatttttctttccacttgaaattggaatcacccatacatgctggtat--agtttcaaaagcatcatttgtgaatcaaattgataaatcttctctgttatcag
||| || ||||||||||| ||||||||||||||||||||||| |||||||| ||  |||| || || ||| ||||||||     ||  ||  ||||||    |||     || ||    |   |      ||||   ||||  | ||| |  |  || |     |     ||||||| | |  ||| |                                
TGTTCTCTATGAAGTCTTTCCAATGTCATTCTTGATGGAACAAGCAGGAGGTCAAGCTTTTACTGGAAAGCAACGGgtat----caactcgattaact--ttctg----cttatcaaccaaaatataagtcact---aattctagtcatctgttaattccaacttcagaattcaaaaaccttctttttt-------------------------------

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|31474714|gb|CD416742.1|CD416742
EST:     CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG                         GCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
genomic: CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgtaatttaca ... ctgttatcagGCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
EST: gi|26269057|gb|CA820120.1|CA820120
EST:     CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG                         GCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
genomic: CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgtaatttaca ... ctgttatcagGCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
EST: gi|15204366|gb|BI427134.1|BI427134
EST:     CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG                         GCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
genomic: CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgtaatttaca ... ctgttatcagGCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
EST: gi|31457542|gb|CD399570.1|CD399570
EST:     CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG                         GCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
genomic: CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgtaatttaca ... ctgttatcagGCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
EST: gi|31473114|gb|CD415142.1|CD415142
EST:     CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG                         GCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
genomic: CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgtaatttaca ... ctgttatcagGCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
EST: gi|22928833|gb|BU545972.1|BU545972
EST:     CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG                         GCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
genomic: CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgtaatttaca ... ctgttatcagGCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
EST: gi|31469604|gb|CD411632.1|CD411632
EST:     CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG                         GCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
genomic: CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgtaatttaca ... ctgttatcagGCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
EST: gi|192304055|gb|FG993885.1|FG993885
EST:     CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACAG                         GCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
genomic: CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgtaatttaca ... ctgttatcagGCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
EST: gi|151398810|gb|EV268681.1|EV268681
EST:     CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG                         GCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
genomic: CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgtaatttaca ... ctgttatcagGCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
EST: gi|31456318|gb|CD398346.1|CD398346
EST:     CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCCAGGAACGG                         GCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
genomic: CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgtaatttaca ... ctgttatcagGCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
EST: gi|7692550|gb|AW760653.1|AW760653
EST:     CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG                         GCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
genomic: CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgtaatttaca ... ctgttatcagGCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
EST: gi|21675556|gb|BQ627907.1|BQ627907
EST:     CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG                         GCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT
genomic: CATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgtaatttaca ... ctgttatcagGCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGGgtaatttacatttcttttaactgacactgacaatttttctcttatttttctttccacttgaaattggaatcacccatacatgctggtatagtttcaaaagcatcatttgtgaatcaaattgataaatcttctctgttatcag

- - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA