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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgacatttattaagtttagtttgataaatctatgattatatttccctaccaatgagtttctcttgagtatttacattcacacactgacttgagttagttatttgattgtgcttttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCATCATGGTGGCTTACAACAACAAGAAATATTACATAGATATTATAGAAACT

Basic information

species Glycine max
transcript GLYMA08G05030.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G05030.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G114220_T01 (Zea mays), 3'ss of exon 7
gtgagttgacatttattaagtttagtttgataaatctatgattatatttccctaccaatgagtttctcttgagtatttacattcacacactgacttgagttagttatttgattgtgcttttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCATCATGGTGGCTTACAACAACAAGAAATATTACATAGATATTATAGAAACT
|| ||   || ||||  || ||  ||   ||||    ||  | | | ||| || |       |||||||||    |   | ||  ||  || |          ||| ||| |  |   ||||    |||||| |||| ||| || || ||||| |||||||| || || ||||| ||||||||||| || |||||||||||  ||||||| || |||||| | ||||| 
gtaaggaaaccttta--aaatt--gtcctataa--tgatcttgaaaattctcttc------atttctcttggcattaggcgttatcattctca----------ttacttgctgttaaattttc---cagCTTGGAAAAAACTTTAAGAAATTTCTCCTGCTTAACCACGGGAGACAGCATCATGGTAGCCTACAACAACAAACAATATTATATTGATATTGTTGAAACA

upper sequence: GLYMA08G05030.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv03s0038g00750.t01 (Vitis vinifera), 3'ss of exon 7
gtgagttgacatttattaagtttagtttgataaatctatgattatatttccc-taccaatgagtttctcttgagtatttacattcacacactgacttgagttagttatttgattgtgcttttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCATCATGGTGGCTTACAACAACAAGAAATATTACATAGATATTATAGAAACT
                              ||  | | |||| | || ||   | |  ||   | ||  || | |   ||  |  |     |    | | |||  | |||   | |  ||| | ||||||||| || |||||| | ||||| ||||||||||| || ||||||||||| ||||||||||| || || || ||||||||||||||||||||| |||| || 
-----------------------------ttatctttttgataaaatatctgatgctcatctatgtcattt-aatggatatgtgtagcaggtacactaatttatcttttttcatttcttttataatgcagCTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTATCATGGTGGCATATAATAATAAGAAATATTACATAGATATTGTAGAGACA

upper sequence: GLYMA08G05030.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ38251 (Selaginella moellendorffii), 3'ss of exon 3
gtgagttgacatttattaagtttagtttgataaatctatgattatatttccctaccaatgagtttctcttgagtatttacattcacacactgacttgagttagttatttgattgtgcttttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCATCATGGTGGCTTACAACAACAAGAAATATTACATAGATATTATAGAAACT
                                                        | |||| | |          ||  | | || |    |   |   |    |||   || |   ||  | ||||| |||||||| ||  |||||||||| || ||| | |||   || || | |||||||||||| |||||||||||||| || ||||| |||||| | ||| | 
-----------------------------------------------------gtaagtgaggtgccaccagcc--ttgtacttactctgctaacagctctccaaattccgttttttcttgctttgcagATTAGAAACCACGCTGAGGAATTTCTCGTGCCTCACTGTGGGTGACAACATCATGGTGGCGTACAACAACAAGAAGTACTACATTGATATTGTGGAAGCC

upper sequence: GLYMA08G05030.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ14970 (Selaginella moellendorffii), 3'ss of exon 3
gtgagttgacatttattaagtttagtttgataaatctatgattatatttccctaccaatgagtttctcttgagtatttacattcacacactgacttgagttagttatttgattgtgcttttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCATCATGGTGGCTTACAACAACAAGAAATATTACATAGATATTATAGAAACT
                                                        | | || | |          ||  | | || |    |   |  ||    |||   ||     ||  | ||||| |||||||| ||  |||||||||| || ||| | |||   || || | |||||||||||| |||||||||||||| || ||||| |||||| | ||| | 
-----------------------------------------------------gtaagtaaggtgccaccagcc--ttgtacttactctgctaacagctttccaaattccgtttcttcttgctttgcagATTAGAAACCACGCTGAGGAATTTCTCGTGCCTCACTGTGGGTGACAACATCATGGTGGCGTACAACAACAAGAAGTACTACATTGATATTGTGGAAGCC

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|151397988|gb|EV267861.1|EV267861
EST:     TTACAGCCTCACACAAAAGACTTCTTGGATACTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|19269563|gb|BM885819.1|BM885819
EST:     TTACAGCCCCACACAAAAGACTTTTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|254318174|gb|GR832342.1|GR832342
EST:     TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|9563895|gb|BE473404.1|BE473404
EST:     TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|192296041|gb|FG993404.1|FG993404
EST:     TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|37994740|gb|CF806346.1|CF806346
EST:     TTACAGCCCCACACAAAAGACTTTTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|192325065|gb|FK016176.1|FK016176
EST:     TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|15816027|gb|BI788302.1|BI788302
EST:     TTACAGCCCCACACAAAAGACTTTTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|16996631|gb|BM086003.1|BM086003
EST:     TTACAGCCCCACACAAAAGACTTTTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|209712046|gb|BW674191.1|BW674191
EST:     TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|192309316|gb|FK000524.1|FK000524
EST:     TTACAGCCCCACACAAAAGACTTTTTGGATATTTCCGATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|16348528|gb|BI974123.1|BI974123
EST:     TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|192326508|gb|FK018815.1|FK018815
EST:     TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|254313714|gb|GR831343.1|GR831343
EST:     TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|298172847|gb|HO019831.1|HO019831
EST:     TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTT
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTT
EST: gi|17153552|gb|BM143485.1|BM143485
EST:     TTACAGCCCCACACAAAAGACTTTTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|213604953|gb|DB956328.1|DB956328
EST:     TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAG
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAG
EST: gi|192330755|gb|FK022018.1|FK022018
EST:     TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAA-AACATTGAGGAATTTTTCCTGCTTGGCTACTGGAGATAGCAT
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|24205916|gb|BU965169.1|BU965169
EST:     TTACAGCCCCACACAAAAGACTTTTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|213599556|gb|DB968353.1|DB968353
EST:     TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttacattcacacactgacttgagttagttatttgattgtgcttttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCATCATGGTGGCTTACAACAACAAGAAATATTACATAGATATTATAGAAACT
                                        tgctttttt  CT-rich tract
                         ttagttatttgatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgacatttattaagtttagtttgataaatctatgattatatttccctaccaatgagtttctcttgagtatttacattcacacactgacttgagttagttatttgattgtgcttttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCATCATGGTGGCTTACAACAACAAGAAATATTACATAGATATTATAGAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA