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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattattctactgttgtgatcttttattaatgacatcactgtacagagagagaaagagagggttgattagaatgcagtttgatgtagctgagttatgcttttggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG

Basic information

species Glycine max
transcript GLYMA08G22140.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 19
gtattattctactgttgtgatcttttattaatgacatcactgtacagagagagaaagagagggttgatt-agaatgcagtttgatgtagctgagttatgcttttggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG
          | | ||||   || | |||||    |||  ||| | |         | |  | |   || |||    |   | || |  |||  ||  ||  |  |||| |  || || || || |||||  ||||||| ||||| ||||| || ||||| ||  |||| ||||| |||||||||||||| || |||||||| 
-------gtaagtcttgtttgctgtgattaa----atccttgttctg---------gtgctgttcctttgagagctaaacattatctt-ctgtattcggcact--gcagTAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAA

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 20
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 20
gtattattctactgttgtgatcttttattaatgacatcactgtacagagagagaaagagagggttgattagaatgcagtttgatgtagctgagttatgcttttggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG
                || ||   ||| || | || | |  ||   || |   |||       || ||     |   |||   ||| |      |||  |||   ||| || ||||| ||||| |||||| | ||||| ||||| ||||| || ||||| || || |||||||| ||  ||||||| ||||||||||| |||
----------------gtaattcattagtagtcacttgagagtttggaaaatcaaa-------tttatgcacctttggttaactgt-gtgacaatattttttcctcagTAACCGGATACCAGAAGCTGCTCTGATGGCACGATCATATCTTCCGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAG

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
--------------------------------------------gtattattctactgt-tgtgatcttttattaatgacatcactgtacagagagaga----aagagagggttgattagaatgcagttt---gatgtagctgagttatgcttt-tggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG
                                             || || | || |     |   ||| | | | | |    ||  ||  | |  ||     | ||    |    ||   ||  |||||   |||    ||  | |||| | | | |||| |||||||| || || |||||||||||||| ||||| || || |||||||||||  |||||||| |  | ||||||||||| || ||||  |||
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatggtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 20
gtattattctactgttgtgatcttttattaatgacatcactgtacagagagagaaagagagggttgattaga-atgcagttt----gatgtagctgagttatgcttttggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG
                        | |||  ||   | |||| | | |  |  | | |||  ||||   ||| || |   ||    ||||   ||||   || || || ||||||||||||| || ||||||||||| ||||| || || ||||| ||||||||||||||||||||||| ||  | ||||| ||||| || | ||||
-----------------------gtaattgttgttgttactgcaaacatgggaacaaagatagttgtggagatattccacttttgggatgatactgaagcattctctttgcagCAATCGGATCCCTGAGGCTGCTTTGATGGCACGGTCTTATCTTCCAAGCAAGGTCTCAGAGATAGTCGCTCTGTGGAGGAAAGACCTTAATAAG

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|151397194|gb|EV267067.1|EV267067
EST:     TTATTCATGTTGGGTAAACTTGAGGACTGCCTTCAACTTTTGGTAGAAAG                         CAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAA
genomic: TTATTCATGTTGGGTAAACTTGAGGACTGCCTTCAACTTTTGGTAGAAAGgtattattct ... cttttggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAA
EST: gi|151411223|gb|EV281034.1|EV281034
EST:     TTATTCATGTTGGGTAAACTTGAGGACTGCCTTCAACTTTTGGTAGAAAG                         CAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAA
genomic: TTATTCATGTTGGGTAAACTTGAGGACTGCCTTCAACTTTTGGTAGAAAGgtattattct ... cttttggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagagagggttgattagaatgcagtttgatgtagctgagttatgcttttggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG
                        gtttgat  putative branch site (score: 5)
                                           tgctttt  putative PPT
             attagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattattctactgttgtgatcttttattaatgacatcactgtacagagagagaaagagagggttgattagaatgcagtttgatgtagctgagttatgcttttggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA