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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagcatttttctattattgttgaaataccaaacattgttgtgtgtctgtgtgtaagcgtgtttattgtatggtgtactcaaattttcccattttttaatatgtttagtgtttaattatttttcttatctttttgttgagacttgataaggttctggttgggtggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAATTATGAAGTAGGAAATATGATTGCTGAAGCATTGAGCAGAGTTGGTAGAA

Basic information

species Glycine max
transcript GLYMA08G18760.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g02380.2 (Oryza sativa), 3'ss of exon 5
gtgaagcatttttctattattgttgaaataccaaacattgttgt-gtgtctgtgtgtaagc--gtgtttattgtatggtgtactcaaattttccca-ttttttaatatgtttagtgtttaattatttttcttatctttttgttgagacttgataaggttctggttgggtggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAATTATGAAGTAGGAAATATGATTGCTGAAGCATTGAGCAGAGTTGGTAGAA
|| ||  | |  ||      |  ||   | |  ||  || | || |||  |||| | || |  |||||| ||| |     | || |  |   |  | |    | | ||| ||  | | ||  || | |     | ||||||||     |  | ||     |   | |      |  |||||||||| |||||| | || ||||| || ||||||||||| || |||||||||||| | || |||||||| || || ||  ||||||  ||||| || |
gtaaaataatcgtcaggctctaatgcttt-cagaatgttttagttgtggttgtg-gcaacctggtgtttgttgcaaca-atgcttagctagactgagtcaaatcagatgatt--tatctatgtagtatatgcttttttttgttctacttataaaaaacattttcttg-----ctttagGTTGAAGACAGTGAGCTTGCGGATGTTGCTGCAGTCAGTGCTGGCAACAATTATGAAATCGGTAATATGATAGCAGAGGCTATGAGCAAGGTTGGCAGGA

upper sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 4
lower sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 5
gtgaagcatttttctattattgttgaaataccaaacattgttgtgtgtctgtgtgtaagcgtgtttattgtatggtgtactcaaattttcccattttttaatatgtttagtgtttaattatttttcttatctttttgttgagacttgataaggttctggttgggtggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAATTATGAAGTAGGAAATATGATTGCTGAAGCATTGAGCAGAGTTGGTAGAA
                                                                                      ||    | ||  | | ||  |||   | ||  |  ||||| | |  ||| |  ||  |||||| | ||     ||   |||||||||||||||||| |||||  | |||||||| |||||||| |||||||| |||||||| |||||||| ||||||||||| |||||| ||   | ||||||| | |
-----------------------------------------------------------------------------------gtattgttgacttaattagattcttaa--tctagct-cttttcatgtgctttagaggattcttgatcatgtagctcttttctggattgcagGTTGAAGACAGTGAACTAGCAGATGTTGCAGCAGTTAGTGCAGGAAACAATTACGAAGTAGGCAATATGATTGCAGAAGCAATGGCAAAAGTTGGTCGTA

upper sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgaagcatttttctattattgttgaaataccaaacattgttgtgtgtctgtgtgtaagcgtgtttattgtatggtgtactcaaattttcccattttttaatatgtttagtgtttaattatttttcttatctttttgttgagacttgataaggttctggttgggtggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAATTATGAAGTAGGAAATATGATTGCTGAAGCATTGAGCAGAGTTGGTAGAA
                                                                                    |  |  | ||| |   | |   ||  |  ||  | |||||||     | | |    |||     ||| | |   ||     | | |  |||||||||| |||||  | || ||||||||||| || ||||| || || ||  | ||||| |||| |||||||||||||||| |||||| ||| || || |
----------------------------------------------------------------------------------gtaagtaactattatgcta-aaacttccttcttcttaatttttcgagagtctatagcaagatggtctaaaggttatgtcattggaaatatagGTTGAAGACAGTGAACTTGCTGATGTGGCAGCTGTTAGTGCGGGTAATAACCACGAAGTTGGAAGTATGATTGCTGAAGCAATGAGCAAAGTGGGCAGGA

upper sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 4
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 5
gtgaagcatttttctattattgttgaaataccaaacattgttgtgtgtctgtgtgtaagcgtgtttattgtatggtgtactcaaattttcccattttttaatatgtttagtgtttaattatttttcttatctttttgttgagacttgataaggttctggttgggtggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAATTATGAAGTAGGAAATATGATTGCTGAAGCATTGAGCAGAGTTGGTAGAA
                                                                                       || | | ||| ||  |   |   | ||| | ||| ||     |||||||    ||  |        |    ||   || ||| | |||||||||| |||||  | |||||||| ||||| || ||||| || |||||  | ||| | ||||||||||||||||||||| |||||| ||| || || |
--------------------------------------------------------------------------------------gtttcaaatttatagaactctctttcttttaatatgttaagagtctttttcaaaaggttc---tgaatgtaagtcatgtcgat-gtagGTTGAAGACAGTGAACTTGCAGATGTTGCAGCTGTTAGTGCGGGTAACAACGACGAAATTGGAAATATGATTGCTGAAGCAATGAGCAAAGTGGGCAGGA

upper sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 5
gtgaagcatttttctattattgttgaaataccaaacattgttgtgtgtctgtgtgtaagcgtgtttattgtatggtgtactcaaattttcccattttttaatatgtttagtgtttaattatttttcttatctttt-tgttgagacttgataaggttctggttgggtggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAATTATGAAGTAGGAAATATGATTGCTGAAGCATTGAGCAGAGTTGGTAGAA
                         || |   ||| | | ||    |    || ||     ||   ||| | |  | || || | | ||    |  ||| | || || |  ||| | || ||  | ||||||    |||  ||  |  | |  ||     |  |||  ||  ||||||||||| |||||| | |||||||| ||||| || |||||||| |||||  ||||||| |||||||||||||| |||||| |||| | ||| ||| |||
-----------------------gtaattgagaaatactatttcaaggtcttgcgttgat-tgagaattatgtc-tctagtctagtcttaagttcatttgaaattttaaaagttcattt-ttacttttatctagaatgtctaggatctaaacagt---aatatggt--atcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAACCATGAAGTGGGAAATATGATTGCCGAAGCAATGAGTAAAGTGGGTCGAA

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|120530535|gb|EH258668.1|EH258668
EST:     AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAG                         GTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT
genomic: AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAGgtgaagcatt ... tggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT
EST: gi|193653960|gb|FK596948.1|FK596948
EST:     AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAG                         GTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT
genomic: AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAGgtgaagcatt ... tggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT
EST: gi|208211632|gb|GE010369.1|GE010369
EST:     AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAG                         GTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT
genomic: AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAGgtgaagcatt ... tggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT
EST: gi|208131083|gb|GD927190.1|GD927190
EST:     AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAG                         GTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT
genomic: AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAGgtgaagcatt ... tggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT
EST: gi|208120233|gb|GD916640.1|GD916640
EST:     AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAG                         GTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT
genomic: AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAGgtgaagcatt ... tggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT
EST: gi|120530550|gb|EH258683.1|EH258683
EST:     AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAG                         GTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT
genomic: AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAGgtgaagcatt ... tggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT
EST: gi|17401201|gb|BM177983.1|BM177983
EST:     AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAG                         GTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT
genomic: AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAGgtgaagcatt ... tggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT
EST: gi|20207910|gb|BQ133999.1|BQ133999
EST:     AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAG                         GTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT
genomic: AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAGgtgaagcatt ... tggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT
EST: gi|15201304|gb|BI424801.1|BI424801
EST:     AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAG                         GTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT
genomic: AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAGgtgaagcatt ... tggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT
EST: gi|192323269|gb|FK015275.1|FK015275
EST:     AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAG                         GTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT
genomic: AGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAGgtgaagcatt ... tggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttcttatctttttgttgagacttgataaggttctggttgggtggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAATTATGAAGTAGGAAATATGATTGCTGAAGCATTGAGCAGAGTTGGTAGAA
                       acttgat  putative branch site (score: 5)
       ttatcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagcatttttctattattgttgaaataccaaacattgttgtgtgtctgtgtgtaagcgtgtttattgtatggtgtactcaaattttcccattttttaatatgtttagtgtttaattatttttcttatctttttgttgagacttgataaggttctggttgggtggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAATTATGAAGTAGGAAATATGATTGCTGAAGCATTGAGCAGAGTTGGTAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG