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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtggaagttatgtttcttatataatccatttaaaattcgttttcttttgatttagaagaaacaaaaggggaaggatttggtggttgattgcattacatcgtttgccattatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGGCTATTGGAACGGGCAAAGTGGCCACTCCCCAGCAAGCTCAGGAAGTACA

Basic information

species Glycine max
transcript GLYMA19G36990.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G36990.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g36450.2 (Oryza sativa), 3'ss of exon 6
gtagtggaagttatgtttcttatataatccatttaaaattcgttttctt---ttgatttagaagaaacaaaaggggaaggatttggtggttgattgcattacatcgtttgccattatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGGCTATTGGAACGGGCAAAGTGGCCACTCCCCAGCAAGCTCAGGAAGTACA----
                                | | ||||| |  ||||   || | |||  |       | | |     ||    ||       |  | |  |         ||  || ||||     || | | |||||   |  | || ||||||||||| ||||| |||||||||||||| || ||||| || |||||  |||||||||||||||| ||    
-------------------------------gtgacaattcttcatcttgagttaaattaataatggttgatgagcctacatcatctgaagacaagattcatgtatcaacatgttgctttcagacagTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCATGCT

upper sequence: GLYMA19G36990.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g36450.1 (Oryza sativa), 3'ss of exon 6
gtagtggaagttatgtttcttatataatccatttaaaattcgttttctt---ttgatttagaagaaacaaaaggggaaggatttggtggttgattgcattacatcgtttgccattatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGGCTATTGGAACGGGCAAAGTGGCCACTCCCCAGCAAGCTCAGGAAGTACA
                                | | ||||| |  ||||   || | |||  |       | | |     ||    ||       |  | |  |         ||  || ||||     || | | |||||   |  | || ||||||||||| ||||| |||||||||||||| || ||||| || |||||  |||||||||||||||| ||
-------------------------------gtgacaattcttcatcttgagttaaattaataatggttgatgagcctacatcatctgaagacaagattcatgtatcaacatgttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCA

upper sequence: GLYMA19G36990.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G852968_T02 (Zea mays), 3'ss of exon 6
gtagtggaagttatgtttcttatataatccatttaaaattcgttttcttttgatttagaagaaacaaaaggggaaggatttggtggttgattgcattacatcgtttgccattatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGGCTATTGGAACGGGCAAAGTGGCCACTCCCCAGCAAGCTCAGGAAGTACA
   ||| || || |   |||||   | |   ||||      |  ||||   ||   ||  |  |   |  |     | ||  |  |||||| ||||  |      ||    |  || |||||    || | | ||||| | |  |||| ||||||||||| ||||| |||||||||||||| || ||||| || |||||  ||||||| |||||||| ||
---gtgaaatttcttcatcttagg-attttttttatgg---gcgttctagagaagaagttgggaggcattgatttagcttgaggtgttgat-gcat-gcgcaacatgtatctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAGCAAGCCCAGGAAGTTCA

upper sequence: GLYMA19G36990.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G002807_T01 (Zea mays), 3'ss of exon 6
gtagtggaagttatgtttcttatataatccatttaaaattcgttttcttttgatttagaagaaacaaaaggggaaggatttggt---ggttgattgcat-tacatcgtttgccattatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGGCTATTGGAACGGGCAAAGTGGCCACTCCCCAGCAAGCTCAGGAAGTACA
             ||   |||   | |||  || | ||    |||| ||   |||    ||||       || |  |||||  |    | || |      ||       ||    |   | |||||    || | | |||||   |  |||| |||||||| || ||||| |||||||||||||| || ||||| || |||||  | ||||| |||||||| ||
------------gtgaaactttcttcatc--ttaagaaacttttttattggcattctagagaagtttgtaggcattgatttaatctgaggtgttgatgcatatgcaacatgtatctgcctgcagATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAACAAGCCCAGGAAGTTCA

upper sequence: GLYMA19G36990.2 (Glycine max), 3'ss of exon 6
lower sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 5
gtagtggaagttatgtttcttatataatccatttaaaattcgttttcttttgatttagaagaaacaaaaggggaaggatttggtggttgattgcattacatcgtttgccattatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGGCTATTGGAACGGGCAAAGTGGCCACTCCCCAGCAAGCTCAGGAAGTACA
                        |||  |  ||  | ||  |||  ||    | |        ||||   |   | | |   |   | |  ||| ||  |  ||||    ||||| ||||||| || |||||||||||||| || ||| ||||||| || ||||||||||| |||||||| || ||||| ||  |||| |||||||| || ||||| ||
-----------------------gtaacactcttgtattttctttgattaccctctcctgttcccaaacatgtctgaactcaat---taacagcagtaagttatttg----tattttcagATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGGCAATTGGAACTGGTAAAGTTGCATCTCCTCAGCAAGCACAAGAAGTCCA

upper sequence: GLYMA19G36990.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 6
gtagtggaagttatgtttcttatataatccatttaaaattcgttttcttttgatttagaagaaacaaaaggggaaggatttggtggttgattgcattacatcgtt----tgccattatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGGCTATTGGAACGGGCAAAGTGGCCACTCCCCAGCAAGCTCAGGAAGTACA
     | ||||| | || || || |  ||  | | |      | | || | | |||        |    |   |  ||  | || |    ||   | |||||| |    | | || ||   ||||||| || || || |||||  |  | |||||||||||||| || || |||||||||||||| || ||||||||||| |||| ||| || |||||||||||
-----gcaagttctcttgctgatgttctctttctcatgga-atgtactgtcgttttgtggtcctcttgtgaaaagagaacttgttgactcttttgtaacatcgctcttgttcaatcatgcgcagATGCTGTACCCAGTTGGGATGATGTAGTTATTGCATATGAGCCGGTTTGGGCTATTGGAACTGGTAAAGTGGCCACACCCCTGCAGGCACAGGAAGTACA

upper sequence: GLYMA19G36990.2 (Glycine max), 3'ss of exon 6
lower sequence: EFJ10235 (Selaginella moellendorffii), 3'ss of exon 6
gtagtggaagttatgtttcttatataatccatttaaaattcgttttcttttgatttagaagaaacaaaaggggaaggatttggtggttgattgcattacatcgtttgccattatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGGCTATTGGAACGGGCAAAGTGGCCACTCCCCAGCAAGCTCAGGAAGTACA
                               | | |||     ||||||||| ||     |   |    |  ||||  |||| |      |||||  || |   |  |      ||  ||| ||  || || ||||||||||| | || ||||| || || |||||||||||||| || || |||||||| || || || |||||||| |||||||| ||
------------------------------gtatgaaaacttgtttcttttgttt-----gtttc----gctgaagcttttgtt------ttgca--acgttactctc------ttgtagAGGCGATTTCTGGCTGGGACAACGTGGTCATTGCGTACGAGCCTGTATGGGCTATCGGTACTGGCAAAGTCGCAACACCGCAGCAAGCGCAGGAAGTTCA

upper sequence: GLYMA19G36990.2 (Glycine max), 3'ss of exon 6
lower sequence: EFJ12536 (Selaginella moellendorffii), 3'ss of exon 6
gtagtggaagttatgtttcttatataatccatttaaaattcgttttcttttgatttagaagaaacaaaaggggaaggatttggtggttgattgcattacatcgtttgccattatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGGCTATTGGAACGGGCAAAGTGGCCACTCCCCAGCAAGCTCAGGAAGTACA
                               | | |||     ||||||||| ||     |   |    |  ||||  |||| |      |||||  || |   |  |      ||  ||| ||  || || ||||||||||| | || ||||| || || |||||||||||||| || || |||||||| || || || |||||||| |||||||| ||
------------------------------gtatgaaaacttgtttcttttgttt-----gtttc----gctgaagcttttgtt------ttgca--acgttactctc------ttgtagAGGCGATTTCTGGCTGGGACAACGTGGTCATTGCGTACGAGCCTGTATGGGCTATCGGTACCGGCAAAGTCGCAACACCGCAGCAAGCGCAGGAAGTCCA

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|192294177|gb|FG986266.1|FG986266
EST:     AGCTGGAAAAACTTTTGATGTTTGTTTTCAGCAATTGAAGGCTTATGCAG                         ATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGG
genomic: AGCTGGAAAAACTTTTGATGTTTGTTTTCAGCAATTGAAGGCTTATGCAGgtagtggaag ... ttatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGG
EST: gi|20814775|gb|BQ299253.1|BQ299253
EST:     AGCTGGAAAAACTTTTGATGTTTGTTTTCAGCAATTGAAGGCTTATGCAG                         ATGCAGTTCCTAGCTGGGACAACATTGTGATTGCATATGAACCTGTATGGG
genomic: AGCTGGAAAAACTTTTGATGTTTGTTTTCAGCAATTGAAGGCTTATGCAGgtagtggaag ... ttatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGG
EST: gi|8283483|gb|BE021042.1|BE021042
EST:     AGCTGGAAAAACTTTTGATGTTTGTTTTCAGCAATTGAAGGCTTATGCAG                         ATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGG
genomic: AGCTGGAAAAACTTTTGATGTTTGTTTTCAGCAATTGAAGGCTTATGCAGgtagtggaag ... ttatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGG
EST: gi|12689031|gb|BG155376.1|BG155376
EST:     AGCTGGAAAAACTTTTGATGTTTGTTTTCAGCAATTGAAGGCTTATGCAG                         ATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGG
genomic: AGCTGGAAAAACTTTTGATGTTTGTTTTCAGCAATTGAAGGCTTATGCAGgtagtggaag ... ttatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGG
EST: gi|15204307|gb|BI427075.1|BI427075
EST:     AGCTGGAAAAACTTTTGATGTTTGTTTTCAGCAATTGAAGGCTTATGCAG                         ATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGG
genomic: AGCTGGAAAAACTTTTGATGTTTGTTTTCAGCAATTGAAGGCTTATGCAGgtagtggaag ... ttatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGG
EST: gi|8284792|gb|BE022351.1|BE022351
EST:     AGCTGGAAAAACTTTTGATGTTTGTTTTCAGCAATTGAAGGCTTATGCAG                         ATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGG
genomic: AGCTGGAAAAACTTTTGATGTTTGTTTTCAGCAATTGAAGGCTTATGCAGgtagtggaag ... ttatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGG
EST: gi|192326679|gb|FK018521.1|FK018521
EST:     AGCTGGAAAAACTTTTGATGTTTGTTTTCAGCAATTGAAGGCTTATGCAG                         ATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGG
genomic: AGCTGGAAAAACTTTTGATGTTTGTTTTCAGCAATTGAAGGCTTATGCAGgtagtggaag ... ttatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaggggaaggatttggtggttgattgcattacatcgtttgccattatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGGCTATTGGAACGGGCAAAGTGGCCACTCCCCAGCAAGCTCAGGAAGTACA
                   ggttgat  putative branch site (score: 5)
                                            attatttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtggaagttatgtttcttatataatccatttaaaattcgttttcttttgatttagaagaaacaaaaggggaaggatttggtggttgattgcattacatcgtttgccattatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGGCTATTGGAACGGGCAAAGTGGCCACTCCCCAGCAAGCTCAGGAAGTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA