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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctttcccactagtccacacaattttgtttctcctaatgaatccaatattttctttaactttctaatgagtattgtgaattccagATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGATGGTTCATCATTTACTGGTGATGTGGAAGCAGTGAATCCA

Basic information

species Glycine max
transcript GLYMA09G35050.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G35050.4 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g47400.2 (Oryza sativa), 3'ss of exon 4
---gtctttcccactagt-ccacacaattttgtttctcctaatgaatccaatattttctttaactttct--aatgagtattgtgaattc--------cagATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGATGGTTCATCATTTACTGGTGATGTGGAAGCAGTGAATCCA
    |   |      | | | | | | | || |       || | |   | || | |  || || | ||  |  || |  |||| | ||        ||||||||||||| |||||||   |||||||| |||| |||||||| ||||| || || || |||||||||  |||  |||| 
tatatgaatgtggacaatgctagaaagtcttataatatgaaacggagggagtagtatagttcacatgcttgatcgattcctgtgcaatcatcaaaaccagATTTCTACAATTGGAACAAGGTCAAGGTTCGGTACTGTGATGGGTCATCTTTCACCGGCGATGTGGAAAAAGTAGATCCT

upper sequence: GLYMA09G35050.4 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0087g00400.t01 (Vitis vinifera), 3'ss of exon 4
------gtctttcccactagtccacacaattttgtttctcctaatg-aatccaatattttctttaactttctaatgagtattgtgaattccagATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGATGGTTCATCATTTACTGGTGATGTGGAAGCAGTGAATCCA
       ||     | | | |   || |  | |  |  |  | ||| ||||    |  ||||   |   ||||||    |||   |  |||||| ||||||||||||||||  |||||||||||||| || |||||  | || ||||| || ||||| ||||||||  |||| 
gtaccactcaaaatcgccaattggcatagctct--tcttgttgatgtaatctttgagattctcccaagctctaatctccattccaacatccagACTTCTACAACTGGAACAAGATCAAGGTTAGGTACTGCGATGGGGCCTCCTTTACGGGCGATGTAGAAGCAGTTGATCCT
















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|213597073|gb|DB968168.1|DB968168
EST:     GCTAATTGCCTTTTCAGGAATTTTGAATAACAGGGAAATGTTTAATCCAG                         ATTTCTACAACTGGTACAGAATCAAGGTTAGGTATTGTGACGGGTCATCAT
genomic: GCTAATTGCCTTTTCAGGAATTTTGAATAACAGGGAAATGTTTAATCCAGgtctttccca ... tgaattccagATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGATGGTTCATCAT
EST: gi|18733683|gb|BM527753.1|BM527753
EST:     GCTAATTGCCTTTTCAGGAATTTTGAATAACAGGGAAATGTTTAATCCAG                         ATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGATGGTTCATCAT
genomic: GCTAATTGCCTTTTCAGGAATTTTGAATAACAGGGAAATGTTTAATCCAGgtctttccca ... tgaattccagATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGATGGTTCATCAT
EST: gi|21888360|gb|BQ741573.1|BQ741573
EST:     GCTAATTGCCTTTTCAGGAATTTTGAATAACAGGGAAATGTTTAATCCAG                         ATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGATGGTTCATCAT
genomic: GCTAATTGCCTTTTCAGGAATTTTGAATAACAGGGAAATGTTTAATCCAGgtctttccca ... tgaattccagATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGATGGTTCATCAT
EST: gi|9986444|gb|BE660552.1|BE660552
EST:     GCTAATTGCCTTTTCAGGAATTTTGAATAACAGGGAAATGTTTAATCCAG                         ATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGACGGTTCATCAT
genomic: GCTAATTGCCTTTTCAGGAATTTTGAATAACAGGGAAATGTTTAATCCAGgtctttccca ... tgaattccagATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGATGGTTCATCAT
EST: gi|9898765|gb|BE607733.1|BE607733
EST:     GCTAATTGCCTTTTCAGGAATTTTGAATAACAGGGAAATGTTTAATCCAG                         ATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGATGGTTCATCAT
genomic: GCTAATTGCCTTTTCAGGAATTTTGAATAACAGGGAAATGTTTAATCCAGgtctttccca ... tgaattccagATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGATGGTTCATCAT
EST: gi|37995321|gb|CF806910.1|CF806910
EST:     GTTTAATCCAG                         ATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGACGGTTCATCAT
genomic: GTTTAATCCAGgtctttccca ... tgaattccagATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGATGGTTCATCAT
EST: gi|9820186|gb|BE555696.1|BE555696
EST:     GCTAATTGCCTTTTCAGGAATTTTGAATAACAGGGAAATGTTTAATCCAG                         ATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGATGGTTCATCAT
genomic: GCTAATTGCCTTTTCAGGAATTTTGAATAACAGGGAAATGTTTAATCCAGgtctttccca ... tgaattccagATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGATGGTTCATCAT
EST: gi|15287443|gb|BI471334.1|BI471334
EST:     GCTAATTGCCTTTTCAGGAATTTTGAATAACAGGGAAATGTTTAATCCAG                         ATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGACGGTTCATCAT
genomic: GCTAATTGCCTTTTCAGGAATTTTGAATAACAGGGAAATGTTTAATCCAGgtctttccca ... tgaattccagATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGATGGTTCATCAT
EST: gi|15664114|gb|BI701485.1|BI701485
EST:     GCTAATTGCCTTTTCAGGAATTTTGAATAACAGGGAAATGTTTAATCCAG                         ATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGACGGTTCATCAT
genomic: GCTAATTGCCTTTTCAGGAATTTTGAATAACAGGGAAATGTTTAATCCAGgtctttccca ... tgaattccagATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGATGGTTCATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcctaatgaatccaatattttctttaactttctaatgagtattgtgaattccagATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGATGGTTCATCATTTACTGGTGATGTGGAAGCAGTGAATCCA
                              ttctaat  putative branch site (score: 2)
              aatattttctttaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctttcccactagtccacacaattttgtttctcctaatgaatccaatattttctttaactttctaatgagtattgtgaattccagATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGATGGTTCATCATTTACTGGTGATGTGGAAGCAGTGAATCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG