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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggctccttgtgtgttttaagtgttgcatgactgtagctatgtttctggagtttttttaatttaaattttaatatatatgttcatgctttgttttaaatagGTTCATATGGAGAGGTATACCATGCCGACTGGAATGGCACA

Basic information

species Glycine max
transcript GLYMA20G37330.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g29540.1 (Oryza sativa), 3'ss of exon 4
ggctccttgtgtgttttaagtgttgcatgactgtagctatgtttctggagtttttttaatttaaattttaatatatatgttcatgctttgttttaa---atagGTTCATATGGAGAGGTATACCATGCCGACTGGAATGGCACA
   |     ||||||||  | ||| | |   || |        ||| | |||  | ||  || || | ||  | |  |      | ||  || |||    ||||||| |||||||| |||||||||||||| |||||||| || 
---taagcatgtgtttttggagtttcttttgtgcattaggagctcttgtgttgctatatctttaaatatatgacaattaaaagagtttccttgtaatttgtagGTTCGTATGGAGAAGTATACCATGCCGATTGGAATGGAACT

upper sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G175563_T01 (Zea mays), 3'ss of exon 4
ggctccttgtgtgttttaagtgttgcatgactgtagctatgtttctggagtttttttaatttaaattttaatatata---tgttcat-gctttgtttta---aatagGTTCATATGGAGAGGTATACCATGCCGACTGGAATGGCACA
       | ||  |||||   |||| ||    || |    ||| || ||  ||      |    || |    ||  |   | || || | |||| ||     ||||||||||||||||||||| |||| ||| ||||||||||| || 
-------tatgctttttattagttgaataggagtgggctggttgcttgaacttgcaccttcctgatctctgcatgaaaactattgattgatttgcttcgttcaatagGTTCATATGGAGAGGTTTACCGTGCTGACTGGAATGGAACC

upper sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G038982_T01 (Zea mays), 3'ss of exon 4
----------------------------------------------------------------------------ggctccttgtgtgttttaa-gtgttgcatgactgtagctatgtttctggagtttttt-taatttaaattttaatatatatgtt-catg--ctttgttttaaatagGTTCATATGGAGAGGTATACCATGCCGACTGGAATGGCACA
                                                                               |     ||||||  |  || || || |    ||||| || |      ||||||| | |  | |||   | |   |  ||| ||||  |||   |||  |||||||||||||||||||| |||| ||| ||||||||||| |||
gtacttattttgctaccaagttttgatatacactgtgctgcttttgaactaacaactttgacctgttttggaaactaattttaaatgtgttgaactgtatttcaagttgttagctttgatggacatgttttttattagctgaataggagtgggttggtttcatgaacttgcatttttatagGTTCATATGGAGAGGTTTACCGTGCTGACTGGAATGGAACA

upper sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0030g01440.t01 (Vitis vinifera), 3'ss of exon 4
ggctccttgtgtgttttaagtgttgcatgactgtagctatgtttctggagtttttttaatttaaat--tttaatatatatgttcatgctttgttttaaatagGTTCATATGGAGAGGTATACCATGCCGACTGGAATGGCACA
  ||  ||| |     |   ||| |  |  |  |       || |   |   |  || ||||  ||  |||   ||   | |||||| |||||| | |||||| || ||||||||||| |||||||  || ||||||||||||
-tcttattg-gaagaatggttgtagtgtttcaatctgagcattgcaatatgctcatttatttggatgttttctgattattattcatgttttgttgtcaatagGCTCGTATGGAGAGGTCTACCATGGTGATTGGAATGGCACA

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|6566093|gb|AW233853.1|AW233853
EST:     ATGTGAGATTCCATGGGAGGATCTGGTTCTTGGTGAAAGAATTGGTATAG                         GTTCATATGGAGAGGTATACCATGCCGACTGGAATGGCACA
genomic: ATGTGAGATTCCATGGGAGGATCTGGTTCTTGGTGAAAGAATTGGTATAGgtaatgccgt ... ttttaaatagGTTCATATGGAGAGGTATACCATGCCGACTGGAATGGCACA
EST: gi|9564976|gb|BE474476.1|BE474476
EST:     TCTGGTTCTTGGTGAAAGAATTGGTATAG                         GTTCATATGGAGAGGTATACCATGCCGACTGGAATGGCACA
genomic: TCTGGTTCTTGGTGAAAGAATTGGTATAGgtaatgccgt ... ttttaaatagGTTCATATGGAGAGGTATACCATGCCGACTGGAATGGCACA
EST: gi|33389731|gb|CA852938.1|CA852938
EST:     ATGTGAGATTCCATGGGAGGATCTGGTTCTTGGTGAAAGAATTGGTATAG                         GTTCATATGGAGAGGTATACCATGCCGACTGGAATGGCACA
genomic: ATGTGAGATTCCATGGGAGGATCTGGTTCTTGGTGAAAGAATTGGTATAGgtaatgccgt ... ttttaaatagGTTCATATGGAGAGGTATACCATGCCGACTGGAATGGCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggagtttttttaatttaaattttaatatatatgttcatgctttgttttaaatagGTTCATATGGAGAGGTATACCATGCCGACTGGAATGGCACA
                    ttttaat  putative branch site (score: 3)
                                        ctttgtttt  putative PPT
     tttttttaatttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggctccttgtgtgttttaagtgttgcatgactgtagctatgtttctggagtttttttaatttaaattttaatatatatgttcatgctttgttttaaatagGTTCATATGGAGAGGTATACCATGCCGACTGGAATGGCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG