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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttagctaagcctagatttattgtttgatggaagttttgatttattcatctagttctcgtcataacaaacttaaattattgaattttgttgtatttatagAAGTAGCAGTGAAATGTCAACAAGGGACATACAAAAGATGGTTCAAGCACTTCCACAGTACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG

Basic information

species Glycine max
transcript GLYMA11G03230.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G03230.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os04g18030.3 (Oryza sativa), 3'ss of exon 14
-ttta-gctaagcctagatttattgtttgatggaagttttgatt-tattcatctagttctcgtcataaca-aacttaaattattgaattttgttgtatttat-agAAGTAGCAGTGAAATGTCAACAAGGGACATACAAAAGATGGTTCAAGCACTTCCACAGTACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
 || | | ||  |  |||||| || | || || |    ||  || | || ||    | ||  || |     ||  |||||  |||     |||| ||||| | |||| | |  | ||  | ||||| |  ||  | ||||| ||||||||||| ||||| ||||||||||| ||||||||||||||  | || ||||| |||
gttaatggtattcaaagatttgttttatgttgaattaattatttctgttgataggatccttttctttttgtaatgtaaatgcttg-----tgttatatttgtcagAAATGGTGGAGATTTATCAACCAAAGAGTTGCAAAAAATGGTTCAAGCTCTTCCGCAGTACAGTGATCAAATTGACAAGCTTGCGCTTCATGTTGAG

upper sequence: GLYMA11G03230.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os02g25580.2 (Oryza sativa), 3'ss of exon 8
-tttagctaagcctagatttattgtttgatggaagttttgatttattcatctagttctcgtcataacaaactta-aattattgaattttgttgtatttat-agAAGTAGCAGTGAAATGTCAACAAGGGACATACAAAAGATGGTTCAAGCACTTCCACAGTACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
 ||||  |   | |  || |   |||  |||     |    ||| ||  |   ||||| | | ||  |   | |   | ||||  |  ||||  | |||  |||| | |  | || || || |  || ||  | ||||| ||||||||||| |||||||||||||| || |||||||| ||||| || || ||||| |||
atttatttggacatgtatgttgagttgcatgag---tccattttgtttgtaatgttcttgacttattattttaatggtcattgcttcatgtttaaattaccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCTTCCACAGTACAGCGATCAAATTGAGAAGCTTTCTCTTCATGTTGAG

upper sequence: GLYMA11G03230.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 12
tttagctaagcctagatttattgtttgatggaagttttgatttattcatctagttctcgtcataacaaacttaaattattgaattttgttgtatttat---agAAGTAGCAGTGAAATGTCAACAAGGGACATACAAAAGATGGTTCAAGCACTTCCACAGTACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
  |  ||   || |     ||| | | |   | ||| | |  |  |  | |   | | |   |   ||     | | |||| ||||   | | |||     ||||      | ||| | || ||||| ||  ||||||| |||||||| || ||||||||||||||||| |||||||| ||||| ||||| ||||| |||
actgactt--ccaaacacgattttgttagctatgttcttaacttcttgtttcaatgttgatttg-taattaggattgattgcatttccctttcttttcatcagAACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCTTCCACAGTACAGTGATCAAATTGATAAGCTTTCCCTGCATGTTGAG

upper sequence: GLYMA11G03230.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G012942_T01 (Zea mays), 3'ss of exon 12
tttagctaagcctagatttattgtttgatggaagttttgatttattcat--ctagttc--tcgtcataacaaac-ttaaattattgaattttgttgtatttatagAAGTAGCAGTGAAATGTCAACAAGGGACATACAAAAGATGGTTCAAGCACTTCCACAGTACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
         ||| ||   |  |||| | |  |||| ||   |  || ||  ||   ||  | |   |    ||| || | | || | || |  ||  | |   |||  | |  | ||  | || || | | |  | || || ||||||||||| |||||||| |||||||| ||||||||||||||| |||| ||||| |||
----aaagggccaagcaatgctgttagcta-aagtattagctgcttgatagctgtgtcaatggatctggttaacatttattcataggatctattttgagtgtcagATCTGGTGGAGAGTTATCTACCAAGCAGTTGCAGAAAATGGTTCAAGCTCTTCCACAATACAGTGATCAAATTGACAAGCTCACCCTTCATGTTGAG

upper sequence: GLYMA11G03230.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 12
tttagctaagcctagatttat-tgtttgatggaagtt--ttgatttattcatctagttctcgtcataacaaacttaaattattgaattttgttgtatttatagAAGTAGCAGTGAAATGTCAACAAGGGACATACAAAAGATGGTTCAAGCACTTCCACAGTACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
 |||  | |  |||  || || | | || |  |  ||  ||| ||     |    ||  ||          |   |  || ||  | | | ||   ||  ||||  | |   |||  | || ||||| ||  | || ||||||||||||||| | |||||||||||||||||||||||||||||||| ||||| ||||||
cttacattactctacgttgatctatgtggtatactttatttggttagagaagtaggtcttctctccttttgatcaattttgtttgactctttt---ttcttagAGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAG

upper sequence: GLYMA11G03230.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 12
------tttagctaagcctagat----ttattgtttgatggaagttttgatttattcatctagttctcgtcataacaaacttaaattattgaattttgttgtatttatagAAGTAGCAGTGAAATGTCAACAAGGGACATACAAAAGATGGTTCAAGCACTTCCACAGTACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
       || |  |   || | |    ||  |  ||||||  ||| |  ||| |  |   || | |  |   |   || ||  || |||| |  | |||| | |    ||| || |  ||||| |||| ||||||||| | |||||||||||||||||  | ||||| || ||||| |||||||| ||||| ||||||||||| |||
atgtatctttgtgatatctggttaatctttctacttgatgccagtgt--attcagaccagtaatccaggatgtgttaacct--aaatattta--tctgttatgt----agAGGTGGTGGTGAATTGTCTACAAGGGACTTGCAAAAGATGGTTCAAGCTTTGCCACAATATAGTGAGCAAATTGAGAAGCTTTCCCTCCATGTTGAG

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|21602829|gb|BQ613160.1|BQ613160
EST:     ACCAACTTCATTTCGAAGAACAAAGCTGCACAAATACAACATGGTTCAAA                         AAGTAGCAGTGAAATGTCAACAAGGGACATACAAAAGATGGTTCAAGCACT
genomic: ACCAACTTCATTTCGAAGAACAAAGCTGCACAAATACAACATGGTTCAAAgtgagtgata ... gtatttatagAAGTAGCAGTGAAATGTCAACAAGGGACATACAAAAGATGGTTCAAGCACT
EST: gi|254335298|gb|GR846795.1|GR846795
EST:     ACCAACTTCATTTCGAAGAACAAAGCTGCACAAATACAACATGGTTCAAA                         AAGTAGCAGTGAAATGTCAACAAGGGACATACAAAAGATGGTTCAAGCACT
genomic: ACCAACTTCATTTCGAAGAACAAAGCTGCACAAATACAACATGGTTCAAAgtgagtgata ... gtatttatagAAGTAGCAGTGAAATGTCAACAAGGGACATACAAAAGATGGTTCAAGCACT
EST: gi|20497874|gb|BQ272804.1|BQ272804
EST:     ACCAACTTCATTTCGAAAAACAAAGCTGCACAAATACAACATGGTTCAAA                         AAGTAGCAGTGAAATGTCAACAAGGGACATACAAAAGATGGTTCAA
genomic: ACCAACTTCATTTCGAAGAACAAAGCTGCACAAATACAACATGGTTCAAAgtgagtgata ... gtatttatagAAGTAGCAGTGAAATGTCAACAAGGGACATACAAAAGATGGTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatctagttctcgtcataacaaacttaaattattgaattttgttgtatttatagAAGTAGCAGTGAAATGTCAACAAGGGACATACAAAAGATGGTTCAAGCACTTCCACAGTACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
              tcataac  putative branch site (score: 2)
                ataacaaacttaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttagctaagcctagatttattgtttgatggaagttttgatttattcatctagttctcgtcataacaaacttaaattattgaattttgttgtatttatagAAGTAGCAGTGAAATGTCAACAAGGGACATACAAAAGATGGTTCAAGCACTTCCACAGTACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - -ctaagcc
- - - - - - - - - - ttgtttg