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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attataatgtttatttgcaaatattattgtcattattatatgttaacattatatgggtcaatcgctaattgaaatattcgtttggtttgtggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG

Basic information

species Glycine max
transcript GLYMA09G14380.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G14380.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g55250.1 (Oryza sativa), 3'ss of exon 4
-----attataatgtttatttgcaaatattattgtcattattatatgttaacattatatgggtcaatcgctaattgaaatattcgtttggtttgtggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG
     ||  | || | |  | ||  |||   |||     |  | |   ||   | | | || ||| |  |  | ||||||     | |||  | | |  |  ||||| ||||||||||| ||||| || |||||||| ||||| ||||||||||| |||||||||||||||
catccatcttcatatct--tagctgatagggttgct-ccagcacaaagtagagtgacacggatcactgtc--actgaaatgacgatgtggaatttcgttttgcagACCGACAAGGCATCGATGCTCGACGAGATCATTGATTATGTGAAGTTCCTCCAGCTCCAAGTCAAG

upper sequence: GLYMA09G14380.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g08500.1 (Oryza sativa), 3'ss of exon 3
attataatgtttatttgcaaatattattgtcattattatatgttaacattat-atgggtcaatcgc--taattgaa-atattcgtttggtttg--tggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG
        |   ||| |     | | |||||||  || | | || ||||  | |||    ||  |   | ||||||   | |  |||| ||||  |    |  ||||| |||||||| || ||||| || ||||||||||| ||||| ||||||||||||||||||||||||
-----tgggcgcattcgtgcccaattttgtcatcgtttt-tcttgacatcttgatgaagaaaatgaagtgattgaatggagttctttgatttgattttgcttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTGCAGCTCCAAGTCAAG

upper sequence: GLYMA09G14380.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g25040.1 (Oryza sativa), 3'ss of exon 4
------------attataatgtttatttgcaaatattattgtcattattatatgttaacattatatgggtcaatcgctaattgaaatattcgtttggtttgtgg--aatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG-------------------------
              | |   |||         | ||||   || |  | |  || | |  | || |    |||  |    |     | |  || |   |||  |   ||| ||||| |||||||| |||||||| || ||||||||||| ||||| |||||||| || ||||||||||||                         
cgacgctcgctttcttttcagttccccatttgagattaacctcttcgtgaattgctcatctcatct----caagtgtgtgtgtgtgtgtgtgtctttcttggagTTGATG-CAGACGGACAAGGCTTCCATGCTGGACGAGATCATCGACTACGTCAAGTTCCTACAACTCCAAGTCAAGGCAAGCACGTACACTAAATTACTAA

upper sequence: GLYMA09G14380.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G316758_T01 (Zea mays), 3'ss of exon 3
attataatgtttatttgcaaa--tattattgtc---attattatatgttaacattatatgggtcaatcgctaattgaaatattcgtttggtttgtggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG
         || ||   || |  |   || |     | || ||    | |   |         | ||||     ||    || ||| |||  | | |  |  ||||| ||||||||||| ||||| |||||||| || || |||||||||||||| |||||||||||||||
----cgtctttgatcgacagagcttccatggcacaaactaataagactcattgtcgctgaaaacgatcgtgccgtgtgtcat-cgtatggaattttgttttgcagACCGACAAGGCATCGATGCTTGATGAGATTATTGACTACGTGAAGTTCCTCCAGCTCCAAGTCAAG

upper sequence: GLYMA09G14380.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G350165_T01 (Zea mays), 3'ss of exon 4
attataatgtttatttgcaaatattattgtcattattatatgttaacattatatgggtcaatcgctaattgaaatattcgtttggt-ttgtggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG
 || |  |  |    | ||     |||  || || |  | | ||  |  |  |         ||   | |||   ||    |   | |  || |    ||||| |||||||| || ||||| || |||||| |||| ||||| |||||||| |||||||||||||||
cttgtcgtaatgtcgtccaccctctatcctccttttcgt-tcttcgcgcttgacttcctcgccgacgactgatccatcatctcaatgtcttgtatctgcagACGGACAAGGCGTCGATGCTGGACGAGATCGTCGACTACGTCAAGTTCCTTCAGCTCCAAGTCAAG

upper sequence: GLYMA09G14380.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G067654_T01 (Zea mays), 3'ss of exon 4
---------------------------attataatgtttatttgcaaatattattgtca-ttattatatgttaacattatatgggtcaatcgctaattgaaatattcgtt-tggtttgtggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG
                            |  |     || | |     |    | ||||   || |   |  |||| |  |  ||  |   | |   ||      ||||  | ||||||||  |  ||||| |||||||| || ||||| || ||||||||||| ||||| | |||| |||||||||||||||||
gtcggcatcccccctctagctagctagctcctttctcttctctctcgctcgcgtcgtcaacaatcaacagacaacactgaaatggcgacgtggtg--tgggtcggtcgtcgttgtttgtggttttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAGGTTCTTGCAGCTCCAAGTCAAG

upper sequence: GLYMA09G14380.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G027563_T02 (Zea mays), 3'ss of exon 3
attataatgtttatttgcaaatattattgtcattattatatgttaacattatatgggtcaatcgctaattgaaatattcgtttggtt---tgtggaatg---acagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG
    |   | ||  |  |  |    | |    |  | |  | || |    || | | ||  |   |  |  | || || | |||| |   || |   ||    ||||| |||||||| || ||||| || ||||||||||| ||||| |||||||| |||||||||      
----ttgcgcttgctcactcac-cgagtacagtactgaactattgat-ccatcttgctctgtgttttctcaatatcttggattggatgcctgcgccgtgcatgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTACAGCTCCAA------

upper sequence: GLYMA09G14380.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G24260.1 (Arabidopsis thaliana), 3'ss of exon 3
---attataatgtttatttgcaaatattattgtcattattatatgttaacattatatgggtcaatcgctaattgaaatattcgtttggtttgtggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG
     || |||  | |  |  || || |   || || |  ||  ||||  ||   |    | |     |  ||    ||||   || || |    |  ||||||||||||||||||| ||||| ||||||||||| ||||| || |||||  | || ||||||||||||
taggctacaataataaagt-taactaatgcagtaataa--atgagttaggatctcagttctgacagttttgtttttgtattttatttgtataataatggacagACAGACAAGGCATCGATGCTCGATGAGATCATAGATTATGTCAAGTTTTTACAACTCCAAGTCAAG

upper sequence: GLYMA09G14380.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G30980.1 (Arabidopsis thaliana), 3'ss of exon 3
attataatgtttatttgcaaatattattgtcattattatatgttaacattatatgggtcaatcgctaattgaaatattcgtttggtt-----tgtggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG
  ||     || |||   |||| | ||||  | || ||  |  |||    ||   |   ||| |||||      | ||  | | |||     |    | | |||||||||||| ||||| ||||| |||||||| |||||||| || |||||| | |||||||||||||||
--tagctaattaattctaaaatttaattgataataatacttaataaacagatgcag---aattgctaacaaggttttttttattgttaaaaataataattaacagACAGACAAAGCATCAATGCTCGATGAGATTATCGATTATGTCAAGTTCTTACAGCTCCAAGTCAAG

upper sequence: GLYMA09G14380.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0037g00040.t01 (Vitis vinifera), 3'ss of exon 4
---attataatgtttatttgcaaatattat-tgtcattattatatgttaacattatatgggtcaatcgctaattga-aatattcgtttggtttgtggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG
     | |   |       || | |  |   |  |   |  |  | ||    || ||    | |||    ||| || ||| || | | ||   |||||||||||||| |||||||| || ||||| ||||||||||| || || || || ||||||||||||||||| |||
cccggtctcgagcagtgcggcgagtcatgcgtagcgaaaccacctattttatttttac--tttaatacgaaatcgataatgttgggtggg---gtggaatgacagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG

upper sequence: GLYMA09G14380.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S173_83V6.1 (Physcomitrella patens), 3'ss of exon 3
--attataatgt-ttatttgcaaatattattgtcattattatatgttaacattatatgggtcaatcgctaattgaaatattcgtttggtttgtggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG
  |   |  ||| || ||| ||  || | ||  | |     ||| |||| ||   ||  |  ||    | ||  ||   |     || | | ||     |||||| || ||||| || ||||| ||||| |||||||||||||| ||||||||||| |||||||| |||
gaaacttcgtgtatttttttcatctact-ttcacttgggcttattttaaaatctaattag--aagaaatgatccaatcctcttactgctgtctgtggatacagACGGATAAGGCGTCGATGCTGGATGAAATCATCGATTACGTCAAGTTCCTGCAACTCCAAGTAAAG

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|4396207|gb|AI495204.1|AI495204
EST:     TCGCAGAGAGAATGAAGGCCCTACAGGAACTGGTTCCCAATGCCAACAAG                         ACAGACAAGGCATCCATGCTAGAT-AGATCAT
genomic: TCGCAGAGAGAATGAAGGCCCTACAGGAACTGGTTCCCAATGCCAACAAGgtaaatgccc ... ggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCAT
EST: gi|14990392|gb|BI316065.1|BI316065
EST:     TCGCAGAGAGAATGAAGGCCCTACAGGAACTGGTTCCCAATGCCAACAAG                         ACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTG
genomic: TCGCAGAGAGAATGAAGGCCCTACAGGAACTGGTTCCCAATGCCAACAAGgtaaatgccc ... ggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattatatgggtcaatcgctaattgaaatattcgtttggtttgtggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG
                    taattgaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attataatgtttatttgcaaatattattgtcattattatatgttaacattatatgggtcaatcgctaattgaaatattcgtttggtttgtggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - -tttgcaa