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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggttatcttgaatcttatataccaaaaagattcatgcttttgtgttgtgatatatttttattttttgatacatttgccttttcttatgtatctatatgaagcttcattacatagaacatacatatgccataattttgttgattattttgataatttttatatatgtccagTCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCACCGATAGAAAAGAGAAGACACCTGCAAAGGCTGAAACAACAGCATTGCA

Basic information

species Glycine max
transcript GLYMA11G36000.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g07570.1 (Oryza sativa), 3'ss of exon 6
gtacggtt----atcttgaatcttatataccaaaaagattcatgcttttgtgttgtgatatatttttattttttgatacatttgccttttcttatgtatctatatgaagcttcattacatagaacatacatatgccataattttgttgattattttgataatttttatatatgtccagTCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCACCGATAGAAAAGAGAAGACACCTGCAAAGGCTGAAACAACAGCATTGCA
|||   |     |||||   |  ||| |    || |   ||     |||   || || |  |||     || ||| |  | |||    | | | |  ||||   | |   ||  | ||  | |  ||  ||     || | | |||  | |    | ||    | | | | |   |||||||||||||||| ||||| || || || ||| | ||| | ||  |||| |||||||| || |||||||||||||| ||||| || || |    ||||  
gtaaaatctacaatctttggttatatttgtataacaacatcgccagtttacattctgcttgattcaacattgttgctttagttgatgatgccttt-catctgagtaacattt--tcactca-actatttattattgattaatctgtctaatcccatcatttggtctttctgttgtcagTCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTACCGATAGGAAGGAGAAGACACCTGCCAAGGCCGAGACCAATTTATTGTT

upper sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 6
lower sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 6
gtacggttatcttgaatcttatataccaaaaagattcatgcttttgtgttgtgatatatttttattttttgatacatttgccttttcttatgtatctatatgaagcttcattacatagaacatacatatgccataattttgttgattattttgataatttttatatatgtccagTCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCACCGATAGAAAAGAGAAGACACCTGCAAAGGCTGAAACAACAGCATTGCA
                                                                                              |   ||  || |    ||| |||       ||| | |  |  ||||  | |  |   ||      | | | |   | ||||||||||||| || ||||||||||| |||||||| ||||| ||  |||| |  ||  | ||||| |||||||| || |||||||||||| | |  |||  
---------------------------------------------------------------------------------------------gtaagtaccaaacaaacttatataatcagatcatttactctgtttttacttacaaccgtg------tctgtttggtttcagTCATTGGAGACGTGAGAGGAAGAGGGTTAATGGTTGGGATTGAGCTTGTGAGTGACCGGAAAGACAAGACACCAGCCAAGGCTGAAACATCTGTCTTGTT

upper sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 6
gtacggttatcttgaatcttatataccaaaaagattcatgcttttgtgttgtgatatatttttattttttgatacatttgccttttcttatgtatctatatgaagcttcattacatagaacatacatatgccataattttgttgattattttgataatttttatatatgtccagTCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCACCGATAGAAAAGAGAAGACACCTGCAAAGGCTGAAACAACAGCATTGCA
                                                         | ||  |   ||||||   | ||| | ||| | | |  ||  ||  ||| | ||      |  ||  ||| |  |||  | || ||   ||| |   |||   || | | |   |||| || ||||| ||||||||||| ||  ||||||||||| | ||| |||| || || |||||||||||||| ||||| || || |||||  |||  |||  
--------------------------------------------------------aagttcaaacctttgat---tctgcttcttcctttct--ctgaattgagcattat------ggccagtcat-tttcatggtgttctta--tatct-attaaaccttgtttct---cagTTATCGGAGACGTAAGAGGAAGGGGTCTAATGGTGGGGGTGGAACTTGTGACTGACAGAAAAGAGAAGACCCCTGCCAAAGCAGAAACTGCAGTTTTGTT

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|9820018|gb|BE555531.1|BE555531
EST:     TGGTTCTCACTTGATTCAGCGTTTAAGATCCCTGATGCAAATACATGACA                         TCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATNTGTCA
genomic: TGGTTCTCACTTGATTCAGCGTTTAAGATCCCTGATGCAAATACATGACAgtacggttat ... atatgtccagTCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCA
EST: gi|16341987|gb|BI967582.1|BI967582
EST:     TGGTTCTCACTTGATTCAGCGTTTAAGATCCCTGATGCAAATACATGACA                         TCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCA
genomic: TGGTTCTCACTTGATTCAGCGTTTAAGATCCCTGATGCAAATACATGACAgtacggttat ... atatgtccagTCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCA
EST: gi|193352675|gb|FK315965.1|FK315965
EST:     TGGTTCTCACTTGATTCAGCGTTTAAGATCCCTGATGCAAATACATGACA                         TCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCA
genomic: TGGTTCTCACTTGATTCAGCGTTTAAGATCCCTGATGCAAATACATGACAgtacggttat ... atatgtccagTCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCA
EST: gi|6726423|gb|AW310777.1|AW310777
EST:     TGGTTCTCACTTGATTCAGCGTNTAAGATCCCTGATGCAAATACATGACA                         TCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCA
genomic: TGGTTCTCACTTGATTCAGCGTTTAAGATCCCTGATGCAAATACATGACAgtacggttat ... atatgtccagTCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatacatatgccataattttgttgattattttgataatttttatatatgtccagTCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCACCGATAGAAAAGAGAAGACACCTGCAAAGGCTGAAACAACAGCATTGCA
                             ttttgat  putative branch site (score: 4)
             ataattttgttgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggttatcttgaatcttatataccaaaaagattcatgcttttgtgttgtgatatatttttattttttgatacatttgccttttcttatgtatctatatgaagcttcattacatagaacatacatatgccataattttgttgattattttgataatttttatatatgtccagTCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCACCGATAGAAAAGAGAAGACACCTGCAAAGGCTGAAACAACAGCATTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG