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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattgaatttgagatgtattaaataaaaccgtattaacatgtcttcctatttatcattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGGTTCAGAAAG

Basic information

species Glycine max
transcript GLYMA03G39290.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 14
gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattgaatttgagatgtattaaataaaaccgtattaacatgtcttcctatttatcattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGGTTCAGAAAG
               ||  | | | |||||  | |||| |    ||     | |||  |||      | ||          ||| |||    | | | | ||| ||||      |  ||  |||| || || ||||| |||||||||||||| |||| | | ||||| |||||||||||||||||| | || ||||| |||||   ||||||  | || 
---------------gtaagcagaggtatt--actttcgtaccgaa-----agttgtctttagttattgttg-------ttgtactaa----tttacttgtttttcata-----tgaagGTTGTTCTCATGTGGAACAAGTAAAGATGGAGATTCATATTTAGTTGAGTGGAATGAAAGTGAAGGATCTATCAAGAGGACATATTCTGGGTTTCGTAAA

upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 15
lower sequence: AT5G27030.2 (Arabidopsis thaliana), 3'ss of exon 13
-----------------------------------------------------------------------gtaagaaggatttgggtgcggataagtat-ttaagtttcatgttcaatggataattgaatttgagatgtattaaataaaaccgtattaacatgtcttcctatttatcattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGGTT-CAGAAAG
                                                                        | |||    ||||  | |     || ||  | ||||   ||| |  | ||   |  ||| | |  | | |    |||       ||  ||   ||| ||  |  |  ||    ||  ||| |||| ||||| ||||| |||||||||||||| || || || ||||| |||||||||||||||||| | ||||| || || || || | ||| |||||| 
gtaagatcttaaactcataaacatttccctcttctataccgcttgttcttcactcctcagtttccaaaatcttcagattcttttgtttactccggaggatactgagtt--gtgtcc--ttgagtttctaatcttatctttctgttttaagtttaccttttcagtgctttctgatgttttttcccccttcagATTGTTCTCTTGTGGAACGAGTAAAGATGGAGATTCTTTCCTAGTTGAGTGGAATGAAAGTGAAGGATCAATTAAAAGGACGTATAAAGAGTTTCAGAAA-

upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 14
-----------------------------------------------------------------gtaagaaggatttgggtgcggataag--tatttaagtttcatgttcaatggataat----tgaatttga---gatgtattaaataaaaccgt----attaacatgt---cttcctatttatcattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGGTTCAGAAAG
                                                                  |   ||   |     |     |||   | ||  ||||   | ||||    ||| |    |   |||||    || |||   | | |||  |    | |||  |||    ||  | ||  || |  | | |  ||| |||| ||||| ||||| ||||||||||| || || ||| | |||||||||||||||||||||||||| || ||||| || || |||||||| ||||||
gtaagattggtgaaattcacaattccagacctaataaaattttattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgctacttttgatcaaatatatctgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG

upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 15
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 14
gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattgaatttgagatgtattaaataaaaccgtattaacatgtcttcctatttatcattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGGTTCAGAAAG
                   |  | | | |   | ||| ||  || ||   |   | |  |  ||| ||||    | ||    |||| |  | ||| ||  ||| || || |     ||| || || ||||||||||| ||||||||||||||||| | ||| || ||||||||||| ||||| || || || ||| | ||||||   || ||| | |||
-------------aatgatgatttactgtcagaatttgatcctccatctttttcttacatgtagaggtatc--gtgaa----tattgatttatctccccttttctctttttgatgttagGCTCTTCTCTTGCGGAACAAGTAAAGATGGAGAGTCTTATCTGGTGGAATGGAATGAGAGTGAGGGTGCAATCAAGCGGACATACTCAGGTTTCCGGAAG

upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 15
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 14
gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattgaatttgagatgtattaaataaaaccgtattaacatgtcttcctatttatcattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGGTTCAGAAAG
           | |  | || || |  | || |||      || |     | || |  |      ||||||    | ||   | ||    | |     | ||  |  |     | |  |||| |||||||| |||||||| ||||||||||| || | ||| || ||||||||||| || ||||| || |||||| | ||||||   || ||| | |||
-----------tcgctttcgaatta--agttgagt---gaatttaggacgtgat-gtgtccatcttgtatttgcgacaatgatttttgattatgaattttttctttgtggacgcca--gACTCTTTTCTTGTGGAACTAGCAAAGATGGAGAATCTTATCTGGTGGAATGGAATGAGAGCGAAGGCGCAATTAAGCGGACATACTCAGGTTTCCGCAAG

upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ37833 (Selaginella moellendorffii), 3'ss of exon 14
gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattgaatttgagatgtattaaataaaaccgtattaacatgtcttcctatttatcattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGGTTCAGAAAG
                                                | |  |    || |    || |  |    ||        ||| |   |          ||   || | ||| || ||||| ||||||||||| || || || || ||||| ||||| || ||||||||||||||||| |  || ||  | || |||| ||| ||| | |||
------------------------------------------------gtttgtctcgttcgtctcgtttctatcgtaa-------gacacgcgctaaacgaggctatgtgttttgtagGCTCTTTTCGTGCGGAACTAGCAAGGAGGGTGACTCATTCCTTGTCGAGTGGAATGAAAGTGAAGGGGTTATCAAACGCACGTACATTGGATTCCGTAAG

upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 14
gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattgaatttgagatgtattaaataaaaccgtattaacatgtcttcctatttatcattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGGTTCAGAAAG
                                                | |  |    ||||    || |  |    ||        ||| |   |          ||   || | ||| || ||||| ||||||||||| || || || || ||||| ||||| || ||||||||||||||||| |  || ||  | || |||| ||| ||| | |||
------------------------------------------------gtttgtctcgtttgtctcgtttctatcgtaa-------gacacgcgctaaacgaggctatgtgttttgtagGCTCTTTTCGTGCGGAACTAGCAAGGAGGGTGACTCATTCCTTGTCGAGTGGAATGAAAGTGAAGGGGTTATCAAACGCACGTACATTGGATTCCGTAAG

upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 14
gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattgaatttgagatgtattaaataaaaccgtattaacatgtcttcctatttatcattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGGTTCAGAAAG
                                                                     ||   |  ||||   ||   || ||   |   |  |  || ||| |  ||| |||||||||| ||||| || || ||||| ||||| |||||||| || ||||||||||||||||| || ||||| |  || |||||||| ||  | || 
--------------------------------------------------------------------gtttgcttcaacct--ttggtatttccatcacatcct--ttgtttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATTAAAAACACCTACAATGGTTTTCGGAAA

upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ17248 (Selaginella moellendorffii), 3'ss of exon 14
gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattgaatttgagatgtattaaataaaaccgtattaacatgtcttcctatttatcattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGGTTCAGAAAG
                                                                     ||   |  ||||   ||   ||   ||||     ||| ||  || |  ||| |||||||||| ||||| || || ||||| ||||| |||||||| || ||||||||||||||||| || || || |  || |||||||| ||  | || 
--------------------------------------------------------------------gtttgcttcaacct--ttggtat---ttccatcacatcctttgttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATAAAAAACACCTACAATGGTTTTCGGAAA

upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ35798 (Selaginella moellendorffii), 3'ss of exon 14
gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattgaatttgagatgtattaaataaaaccgtattaacatgtcttcctatttatcattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGGTTCAGAAAG
                                                | |  |    ||||    || |  |    ||        ||| |   |           |   || | ||| || ||||| ||||||||||| || || || || ||||| ||||| || ||||||||||||||||| || || ||  | || |||| ||| ||| | |||
------------------------------------------------gtttgtctcgtttgtctcgtttctatcgtaa-------gacacgcgctaaacgaggctgtgtgttttgtagGCTCTTTTCGTGCGGAACTAGCAAGGAGGGTGACTCATTCCTTGTCGAGTGGAATGAAAGTGAAGGGGCTATCAAACGCACGTACATTGGATTCCGTAAG

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|9204391|gb|BE330615.1|BE330615
EST:     GCCCCAGGTCATTGGTGTACTACAATGCTTTACAGTGCTGATGGAAGTAG                         ACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCT
genomic: GCCCCAGGTCATTGGTGTACTACAATGCTTTACAGTGCTGATGGAAGTAGgtaagaagga ... atttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtattaaataaaaccgtattaacatgtcttcctatttatcattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGGTTCAGAAAG
                  tattaac  putative branch site (score: 1)
                                           ttatttct  putative PPT
                                  tatttatcattatttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattgaatttgagatgtattaaataaaaccgtattaacatgtcttcctatttatcattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGGTTCAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA