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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacttatgctaagctatgccagtatttgcttggaatcacagatgtcatgtggacataaaatcttgtttattatttggttagGTGATGATCTTAAGTCATGACCGAGAGAGAGGACGAGTAAGTCTTTCCACAAAGAAGTTGGAACCCACGCCTGGTGACATGATTCGCAATCCAAAGCTTG

Basic information

species Glycine max
transcript GLYMA15G14550.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G14550.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 4
-------gtaaacttatgctaagctatgccagtatttgcttggaatcacagatgtcatgtggacataaaatcttgtttattatttggttagGTGATGATCTTAAGTCATGACCGAGAGAGAGGACGAGTAAGTCTTTCCACAAAGAAGTTGGAACCCACGCCTGGTGACATGATTCGCAATCCAAAGCTTG
        |  | |  | ||     |    | || |  ||     | | |||  | |   || || |  || || ||||  ||    |||||| |||||  |||| |||||||| || ||||| || || |||||||| || || ||| | || || || |||||||||||||||||||||||||||||||
gtattttttgcattcgtacttgagaaaagta-tactatctaaagtttatagagctaa---ggccagagtattttttttaa-atgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACTAAAAAGCTTGAGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTG

upper sequence: GLYMA15G14550.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G862107_T01 (Zea mays), 3'ss of exon 4
gtaaacttatgctaagctatgccagtatttgcttggaatcacagatgtcatgtggacataa--aatcttgtttattatttggttagGTGATGATCTTAAGTCATGACCGAGAGAGAGGACGAGTAAGTCTTTCCACAAAGAAGTTGGAACCCACGCCTGGTGACATGATTCGCAATCCAAAGCTTG
    | |   |||  | | |    ||  ||       ||| || |  | |||  |  |  |  |||    | | ||  ||   ||||| |||||  | || |||||||| || ||||| ||||| || ||||| || |||||| | || || || |||||||||||||| |||||||| |||||||
--gtattgtggctgtggt-tcttggttgttatgccatatc-catacttaatggagctaacaccaatgaattctgttgctta--tagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACTAAGAAGCTTGAGCCAACACCTGGTGACATGATCCGCAATCCCAAGCTTG

upper sequence: GLYMA15G14550.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G30510.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaaacttatgctaagctatgccagtatttgcttggaatcacagatgtcatgtggacataaaatcttgtttattatttggttagGTGATGATCTTAAGTCATGACCGAGAGAGAGGACGAGTAAGTCTTTCCACAAAGAAGTTGGAACCCACGCCTGGTGACATGATTCGCAATCCAAAGCTTG
                 ||| |   ||   | ||  |||  ||||||| |     |||  |   | |   | ||| | |   |||| ||||| || ||||| ||||| || |||||| |||||||||| |||||||||||| |||| || || |||||||| |||||||| || ||||| ||||
----------------gtatactcttaaacgttt--aatttcagatgtta---aaacaacagtccctaacttttaat-gtacagGTTATGATATTGAGTCACGACCGTGACAGAGGAAGAGTAAGTCTCTCCACAAAGAAGCTGGAGCCAACACCTGGTGATATGATTCGTAACCCAAAACTTG

upper sequence: GLYMA15G14550.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0077g00450.t01 (Vitis vinifera), 3'ss of exon 4
--------gtaaacttatgctaa-gctatgccagtatttgcttggaatc--acagatgt-catgtggacata---aaatcttgtttattatttggt-tagGTGATGATCTTAAGTCATGACCGAGAGAGAGGACGAGTAAGTCTTTCCACAAAGAAGTTGGAACCCACGCCTGGTGACATGATTCGCAATCCAAAGCTTG
         |||  |  ||  ||  || |  |   ||||  |      |  ||||||    |  || |  ||   |  | |||| | |   ||| | ||||| |||||| | || || ||||| |||||||| || |||||||| || || |||||||| ||||| || ||||| |||||||||||||||||||||||||
gtttgcctataatatactgtcaatactgtcaccaaatttcttccactccctacagataaataaatgtatgtatttattttttgtgtttctcttgctgtagGTTATGATCCTGAGCCACGACCGTGAGAGAGGCCGTGTAAGTCTCTCAACTAAGAAGTTAGAACCTACCCCTGGAGACATGATTCGCAATCCAAAGCTTG

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|18038939|gb|BM307233.1|BM307233
EST:     ACCGTATAACTGATATTGAAACTGTTCTTCAACCTGGTGATATTCTGAAG                         GTGATGATCTTAAGTCATGACCGAGAGAGAGGAAGGGTAAGTCTTTCCACA
genomic: ACCGTATAACTGATATTGAAACTGTTCTTCAACCTGGTGATGTTCTGAAGgtaaacttat ... atttggttagGTGATGATCTTAAGTCATGACCGAGAGAGAGGACGAGTAAGTCTTTCCACA
EST: gi|18038907|gb|BM307201.1|BM307201
EST:     ACCGTATAACTGATATTGAAACTGTTCTTCAACCTGGTGATATTCTGAAG                         GTGATGATCTTAAGTCATGACCGAGAGAGAGGAAGGGTAAGTCTTTCCACA
genomic: ACCGTATAACTGATATTGAAACTGTTCTTCAACCTGGTGATGTTCTGAAGgtaaacttat ... atttggttagGTGATGATCTTAAGTCATGACCGAGAGAGAGGACGAGTAAGTCTTTCCACA
EST: gi|18732823|gb|BM527270.1|BM527270
EST:     ACCGTATAACTGATATTGAAACTGTTCTTCAACCTGGTGATATTCTGAAG                         GTGATGATCTTAAGTCATGACCGAGAGAGAGGAAGGGTAAGTCTTTCCACA
genomic: ACCGTATAACTGATATTGAAACTGTTCTTCAACCTGGTGATGTTCTGAAGgtaaacttat ... atttggttagGTGATGATCTTAAGTCATGACCGAGAGAGAGGACGAGTAAGTCTTTCCACA
EST: gi|7234320|gb|AW569659.1|AW569659
EST:     ACCGTATAACTGATATTGAAACTGTTCTTCAACCTGGTGATGTTCTGAAG                         GTGATGATCTTAAGTCATGACCGAGAGAGAGGACGAGTAAGTCTTTCCACA
genomic: ACCGTATAACTGATATTGAAACTGTTCTTCAACCTGGTGATGTTCTGAAGgtaaacttat ... atttggttagGTGATGATCTTAAGTCATGACCGAGAGAGAGGACGAGTAAGTCTTTCCACA
EST: gi|26269049|gb|CA820112.1|CA820112
EST:     ACCGTATAACTGATATTGAAACTGTTCTTCAACCTGGTGATATTCTGAAG                         GTGATGATCTTAAGTCATGACCGAGAGAGAGGAAGGGTAAGTCTTTCCACA
genomic: ACCGTATAACTGATATTGAAACTGTTCTTCAACCTGGTGATGTTCTGAAGgtaaacttat ... atttggttagGTGATGATCTTAAGTCATGACCGAGAGAGAGGACGAGTAAGTCTTTCCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttggaatcacagatgtcatgtggacataaaatcttgtttattatttggttagGTGATGATCTTAAGTCATGACCGAGAGAGAGGACGAGTAAGTCTTTCCACAAAGAAGTTGGAACCCACGCCTGGTGACATGATTCGCAATCCAAAGCTTG
                          acataaaatcttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacttatgctaagctatgccagtatttgcttggaatcacagatgtcatgtggacataaaatcttgtttattatttggttagGTGATGATCTTAAGTCATGACCGAGAGAGAGGACGAGTAAGTCTTTCCACAAAGAAGTTGGAACCCACGCCTGGTGACATGATTCGCAATCCAAAGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT