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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatggaaattttttaaaaaaaatggggttagtcttctttagggagagaatggggaacttgaattctgatattggtttggtttggtttttggctttgcagGTGGGGGATGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATGGATACTCCAAGAAGCGTGTTTAAAATAGATGCAAACACACCTGGTTCAG

Basic information

species Glycine max
transcript GLYMA02G01990.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G01990.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G02800.1 (Arabidopsis thaliana), 3'ss of exon 2
ttatggaaattttttaaaaaaaatggggttagtcttctttagggagagaatggggaacttgaattctgatattggtttggtttggtttttggctttgcagGTGGGGGATGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATGGATACTCCAAGAAGCGTGTTTAAAATAGATGCAAACACACCTGGTTCAG
         |||||||            ||  ||| ||  |   | | ||    ||  |||       | | ||||||      |||   |  ||   |||| || ||| |||| | ||||||||||||||||||||||||||| |||||||| || |||||||| ||||||||| | ||    ||||  |||||||| |
--------gttttttactttgctctaaattc-tctcctcgaaaaaaaaaaacaagactttgggaaac-agagtggtttaac---gttagcgtgttcatagGTTGGTGATCCTAACATGGACCATGCTTGTTGGGAGAGACCAGAAGACATGGACACACCAAGAAGTGTGTTTAAAGTCGACAAGAACAATCCTGGTTCTG

upper sequence: GLYMA02G01990.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 2
------------ttatggaaattttttaaaaaaaatggggttagtcttctttagggagagaatggggaacttgaattctgatattggtttggtttggtttttggctttgcagGTGGGGGATGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATGGATACTCCAAGAAGCGTGTTTAAAATAGATGCAAACACACCTGGTTCAG
             |   ||  | |  |     |  |  |   |||   ||  |       |  |  |||  || |          |||||     || ||||   | |||||||||| |||||||| ||||| || ||||||||||||||||||||||||||||| ||| |||| || || || ||  ||||   |||||| ||||||||||
gttttgtgttttcttcagatctctgcttctctatttcagagcagttacctacatttgattagagtcgaaaatgcagaggagctgaggttttaacggggtttt---tctgcagGTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATGGACACTTCAAGGAGTGTTTTCAAGGTAGACAGAAACACCCCTGGTTCAG
















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|208044871|gb|GD843661.1|GD843661
EST:     CTGATTATCTTCTCAAAGCCACTGCACGTCCAAACACCATTTATGTTCAG                         GTGGGGGATGCTAAGAAGGACCATGCTTGTTGAGAGAGACCAGAGGACATG
genomic: CTGATTATCTTCTCAAAGCCACTGCACATCCAAACACCATTTATGTTCAGgtcagttaag ... ggctttgcagGTGGGGGATGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATG
EST: gi|192298776|gb|FG988627.1|FG988627
EST:     CTGATTATCTTCTCAAAGCCACTGCACATCCAAACACCATTTATGTTCAG                         GTGGGGGATGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATG
genomic: CTGATTATCTTCTCAAAGCCACTGCACATCCAAACACCATTTATGTTCAGgtcagttaag ... ggctttgcagGTGGGGGATGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATG
EST: gi|193396103|gb|FK361858.1|FK361858
EST:     CTGATTATCTTCTCAAAGCCACTGCACATCCAAACACCATTTATGTTCAG                         GTGGGGGATGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATG
genomic: CTGATTATCTTCTCAAAGCCACTGCACATCCAAACACCATTTATGTTCAGgtcagttaag ... ggctttgcagGTGGGGGATGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATG
EST: gi|208158073|gb|GD954186.1|GD954186
EST:     CTGATTATCTTCTCAAAGCCACTGCACATCCAAACACCATTTATGTTCAG                         GTGGGGGATGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATG
genomic: CTGATTATCTTCTCAAAGCCACTGCACATCCAAACACCATTTATGTTCAGgtcagttaag ... ggctttgcagGTGGGGGATGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATG
EST: gi|193299964|gb|FK268447.1|FK268447
EST:     CTGATTATCTTCTCAAAGCCACTGCACATCCAAACACCATTTATGTTCAG                         GTGGGGGATGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATG
genomic: CTGATTATCTTCTCAAAGCCACTGCACATCCAAACACCATTTATGTTCAGgtcagttaag ... ggctttgcagGTGGGGGATGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATG
EST: gi|193445032|gb|FK405808.1|FK405808
EST:     CTGATTATCTTCTCAAAGCCACTGCACATCCAAACACCATTTATGTTCAG                         GTGGGGGATGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATG
genomic: CTGATTATCTTCTCAAAGCCACTGCACATCCAAACACCATTTATGTTCAGgtcagttaag ... ggctttgcagGTGGGGGATGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATG
EST: gi|208119529|gb|GD920178.1|GD920178
EST:     CTGATTATCTTCTCAAAGCCACTGCACATCCAAACACCATTTATGTTCAG                         GTGGGGGATGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATG
genomic: CTGATTATCTTCTCAAAGCCACTGCACATCCAAACACCATTTATGTTCAGgtcagttaag ... ggctttgcagGTGGGGGATGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaatggggaacttgaattctgatattggtttggtttggtttttggctttgcagGTGGGGGATGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATGGATACTCCAAGAAGCGTGTTTAAAATAGATGCAAACACACCTGGTTCAG
                  ttctgat  putative branch site (score: 3)
             ttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatggaaattttttaaaaaaaatggggttagtcttctttagggagagaatggggaacttgaattctgatattggtttggtttggtttttggctttgcagGTGGGGGATGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATGGATACTCCAAGAAGCGTGTTTAAAATAGATGCAAACACACCTGGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - -aaaaaaa
- - - - - - - - - - - -tggggtt
- - - - - - - - - - - - - - - - - - - - -gggagag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtttgg