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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagtgataaattgtcaaatttttgttatgccttaattttttatttcttcaaattaagttcttgcttggccgagaaaagtaattgtttgaattgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT

Basic information

species Glycine max
transcript GLYMA15G05620.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G05620.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g06340.2 (Oryza sativa), 3'ss of exon 2
----tgagtgataaattgtcaaatttttgttatgccttaattttt-tatttcttcaaattaagttcttgcttggccgagaaaagtaattgtttgaattgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT----------
    |      ||   |  || | | | |  | | ||||    |  |||    |   || || |    ||||       ||  ||  |||| ||  ||||   ||  |||| | || ||  |  |    |||||| ||||||| |||||||||||||| |||||||| || |||||||| || ||||||||||||          
ccctttcaccctaggct--cataatatcgcgacgacttagcaatgatatgcgctatgatgaattcaacgcttaaatcctaatggtgtttgtatggtttgc---agAAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACTGGGCAATATTTCGACTATTGGTCATGCATTGACAAATGTGTAAGTATCT

upper sequence: GLYMA15G05620.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g06340.1 (Oryza sativa), 3'ss of exon 2
----tgagtgataaattgtcaaatttttgttatgccttaatt-ttttatttcttcaaattaagttcttgcttggccgagaaaagtaattgtttgaattgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT
    |      ||   |  || | | | |  | | ||||    |  |||    |   || || |    ||||       ||  ||  |||| ||  ||||   ||  |||| | || ||  |  |    |||||| ||||||| |||||||||||||| |||||||| || |||||||| || ||||||||||||
ccctttcaccctaggct--cataatatcgcgacgacttagcaatgatatgcgctatgatgaattcaacgcttaaatcctaatggtgtttgtatggtttgc---agAAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACTGGGCAATATTTCGACTATTGGTCATGCATTGACAAATGT

upper sequence: GLYMA15G05620.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G122039_T07 (Zea mays), 3'ss of exon 2
---tgagtgataaattgtcaaatttttgttatgccttaattttttatttcttcaaattaa-gttcttgcttggccgagaaaagtaattgtttgaattgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT
   |      ||   ||  ||   | |   ||   ||||| |          || || |   || ||| |    |   ||  ||   ||| ||  ||    |||   ||| | || ||  |  |   ||||||| |||| || |||||||||||||| ||||| |||||||| ||||| || || |||||||||
tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctg--ttat--cagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT

upper sequence: GLYMA15G05620.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G122039_T05 (Zea mays), 3'ss of exon 2
---tgagtgataaattgtcaaatttttgttatgccttaattttttatttcttcaaattaa-gttcttgcttggccgagaaaagtaattgtttgaattgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT----
   |      ||   ||  ||   | |   ||   ||||| |          || || |   || ||| |    |   ||  ||   ||| ||  ||    |||   ||| | || ||  |  |   ||||||| |||| || |||||||||||||| ||||| |||||||| ||||| || || |||||||||    
tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctg--ttat--cagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAA

upper sequence: GLYMA15G05620.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G01090.2 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------------------------tgagtgataaattgtcaaatttttgttatgcct--taattttttatttcttcaaattaagttcttgcttggccgagaaaagtaattgtttgaattgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT----------
                                                               |        | |||     |||  ||  ||| |    || |   ||  | |    |     |  ||||  |     | |  |  |||||     || | ||||||||  | || ||||| || | |||||| ||||| || ||||| |||||||| |||||||||||||| |||  |||| |||||||||||          
gtgaatacgacttgagctgtcactggtcataaccttgttttgcattatacgagtcatttgacatagagagagagttgattgctttcggtgctgcttatctatctcacatcacatggcttcttagtgctgctcagttttaacatcttgttgttgtgggtggttcagGCGTGTGTCAAGAGGATCCAAGATGATGAGTCTGGCCACAAACATTGCACTGGGCAATATTTTGATTACTGGCATTGTGTTGACAAATGTGTAAGTGTGT

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|298198142|gb|HO039681.1|HO039681
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|7639289|gb|AW733615.1|AW733615
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|58014473|gb|CX701215.1|CX701215
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|193393950|gb|FK358081.1|FK358081
EST:     TGAAGAGTCTTGCAAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATAGGTGATGAT
genomic: TGAAGAGTCTTGCAAA-CCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACAT-GGTGATGAT
EST: gi|51343117|gb|CO983850.1|CO983850
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|14999290|gb|BI320299.1|BI320299
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|193431244|gb|FK396850.1|FK396850
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGAT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGAT
EST: gi|12772718|gb|BG237636.1|BG237636
EST:     AACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: AACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|18733830|gb|BM527835.1|BM527835
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|7639244|gb|AW733571.1|AW733571
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|12690066|gb|BG156402.1|BG156402
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|20814521|gb|BQ298999.1|BQ298999
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|7146375|gb|AW508297.1|AW508297
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|17402023|gb|BM178805.1|BM178805
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|22931573|gb|BU548712.1|BU548712
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|58023473|gb|CX710214.1|CX710214
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|10848067|gb|BF070624.1|BF070624
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|151400909|gb|EV270723.1|EV270723
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|13251785|gb|BG362688.1|BG362688
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|18848956|gb|BM568066.1|BM568066
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|6914391|gb|AW395921.1|AW395921
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|151410688|gb|EV280503.1|EV280503
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|18726815|gb|BM523771.1|BM523771
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|18848720|gb|BM567832.1|BM567832
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|254315068|gb|GR830061.1|GR830061
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|151401498|gb|EV271312.1|EV271312
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
EST: gi|23734278|gb|BU765362.1|BU765362
EST:     TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG                         GCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT
genomic: TTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAGgtgtgctttt ... attgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcaaattaagttcttgcttggccgagaaaagtaattgtttgaattgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT
                             aaaagtaattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagtgataaattgtcaaatttttgttatgccttaattttttatttcttcaaattaagttcttgcttggccgagaaaagtaattgtttgaattgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT

tgagtga
- - - - - - - - - - - - - tatgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtttg