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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatggtgtttattgactgccaaaaggatactgaatttgcctttttagtaggtggctttaagttaactaatacttttttatgatctgattttattggcagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTATTAAGGATTTTATGATTCAGGCCGGTGATTTTGTAAAG

Basic information

species Glycine max
transcript GLYMA09G11960.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G11960.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0084g00620.t01 (Vitis vinifera), 3'ss of exon 1
agatggtgtttattgactgccaaaaggatactgaatttgcctttttagtaggtggctttaagttaactaatacttttttatgatctgatt----------ttattggcagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTATTAAGGATTTTATGATTCAGGCCGGTGATTTTGTAAAG
     || ||||||   | | ||    |  |   |||| | | |||    | ||  ||    ||  ||  | |||| || | || ||||           | ||| |||| ||||| ||| | ||||||||||||||||| || || || || || || || || ||||| ||||||||||| ||||||||||| |||
-----gtttttattcttttctaacttcactc---attttcttattttcaggatgatttcctttt--ctttttctttcttcttatttgatgaatacaataatgatttgcagAAAAGCTGGATTACCTGTTGGTTACAAGGGATGCCAGTTCCACAGGGTCATCAAAGATTTCATGATTCAGGCTGGTGATTTTGTCAAG
















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|6719223|gb|AW306870.1|AW306870
EST:     GGCAGTTCTGCACTGGGGAATACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAGTACAGgtactggaac ... ttattggcagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|151409781|gb|EV279589.1|EV279589
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAGTACAGgtactggaac ... ttattggcagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|192325817|gb|FK018039.1|FK018039
EST:     GGCAGTTCTGCACTGGGGAATACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAGTACAGgtactggaac ... ttattggcagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|298167097|gb|HO010536.1|HO010536
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAGTACAGgtactggaac ... ttattggcagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|15286510|gb|BI470401.1|BI470401
EST:     GGCAGTTCTGCACTGGGGAATACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAGTACAGgtactggaac ... ttattggcagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|298172912|gb|HO019896.1|HO019896
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAGTACAGgtactggaac ... ttattggcagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|15814116|gb|BI786391.1|BI786391
EST:     GGCATTTCTGCACTGGGGAATACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAGTACAGgtactggaac ... ttattggcagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|193315557|gb|FK281777.1|FK281777
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGG-CTGCCTGTTGGTTACAAGGGTTGTCAATTTCAT
genomic: GGCAGTTCTGCACTGGGGAGTACAGgtactggaac ... ttattggcagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCAT
EST: gi|192320580|gb|FK011990.1|FK011990
EST:     GGCAGTTCTGCACTGGGGAATACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAGTACAGgtactggaac ... ttattggcagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|298182560|gb|HO031295.1|HO031295
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAGTACAGgtactggaac ... ttattggcagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|208255556|gb|GE052243.1|GE052243
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGCTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAGTACAGgtactggaac ... ttattggcagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|298195597|gb|HO043988.1|HO043988
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAGTACAGgtactggaac ... ttattggcagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|17023477|gb|BM094511.1|BM094511
EST:     GGCAGTTCTGCACTGGGGAATACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAGTACAGgtactggaac ... ttattggcagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|298188736|gb|HO035429.1|HO035429
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAGTACAGgtactggaac ... ttattggcagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|10847406|gb|BF070093.1|BF070093
EST:     GGCAGTTCTGCACTGGGGAATACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAGTACAGgtactggaac ... ttattggcagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtaggtggctttaagttaactaatacttttttatgatctgattttattggcagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTATTAAGGATTTTATGATTCAGGCCGGTGATTTTGTAAAG
                                           ttttatt  CT-rich tract
           tttaagttaactaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatggtgtttattgactgccaaaaggatactgaatttgcctttttagtaggtggctttaagttaactaatacttttttatgatctgattttattggcagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTATTAAGGATTTTATGATTCAGGCCGGTGATTTTGTAAAG

-gatggtg
- - - - - - - - ctgccaa
- - - - - - - - - - - - - gatactg
- - - - - - - - - - - - - - - - - - -tgccttt
- - - - - - - - - - - - - - - - - - - - - - - - - -gtggctt