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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttccaatttatttcccattaaccttctgtcttttgaatgcatgtttttgttattggtttgaggtgcctttttgctaaaatttgcccctaaatggtctagGATCTTCCTAATTATGCTCAGCATACCGTGCCTATTTTCTCTTTGCCACAAGAGTGGCTATGGTGTGAATCATGGTGTGGTAATGCTACAAAATACAAGG

Basic information

species Glycine max
transcript GLYMA08G13400.1
intron # 38
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13400.1 (Glycine max), 3'ss of exon 38
lower sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 15
gttccaatttatttcccattaaccttctgtcttttgaatgcatgtttttgttattggtttgag-gtgcctttttgctaaaatttgcccctaaatggtctagGATCTTCCTAATTATGCTCAGCATACCGTGCCTATTTTCTCTTTGCCACAAGAGTGGCTATGGTGTGAATCATGGTGTGGTAATGCTACAAAATACAAGG-
       | |  |   ||   |      |        |  ||  |     |||  | | |||   ||  |   |||| |  |    | |       |  ||||||| || ||||||||||||||||| ||||| || |||||| | || ||||| ||||||||||||||||| |||||||| ||||| |||||   ||||  
-acatgctgtggtgtgcagagattaatggaagaaactacacaaatgcagtttacagatgtgaacatgtgtgaatgcttacttgcaacacctttatattcagGATCTCCCAAATTATGCTCAGCATACTGTGCCCATATTCTCTCTCCCTCAAGAATGGCTATGGTGTGAATCTTGGTGTGGAAATGCCACAAAG-GCAAGAG

upper sequence: GLYMA08G13400.1 (Glycine max), 3'ss of exon 38
lower sequence: GRMZM5G846198_T01 (Zea mays), 3'ss of exon 8
---gttccaatttatttcccattaaccttctgtcttttgaatgcatgtttttgttattggtttgaggtgcctttttgctaaaatttgcccctaaatggtctagGATCTTCCTAATTATGCTCAGCATACCGTGCCTATTTTCTCTTTGCCACAAGAGTGGCTATGGTGTGAATCATGGTGTGGTAATGCTACAAAATACAAGG-
    ||  ||   |||     ||    |||||| |  ||  | |||  || | |   |       | ||      |||| |  |    | |   |   |  ||||||| || |||||||| || ||||| |||||||| |||||| | || ||||| ||||| ||||||||||| |||||||| ||||| ||||||  ||||  
gacatttgaag--attctgttttttttttctgtttcatgt-tacataattatttctgtataaatggatgttgcaatgcttacttggaacacattaatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAAGAATGGCTGTGGTGTGAATCTTGGTGTGGAAATGCCACAAAA-GCAAGAG

upper sequence: GLYMA08G13400.1 (Glycine max), 3'ss of exon 38
lower sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 35
----------------------------------------------------------------gttccaatttatttccca---ttaaccttctgtcttttg----aatgcatgtttttgttatt---ggtttgaggtgcctttttgctaa-aatttgcccctaaatggtct-agGATCTTCCTAATTATGCTCAGCATACCGTGCCTATTTTCTCTTTGCCACAAGAGTGGCTATGGTGTGAATCATGGTGTGGTAATGCTACAAAATACAAGG
                                                                |||  | |||||||   |   ||   | | || || ||     |   |||| | |   | ||    |||  |||| |     |  | |     || |  ||  | || | |||||||||||||||||||||||||||| || ||||| || ||  | || ||||||||| | ||||||||||| |||||||| || || ||||||  |||||
gcaagttgtataatatggttctctatacttagggctgtaacctttctttggtggtcacactatcgttttactttatttgaaaggcttttgcatttgactcttaccatacaccatgctctgaatctttagagttccaggttcaaacatattgatggcatgtcattattttgtttcagGATCTTCCTAATTATGCTCAGCATACTGTTCCTATATTTTCACTTCCCCAAGAGTGGTTGTGGTGTGAATCCTGGTGTGGAAACGCCACAAAAGCCAAGG

upper sequence: GLYMA08G13400.1 (Glycine max), 3'ss of exon 38
lower sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 36
---gttccaat-ttatttcccattaaccttctgtcttttgaatgcatgttt-ttgttattggtttgaggtgcctttttgctaaaatttgcccctaaatggtctagGATCTTCCTAATTATGCTCAGCATACCGTGCCTATTTTCTCTTTGCCACAAGAGTGGCTATGGTGTGAATCATGGTGTGGTAATGCTACAAAATACAAGG
    |   |||  |   ||   ||| | || | | || ||  ||| || || || || |     | |  ||| ||  | || | |     ||    |   |  |||||||||| || | |||||||||||| ||||| || || ||  | || ||||||||| ||||||||||||||||||| || ||||||||||||| |||||
aacatctgaatgctccatcattttatctttttatgttctgtttgcttgattattattttccaaataatatgcattgct-ctgatagccatcc----acatttcagGATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAAGAGTGGTTATGGTGTGAATCATGGTGCGGAAATGCTACAAAATCCAAGG

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|7042357|gb|AW472251.1|AW472251
EST:     GCAAGGATCCAAATAGTCTAGCCAACTTGGATCAG                         GATCTTCCTAATTATGCTCAGCATACCGTGCCTATTTTCTCTTTGCCACAA
genomic: GCAAGGATCCAAATAGTCTAGCCAACTTGGATCAGgtaagaggtt ... aatggtctagGATCTTCCTAATTATGCTCAGCATACCGTGCCTATTTTCTCTTTGCCACAA
EST: gi|17401326|gb|BM178108.1|BM178108
EST:     TATATGAAACACTAAGCAAGGATCCAAATAGTCTAGCCAACTTGGATCAG                         GATCTTCCTAATTATGCTCAGCATACCGTGCCTATTTTCTCTTTGCCACAA
genomic: TATATGAAACACTAAGCAAGGATCCAAATAGTCTAGCCAACTTGGATCAGgtaagaggtt ... aatggtctagGATCTTCCTAATTATGCTCAGCATACCGTGCCTATTTTCTCTTTGCCACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgttattggtttgaggtgcctttttgctaaaatttgcccctaaatggtctagGATCTTCCTAATTATGCTCAGCATACCGTGCCTATTTTCTCTTTGCCACAAGAGTGGCTATGGTGTGAATCATGGTGTGGTAATGCTACAAAATACAAGG
                       tttttgctaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttccaatttatttcccattaaccttctgtcttttgaatgcatgtttttgttattggtttgaggtgcctttttgctaaaatttgcccctaaatggtctagGATCTTCCTAATTATGCTCAGCATACCGTGCCTATTTTCTCTTTGCCACAAGAGTGGCTATGGTGTGAATCATGGTGTGGTAATGCTACAAAATACAAGG

- - - - - -tttccca
- - - - - - - - - - - - ttctgtc
- - - - - - - - - - - - - - - - - - - -gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - tggtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcccct