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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaaaataagcttaaacaaataggacctatgttcatactaagtctgatcccctttgggaacttttggctaaggtatagcctttttcttttaatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTC

Basic information

species Glycine max
transcript GLYMA16G01230.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 5
ataaaaataagcttaaacaaata-ggacctatgttcatactaagtctgatc-ccctttgggaacttttggctaaggtatagcctttttcttttaatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTC
|||| | | | | ||| || ||| ||| | ||||| | | || | || | || | | | | ||||||||||| ||||||||||||||| ||||| ||||| |||||||||||||| | |||||| ||||||||| | | || || ||
------gtaagttcttatgagcacggattgattgtcaaggactttctttttgttctttgagtgaggcatggtactgaatggttttggtttcatgaaatgcagGTCATTTCAACATTTTTGTTGGAGATCTTAGTCCAGAGGTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTC

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 5
ataaaaataagcttaaacaaataggacctatgttcatactaagtctg-atcccctttgggaacttttggctaaggtatagccttt--ttcttttaatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTC
|| | | || | | || || |||| ||||| | | | ||| || | | |||||||||||| ||||||||||||||| ||||| ||||| ||||| |||||||| || | | | | |||||||||||| | ||| ||||||
--------------------gtaagttttgactttttttaagtgttgcattttgtttgtatgtttttgaggatactcaatgttttagtttccatgagttgcagGTCATTTCAACATTTTTGTTGGAGATCTCAGTCCAGAGGTCACTGATGCAACATTATATCAAAGCTTTTCTGTCTTTTCCAGTTGTTC

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G17370.2 (Arabidopsis thaliana), 3'ss of exon 5
ataaaaataagcttaaacaaataggacctatgttcatactaagtctgatcccctttgggaacttt-tggctaaggtatagcctttttct---tttaatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTC
| | | | | | | | | ||| | |||| | | |||||| | | | | || || || || | | || || ||||||||| | ||| || |||||||| ||| | ||||| |||||||||||||| | ||||||| | ||||| |||||||| || ||||| ||
------gttggttcaca-atcttatgcttgatttcttgctaaaacag---tattttgggtgttctattgatacaataacgcacttctgtgatcttcatgtgcagGTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTC

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 5
-------ataaaaataagcttaaacaaataggacctatgttcatacta-agtctgatccc------ctttgggaacttttggctaaggtatagcctttttcttt--taatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTC
| | || | ||| | | | || || | ||||| | ||||| | | | | | | || || | | | | || |||||| | ||||||||||||||| ||||| || |||||||||||||||||||| ||||||||||||||||||| | ||||| ||||||
gttggtttctgtagtttaattctatgcataagtttcactcttatgctgcaaactgattctatggagttttggcattcatcattgttgatgttgtattcttgtatgatgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC

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|209725663|gb|BW663152.1|BW663152
EST:     TATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG                         GTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTA
genomic: TATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAGgttagttcag ... taatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTA
EST: gi|26058275|gb|CA801189.1|CA801189
EST:     AGAGAGAGGATACGTCAG                         GTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTA
genomic: AGAGAGAGGATACGTCAGgttagttcag ... taatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTA
EST: gi|298165726|gb|HO008697.1|HO008697
EST:     TATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG                         GTCATTACAACATTTTTGTTGGCGATCT
genomic: TATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAGgttagttcag ... taatttgcagGTCATTACAACATTTTTGTTGGCGATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatcccctttgggaacttttggctaaggtatagcctttttcttttaatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTC
                                          ttttaat  putative branch site (score: 3)
 cctttttcttttaatt  CT-rich tract
 tttttcttttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaaaataagcttaaacaaataggacctatgttcatactaagtctgatcccctttgggaacttttggctaaggtatagcctttttcttttaatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- -aaaataa
- - - - - - - aaacaaa
- - - - - - - - - - - - - cctatgt
- - - - - - - - - - - - - - - - - - - - - - - - tcccctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttttgg