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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatatttaagtcctaattctcctctcacttgtgaagtctcaattcacctaatgttgttattggagttttagaagtaaaagttaccattgcatctttcagGCTATCAATTTCTCAAACTTATATGCACCTGAGCATCTAATTATCAATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAAT

Basic information

species Glycine max
transcript GLYMA15G13910.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G13910.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 13
ttatatttaagtcctaattc-tcctctcacttgtgaagtctcaattcacctaatgt-tgttattggagttttagaagtaaaagttaccattgcatctttcagGCTATCAATTTCTCAAACTTATATGCACCTGAGCATCTAATTATCAATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAAT----
 ||| | ||   ||  |  | | |     | ||  | |  | |||  |  ||   | | |||||    | ||  || ||||| | | ||||  | |||||||||||||   || |||||||||||||||||||||||||| || || |||||||||||||| ||||||||||||| |||||||||||||    
gtatgtctacacccacacacatacatatgcatgc-atgcatgaatatatatatcttgtattattacc-tcttgaaactaaaattgatcatttgaactttcagGCTATCTCCTTTTCAAACTTATATGCACCTGAGCATCTGATAATTAATGTGAAAGATGCTGAGAAGTGGGAGAATTTCATTGAGAATGCAG
















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|12772188|gb|BG237115.1|BG237115
EST:     CCAAAGCTCTGAGCCACAGNNNNNNNGTGTATGCACGTGATATGCTTGAG                         GCTATCAATTTCTCAAACTTATATGCACCTGAGCATCTAATTATCAATGTG
genomic: CCAAAGCTCTGAGCCACAGTTTTTTTGTGTATGCACGTGATATGCTTGAGgttagtcatc ... catctttcagGCTATCAATTTCTCAAACTTATATGCACCTGAGCATCTAATTATCAATGTG
EST: gi|15203715|gb|BI426483.1|BI426483
EST:     CCAAAGCTCTGAGCCACAGNNNNNNNGTGTATGCACGTGATATGCTTGAG                         GCTATCAATTTCTCAAACTTATATGCACCTGAGCATCTAATTATCAATGTG
genomic: CCAAAGCTCTGAGCCACAGTTTTTTTGTGTATGCACGTGATATGCTTGAGgttagtcatc ... catctttcagGCTATCAATTTCTCAAACTTATATGCACCTGAGCATCTAATTATCAATGTG
EST: gi|254340469|gb|GR850771.1|GR850771
EST:     CCAAAGCTCTGAGCCACAGNNNNNNNGTGTATGCACGTGATATGCTTGAG                         GCTATCAATTTCTCAAACTTATATGCA-CTGAGCATCTAATTATCAATGTG
genomic: CCAAAGCTCTGAGCCACAGTTTTTTTGTGTATGCACGTGATATGCTTGAGgttagtcatc ... catctttcagGCTATCAATTTCTCAAACTTATATGCACCTGAGCATCTAATTATCAATGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacctaatgttgttattggagttttagaagtaaaagttaccattgcatctttcagGCTATCAATTTCTCAAACTTATATGCACCTGAGCATCTAATTATCAATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAAT
 acctaat  putative branch site (score: 3)
                                             catctttc  putative PPT
                     ttttagaagtaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatatttaagtcctaattctcctctcacttgtgaagtctcaattcacctaatgttgttattggagttttagaagtaaaagttaccattgcatctttcagGCTATCAATTTCTCAAACTTATATGCACCTGAGCATCTAATTATCAATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - -ctcctct
- - - - - - - - - - - - - -acttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagtaaaa