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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatacttttattcttttgttttccaatatactgatttatgttaaagcatatataaggcttttttcctttcttttttttcctcatgcaaaggtttattgcagGCACCTCTTCTTCTTGGCTGTGATGTTAGAAATATAACTAAAGAGACCATGGAGATAGTAGCTAACAAGGAAGTTATTGCAGTTAACCAAG

Basic information

species Glycine max
transcript GLYMA09G40990.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G40990.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G08380.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaatacttttattcttttgttttccaa-tatactgatttatgttaaa--gcatatataaggcttttttcctttcttttttttcctcatgcaaaggtttattgcagGCACCTCTTCTTCTTGGCTGTGATGTTAGAAATATAACTAAAGAGACCATGGAGATAGTAGCTAACAAGGAAGTTATTGCAGTTAACCAAG
         | |    | | ||  | || || |   | |    | |||   ||||||| | |  |    ||  |  | |        ||  | |   | | ||||||| |||||||| ||||| |||||  | ||||| || || ||||| || |||||||| || || ||||||||||| |||||  |||| ||||
--------gtaagctatatattcccgaaatagagaaactctcttcaaacaacatatattaagtctgaaaccaatgatgt--------atatata---tcactgcagGCTCCTCTTCTACTTGGTTGTGACATAAGAAACATGACCAAAGAAACAATGGAGATTGTCGCCAACAAGGAAGTCATTGCTATTAATCAAG
















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|208322312|gb|GE121681.1|GE121681
EST:     GTACAAAAAATGAATATACTGTTCACTTCAGTTTATGGGCCCTTTCCAAG                         GCACCTCTTCTTCTTGGCTGTGATGTTAGAAATATAACTAAAGAGACCATG
genomic: G-ACAAAAAATGAATATACTGTTCACTTCAGTTTATGGGCCCTTTCCAAGgtaatacttt ... tttattgcagGCACCTCTTCTTCTTGGCTGTGATGTTAGAAATATAACTAAAGAGACCATG
EST: gi|208312867|gb|GE111699.1|GE111699
EST:     TGACAAAAAATGAATATACTGTTCACTTCAGTTTATGGGCCCTTTCCAAG                         GCACCTCTTCTTCTTGGCTGTGATGTTAGAAATATAACTAAAGAGACCATG
genomic: TGACAAAAAATGAATATACTGTTCACTTCAGTTTATGGGCCCTTTCCAAGgtaatacttt ... tttattgcagGCACCTCTTCTTCTTGGCTGTGATGTTAGAAATATAACTAAAGAGACCATG
EST: gi|193362616|gb|FK327036.1|FK327036
EST:     TGACAAAAAATGAATATACTGTTCACTTCAGTTTATGGGCCCTTTCCAAG                         GCACCTCTTCTTCTTGGCTGTGATGTTAGAAATATAACTAAAGAGACCATG
genomic: TGACAAAAAATGAATATACTGTTCACTTCAGTTTATGGGCCCTTTCCAAGgtaatacttt ... tttattgcagGCACCTCTTCTTCTTGGCTGTGATGTTAGAAATATAACTAAAGAGACCATG
EST: gi|31458286|gb|CD400314.1|CD400314
EST:     GGGCCCTTTCCAAG                         GCACCTCTTCTTC-TNGCTGTGATGTTAGAAATATAACTAAAGAGACCATG
genomic: GGGCCCTTTCCAAGgtaatacttt ... tttattgcagGCACCTCTTCTTCTTGGCTGTGATGTTAGAAATATAACTAAAGAGACCATG
EST: gi|208328230|gb|GE130060.1|GE130060
EST:     TACTGTTCACTTCAGTTTATGGGCCCTTTCCAAG                         GCACCTCTTCTTCTTGGCTGTGATGTTAGAAATATAACTAAAGAGACCATG
genomic: TACTGTTCACTTCAGTTTATGGGCCCTTTCCAAGgtaatacttt ... tttattgcagGCACCTCTTCTTCTTGGCTGTGATGTTAGAAATATAACTAAAGAGACCATG
EST: gi|193303351|gb|FK272573.1|FK272573
EST:     TGACAAAAAATGAATATACTGTTCACTTCAGTTTATGGGCCCTTTCCAAG                         GCACCTCTTCTTCTTGGCTGTGATGTTAGAAATATAACTAAAGAGACCATG
genomic: TGACAAAAAATGAATATACTGTTCACTTCAGTTTATGGGCCCTTTCCAAGgtaatacttt ... tttattgcagGCACCTCTTCTTCTTGGCTGTGATGTTAGAAATATAACTAAAGAGACCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatataaggcttttttcctttcttttttttcctcatgcaaaggtttattgcagGCACCTCTTCTTCTTGGCTGTGATGTTAGAAATATAACTAAAGAGACCATGGAGATAGTAGCTAACAAGGAAGTTATTGCAGTTAACCAAG
                    tttctttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatacttttattcttttgttttccaatatactgatttatgttaaagcatatataaggcttttttcctttcttttttttcctcatgcaaaggtttattgcagGCACCTCTTCTTCTTGGCTGTGATGTTAGAAATATAACTAAAGAGACCATGGAGATAGTAGCTAACAAGGAAGTTATTGCAGTTAACCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA