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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaaaatactactctcaccttaagtgactgcttaaaccagggcttgtgcaattgttttattgtttctttatgatgatatttgcatggttttcgtgcacagAAGCAAGGAATGGTGAAGGAAGGAGAAGAAGTAGCACTTGTACAAAGTGGTAGGCAACCCATATGGAGGTTCCAATCCACGCACAATATCCAGGTTAGGA

Basic information

species Glycine max
transcript GLYMA09G23150.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G23150.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 11
-------caaaaatactactctcaccttaagtgactgcttaaaccagggcttgtgcaattgttttattgtttctttatgatgatatttgcatggttttcgtgcacagAAGCAAGGAATGGTGAAGGAAGGAGAAGAAGTAGCACTTGTACAAAGTGGTAGGCAACCCATATGGAGGTTCCAATCCACGCACAATATCCAGGTTAGGA
         ||||||  |||   |   || |  |   |  |||      ||  | ||  |    || |     |||   |||||  |   ||   || |    |||||| || || |||||||||||||| || || || |||||||| |||||||| |||||||| || ||| |||  || ||||| || ||||| ||||| ||||
ttgttgctgaaaatag-actgataaaata-gccatgccccaaatatccactattccacatacgatactcaccatttgatatgatgct-atatatattcc----acagAAACATGGTATGGTGAAGGAAGGCGAGGAGGTTGCACTTGTTCAAAGTGGCAGGCAACCTATCTGGCGGTCGCAGTCCACCCATAATATTCAGGTCAGGA

upper sequence: GLYMA09G23150.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 11
------caaaaatactactctcaccttaagtgactgcttaaaccag-ggcttgtgcaattgttttattgtttctt-tatgatgatatttgcatggttttcgtgcacagAAGCAAGGAATGGTGAAGGAAGGAGAAGAAGTAGCACTTGTACAAAGTGGTAGGCAACCCATATGGAGGTTCCAATCCACGCACAATATCCAGGTTAGGA
      |     |  || |      |  || | ||   ||     |      || || ||||  || |  ||||  | | |   | ||||||||       |  |||||||||||| |||||||||||||||||||| || || ||||| || ||||| ||||| || || ||| ||||||||||||| |||||||||||||| ||||
cccacacgtccttggtatttatgtttccag-gcctctgtatgtttgcaaggagtacagttgtgatacttcttctaatgtaaatgtttttgcatg-------tatacagAAGCAAGGGATGGTGAAGGAAGGAGAAGAGGTGGCTCTTGTTCAGAGTGGCAGGCAGCCGATCTGGCGGTTCCAATCCACACACAATATCCAGGTCAGGA
















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|193584462|gb|FK543284.1|FK543284
EST:     TCTGTGACGATTCTGAGGCAACTTTCAGAAGAGCCTTGAATTTGCTGCAG                         AAGCAAGGAATGGTGAAGGAAGGAGAAGAAGTAGCACTTGTACAAAGTGGT
genomic: TCTGTGACGATTCTGAGGCAACTTTCAGAAGAGCCTTGAATTTGCTGCAGgtaatctttg ... tcgtgcacagAAGCAAGGAATGGTGAAGGAAGGAGAAGAAGTAGCACTTGTACAAAGTGGT
EST: gi|208131341|gb|GD931536.1|GD931536
EST:     TCTGTGACGATTCTGAGGCAACTTTCAGAAGAGCCTTGAATTTGCTGCAG                         AAGCAAGGAATGGTGAAGGAAGGAGAAGAAGTAGCACT
genomic: TCTGTGACGATTCTGAGGCAACTTTCAGAAGAGCCTTGAATTTGCTGCAGgtaatctttg ... tcgtgcacagAAGCAAGGAATGGTGAAGGAAGGAGAAGAAGTAGCACT
EST: gi|193487302|gb|FK450939.1|FK450939
EST:     TCTGTGACGATTCTGAGGCAACTTTCAGAAGAGCCTTGAATTTGCTGCAG                         AAGCAAGGAATGGTGAAGGAAGGAGAAGAAAGTAGCACTTGTACAAAGTGG
genomic: TCTGTGACGATTCTGAGGCAACTTTCAGAAGAGCCTTGAATTTGCTGCAGgtaatctttg ... tcgtgcacagAAGCAAGGAATGGTGAAGGAAGGAGAAGAA-GTAGCACTTGTACAAAGTGG
EST: gi|193527829|gb|FK488035.1|FK488035
EST:     CTGTGACGATTCTGAGGCAACTTTCAGAAGAGCCTTGAATTTGCTGACAG                         AAGCAAGGAATGGTGAAGGAAGGAGA
genomic: CTGTGACGATTCTGAGGCAACTTTCAGAAGAGCCTTGAATTTGCTG-CAGgtaatctttg ... tcgtgcacagAAGCAAGGAATGGTGAAGGAAGGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcaattgttttattgtttctttatgatgatatttgcatggttttcgtgcacagAAGCAAGGAATGGTGAAGGAAGGAGAAGAAGTAGCACTTGTACAAAGTGGTAGGCAACCCATATGGAGGTTCCAATCCACGCACAATATCCAGGTTAGGA
                                          ttttcgt  CT-rich tract
         ttttattgtttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaaaatactactctcaccttaagtgactgcttaaaccagggcttgtgcaattgttttattgtttctttatgatgatatttgcatggttttcgtgcacagAAGCAAGGAATGGTGAAGGAAGGAGAAGAAGTAGCACTTGTACAAAGTGGTAGGCAACCCATATGGAGGTTCCAATCCACGCACAATATCCAGGTTAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
-aaaaata
- - - - - -ctctcac
- - - - - - - - - - - - tgactgc
- - - - - - - - - - - - - - - - - - - - - cttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatggt