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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCTTCATGAGACACTAACCTATCAGGAGGTAACTTCCAAAGATCTGTCAGTGATGGACATGACTGCCATAACTTTATGCCAAGAAAATAATATTCCAGgtaagtcacgcagacaaacatttatatgcacttttatatatatatatatatatgttttctaattgttattagtttaaatgtctccttaccctgcccttcctttatggtgcag

Basic information

species Glycine max
transcript GLYMA08G15610.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G15610.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os01g73450.1 (Oryza sativa), 5'ss of exon 6
CGTCTTCATGAGACACTAACCTATCAGGAGGTAACTTCCAAAGATCTGTCAGTGATGGACATGACTGCCATAACTTTATGCCAAGAAAATAATATTCCAGgtaagtcacgcagacaaacatttatatgcacttttatatatatatatatatatgttttctaattgttattagtttaaatgtctccttaccctgcccttcctttatggtgcag
|| |||| |||| |  | | ||| || |||||     | | ||| || ||||| ||||||||||||||||| ||  ||||||||||||| || ||||| ||||||    |    |   || || | ||    || ||| |        | | || |||  | |  || | | ||    |||   ||| |                       
CGCCTTCTTGAGGCTGTGAGCTACCATGAGGTGCAAACAAGAGACCTCTCAGTAATGGACATGACTGCCATTACGCTATGCCAAGAAAACAACATTCCTGgtaag--gagagagctgtcagtt-tctgagacttgataca-------gtgtttgatttgcattctttttaatttggcctgtaatcttgcag---------------------
















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|209728096|gb|BW655331.1|BW655331
EST:     AGTGATGGACATGACTGCCATAACTTTATGCCAAGAAAATAATATTCCAG                         TTATTGTCTTTAATCTTAACAAACCTGGTAACATTGAGAAAGCTATTAAAG
genomic: AGTGATGGACATGACTGCCATAACTTTATGCCAAGAAAATAATATTCCAGgtaagtcacg ... tatggtgcagTTATTGTCTTTAATCTTAACAAACCTGGTAACATTGAGAAAGCTATTAAAG
EST: gi|51336959|gb|CO980825.1|CO980825
EST:     AGTGATGGACATGACTGCCATAACTTTATGCCAAGAAAATAATATTCCAG                         TTATTGTCTTTAATCTTAACAAACCTGGTAACATTGAGAAAGCTATTAAAG
genomic: AGTGATGGACATGACTGCCATAACTTTATGCCAAGAAAATAATATTCCAGgtaagtcacg ... tatggtgcagTTATTGTCTTTAATCTTAACAAACCTGGTAACATTGAGAAAGCTATTAAAG
EST: gi|214008530|gb|DB987435.1|DB987435
EST:     AGTGATGGACATGACTGCCATAACTTTATGCCAAGAAAATAATATTCCAG                         TTATTGTCTTTAATCTTAACAAACCTGGTAACATTGAGAAAGCTATTAAAG
genomic: AGTGATGGACATGACTGCCATAACTTTATGCCAAGAAAATAATATTCCAGgtaagtcacg ... tatggtgcagTTATTGTCTTTAATCTTAACAAACCTGGTAACATTGAGAAAGCTATTAAAG
EST: gi|214009474|gb|DB990102.1|DB990102
EST:     GCCAAGAAAATAATATTCCAG                         TTATTGTCTTTAATCTTAACAAACCTGGTAACATTGAGAAAGCTCAAT-AA
genomic: GCCAAGAAAATAATATTCCAGgtaagtcacg ... tatggtgcagTTATTGTCTTTAATCTTAACAAACCTGGTAACATTGAGAAAGCT-ATTAAA
EST: gi|9903028|gb|BE611996.1|BE611996
EST:     AGTGATGGACATGACTGCCATAACTTTATGCCAAGAAAATAATATTCCAG                         TTATTGTCTTTAATCTTAACAAACCTGGTAACATTGAAAAAGCTATTAAAG
genomic: AGTGATGGACATGACTGCCATAACTTTATGCCAAGAAAATAATATTCCAGgtaagtcacg ... tatggtgcagTTATTGTCTTTAATCTTAACAAACCTGGTAACATTGAGAAAGCTATTAAAG
EST: gi|192301628|gb|FG994364.1|FG994364
EST:     AGTGATGGACATGACTGCCATAACTTTATGCCAAGAAAATAATATTCCAG                         TTATTGTCTTTAATCTTAACAAACCTGGTAACATTGAGAAAGCTATTAAAG
genomic: AGTGATGGACATGACTGCCATAACTTTATGCCAAGAAAATAATATTCCAGgtaagtcacg ... tatggtgcagTTATTGTCTTTAATCTTAACAAACCTGGTAACATTGAGAAAGCTATTAAAG
EST: gi|5509675|gb|AI856233.1|AI856233
EST:     AGTGATGGACATGACTGCCATAACTTTATGCCAAGAAAATAATATTCCAG                         TTATTGTCTTTAATCTTAACAAACCTGGTAACATTGAGAAAGCTATTAAAG
genomic: AGTGATGGACATGACTGCCATAACTTTATGCCAAGAAAATAATATTCCAGgtaagtcacg ... tatggtgcagTTATTGTCTTTAATCTTAACAAACCTGGTAACATTGAGAAAGCTATTAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTCTTCATGAGACACTAACCTATCAGGAGGTAACTTCCAAAGATCTGTCAGTGATGGACATGACTGCCATAACTTTATGCCAAGAAAATAATATTCCAGgtaagtcacgcagacaaacatttatatgcacttttatatatatatatatatatgttttctaattgttattagtttaaatgtctccttaccctgcccttcctttatggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA