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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatgtattccaataattttctgcaacttcatcatcagtgtttgaatttttgagctttgttttgacacaccaaagttaacctaatataattatttctcagCTTCGAGAATCAAAGGGAATGACAACAATCAAATTCCGTCCACATTCTGGAGAG

Basic information

species Glycine max
transcript GLYMA01G29470.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 5
taatgtattccaataattttctgcaacttcatcatcagtgtttgaatttttgagctttgttttgacacaccaaagttaacctaatataattatttctcagCTTCGAGAATCAAAGGGAATGACAACAATCAAATTCCGTCCACATTCTGGAGAG
                      | ||  |   | |||    |  ||||||    | |  |||||    |  ||||| |  ||  | |    ||||   || | || |||||||| || ||||| ||||||||||||||||||||| |||| |||
-------------------gtaggaaaattgccctcatacctctaatttt----cctcattttgctgga--aaagtaacacttctgtg-caattt---agTTGCGTGAATCAAAAGGGATGACCACAATCAAATTCCGTCCACATGCTGGCGAG

upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 13
taatgtattccaataattttctgcaacttcatcatcagtgtttgaatttttgagctttgttttgacacaccaaagtta-acctaatataattatttctcagCTTCGAGAATCAAAGGGAATGACAACAATCAAATTCCGTCCACATTCTGGAGAG
                      |  |    ||| ||     |    ||  | |  ||| |          || |||   |   | | |  | | || |||||| || || |||||||||||||| || |||||||||||||||||| ||||||||
----------------------gtgatcatatcttc----ctccccttcctcaattttctccacgtttctcagagtggtaatgattctgttcaattttcagCTGCGTGAGTCAAAGGGAATGACCACTATCAAATTCCGTCCACATGCTGGAGAG

upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 14
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 13
--taatgtattccaataattttctgcaacttcatcatcagtgtttgaatttttgagctttgttttgacacaccaaagttaacctaatataattatttctcagCTTCGAGAATCAAAGGGAATGACAACAATCAAATTCCGTCCACATTCTGGAGAG
  |  |    |||   ||| |     ||||   | ||  || || ||   ||     || |     | | | |||| || | |   |    || | ||| |||| ||||| |||||||| ||||| || ||||||||||||||||||||||| |||
catttttccatcctgcaatctcaacgaactcagttat--gttttagatgattatgtgttggacaaaatatagcaaattttaaccctttactttgtatcttagCTACGAGAGTCAAAGGGCATGACTACTATCAAATTCCGTCCACATTCTGGGGAG

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|7925052|gb|AW831078.1|AW831078
EST:     TTTCATACTATGTCTATTACTGTTATGCAAATCTTTACACCTTAAACAAG                         CTTCGAGAATCAAATGGAATGAC
genomic: TTTCATACTATGTCTATTACTGTTATGCAAATCTTTACACCTTAAACAAGgtatgtaact ... tatttctcagCTTCGAGAATCAAAGGGAATGAC
EST: gi|254332340|gb|GR846385.1|GR846385
EST:     TTTCATACTATGTCTATTACTGTTATGCAAATCTTTACACCTTAAACAAG                         CTTCGAGAATCAAAGGGAATGACA-CAATCAAATTCCGTCCACATTCTGGA
genomic: TTTCATACTATGTCTATTACTGTTATGCAAATCTTTACACCTTAAACAAGgtatgtaact ... tatttctcagCTTCGAGAATCAAAGGGAATGACAACAATCAAATTCCGTCCACATTCTGGA
EST: gi|9565158|gb|BE474667.1|BE474667
EST:     TTTCATACTATGTCTATTACTGTTATGCAAATCTTTATACCTTAAACAAG                         CTTCGAGAATCAAAGGGAATGACGACAATCAAATTCCGTCCACATTCTGGA
genomic: TTTCATACTATGTCTATTACTGTTATGCAAATCTTTACACCTTAAACAAGgtatgtaact ... tatttctcagCTTCGAGAATCAAAGGGAATGACAACAATCAAATTCCGTCCACATTCTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttgagctttgttttgacacaccaaagttaacctaatataattatttctcagCTTCGAGAATCAAAGGGAATGACAACAATCAAATTCCGTCCACATTCTGGAGAG
                                 acctaat  putative branch site (score: 3)
                                            ttatttctc  putative PPT
                          aaagttaacctaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatgtattccaataattttctgcaacttcatcatcagtgtttgaatttttgagctttgttttgacacaccaaagttaacctaatataattatttctcagCTTCGAGAATCAAAGGGAATGACAACAATCAAATTCCGTCCACATTCTGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA