Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttcttggtaatagtaattggtgatttaacaagtgtgtttttctccattcttttaaaaccctttctgatatgtgaattttgagctttttcttctttcagCACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAATGAAAGCAAAGTCGAAACCCATAAAAAAATTCACTCCGGAGGAGTTGAAT

Basic information

species Glycine max
transcript GLYMA10G33110.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G33110.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g10400.1 (Oryza sativa), 3'ss of exon 3
---------------------------------------------------------------------------------atttcttggtaatagtaattggtgatttaacaagtgtgtttttctccattcttttaaaaccctttctgatatg---tgaattttgagctttttcttctttcagCACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAATGAAAGCAAAGTCGAAACCCATAAAAAAATTCACTCCGGAGGAGTTGAAT
                                                                                 ||   || || ||     |     |  |   |  | ||| || |    |  |||| |  |  |||| || ||    | || | |    |  || || |  |||||| ||| ||||||||||||||||||||||||| ||  | || ||||||||||| ||||| || |||  ||| || ||| |||| || || ||  || ||
gtatgttccatgaaacatttattttctttcttttagtttaatttaacaaggctagtacttcgattcttcataagcattgcgatcatttagtgatctctgtcacatagctgg-atctttgtattgcattgtggttttgagccaatttcagaaattgcctaaactattgtttgatttttgtgacagCACGGATTTGAGACTGAACCAACCAAGGTATGCAACATTGCCAAACATAATGAAGGCAAAATCAAAAGTCATCAAGAAAGTCACCCCCGAAGATCTGGAT

upper sequence: GLYMA10G33110.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G008864_T01 (Zea mays), 3'ss of exon 3
---------------------------------atttcttggtaatagtaattggtgatttaacaagtgtgt-ttttctccattcttttaaaaccctttctga---tatgtgaattttgagctttttcttc-tttcagCACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAATGAAAGCAAAGTCGAAACCCATAAAAAAATTCACTCCGGAGGAGTTGAAT
                                 |  | ||  || |  |  || | ||    | |      |  ||| | || |  |  | || | |   |||   | | | ||   | || ||| ||||   | |||||| ||| ||||||| ||||| ||||||||||| ||| | || ||||||||||| |||||||| |||   || || ||| |    ||  | ||  |   |
gtagggcccaagaaacatttcaatatattgtttacattttattattcttcgttcgagacgggaaatcgaaatactttgttcagtaatgaataaacttgcgtgaacttgtattaacaattagttttgtctttgctgcagCACGGATTTGAGACTTAACCAGCCAAGGTATGCAACTTTGCCGAACATAATGAAGGCAAAGTCCAAAGTTATTAAGAAAGTTGTCCCTAAAGACCTCGGT

upper sequence: GLYMA10G33110.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0049g00470.t01 (Vitis vinifera), 3'ss of exon 4
--atttcttggtaatagtaattggtgatttaacaagtgtgtttttctccattcttttaaaaccctttctgatatgtgaattttgagctttttcttctttcagCACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAATGAAAGCAAAGTCGAAACCCATAAAAAAATTCACTCCGGAGGAGTTGAAT
        ||     | | ||| |  ||    | ||  |   |  |  | |   | |      | |     ||  |||  |   |  || | | || | |||||| ||| ||||||||||||| ||  ||||||| || || |||||||| ||||||||||| |||||    ||||| || ||||||||  |||| ||||||
cagaaagctgactgcaattatttgccata-ggctagcataaatg-caacttggctctgtgtttcatctcattacttgacctgatattttgtacctcatgcagCACTGATTTGAGACTGAACCAGCCTCGGTATGCAACACTCCCCAACATTATGAAAGCAAAATCGAAGGTAATAAAGAAGTTCACTCCACAGGAATTGAAT

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|22931224|gb|BU548363.1|BU548363
EST:     GTTGACGATGGTATTGAAACCGTGTGTCTAAACTTACCAGCAGTAATAAC                         CACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAAT
genomic: GTTGACGATGGTATTGAAACCGTGTGTCTAAACTTACCAGCAGTAATAACgtaagtttga ... cttctttcagCACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAAT
EST: gi|254321572|gb|GR824889.1|GR824889
EST:     GTTGACGATGGTATTGAAACCGTGTGTCTAAACTTACCAGCAGTAATAAC                         CACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAAT
genomic: GTTGACGATGGTATTGAAACCGTGTGTCTAAACTTACCAGCAGTAATAACgtaagtttga ... cttctttcagCACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAAT
EST: gi|254313596|gb|GR831225.1|GR831225
EST:     GTTGACGATGGTATTGAAACCGTGTGTCTAAACTTACCAGCAGTAATAAC                         CACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAAT
genomic: GTTGACGATGGTATTGAAACCGTGTGTCTAAACTTACCAGCAGTAATAACgtaagtttga ... cttctttcagCACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAAT
EST: gi|58017045|gb|CX703787.1|CX703787
EST:     GTTGACGATGGTATTGAAACCGTGTGTCTAAACTTACCAGCAGTAATAAC                         CACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAAT
genomic: GTTGACGATGGTATTGAAACCGTGTGTCTAAACTTACCAGCAGTAATAACgtaagtttga ... cttctttcagCACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAAT
EST: gi|23731635|gb|BU763954.1|BU763954
EST:     GTTGACGATGGTATTGAAACCGTGTGTCTAAACTTACCAGCAGTAATAAC                         CACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAAT
genomic: GTTGACGATGGTATTGAAACCGTGTGTCTAAACTTACCAGCAGTAATAACgtaagtttga ... cttctttcagCACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAAT
EST: gi|58016732|gb|CX703474.1|CX703474
EST:     GTTGACGATGGTATTGAAACCGTGTGTCTAAACTTACCAGCAGTAATAAC                         CACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAAT
genomic: GTTGACGATGGTATTGAAACCGTGTGTCTAAACTTACCAGCAGTAATAACgtaagtttga ... cttctttcagCACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAAT
EST: gi|151395303|gb|EV265174.1|EV265174
EST:     GTTGACGATGGTATTGAAACCGTGTGTCTAAACTTACCAGCAGTAATAAC                         CACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAAT
genomic: GTTGACGATGGTATTGAAACCGTGTGTCTAAACTTACCAGCAGTAATAACgtaagtttga ... cttctttcagCACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattcttttaaaaccctttctgatatgtgaattttgagctttttcttctttcagCACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAATGAAAGCAAAGTCGAAACCCATAAAAAAATTCACTCCGGAGGAGTTGAAT
                  ttctgat  putative branch site (score: 3)
                                ttttgagctttttctt  putative PPT
      ttttaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttcttggtaatagtaattggtgatttaacaagtgtgtttttctccattcttttaaaaccctttctgatatgtgaattttgagctttttcttctttcagCACCGATCTGAGACTGAACCAACCAAGGTATGCTACTCTTCCCAACATAATGAAAGCAAAGTCGAAACCCATAAAAAAATTCACTCCGGAGGAGTTGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - -attggtg
- - - - - - - - - - - - - - - - -gtgtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatatg