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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttaaattgcaccaaaagaattatgaatttgcctgtgtttattttaatatgggtcgtaatagaaatcttgaactcatcatatttgttgagctatttgcttgcgttgactgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACATCAGACGCCCTTGGAGGTTCACGTGCAAATCCAGCTAGGAAGCGGGAGAT

Basic information

species Glycine max
transcript GLYMA09G36050.2
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G36050.2 (Glycine max), 3'ss of exon 20
lower sequence: AT3G63460.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaattttaaattgcaccaaaagaattatgaatttgcctgtgtttattttaatatgggtcgtaatagaaatcttgaactcatcatatttgttgagctatttgcttgcgttgactgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACATCAGACGCCCTTGGAGGTTCACGTGCAAATCCAGCTAGGAAGCGGGAGAT
                                  |  | ||      ||| ||  |   | ||       | |    || |  | | |  |  |   ||   ||   ||  ||||  ||||  || || |  ||| |  |  |||| |||||||||||||||||||||||||| || || || |||||  ||||||| ||| |  ||| |||||| |||||
---------------------------------gtatc-gtacgacgtttcattagcaccttatctctgttttgtttctgagtaaagtcatataatgatcacctcttgtaaactgatccagCCCACCAGAAACCTGTGATAGCAACGTTGACAAGGCTTTTCAATGAGACATCGGAAGCACTGGGAGGCGCACGTGCGAATACTACTAAGAAGCGTGAGAT

upper sequence: GLYMA09G36050.2 (Glycine max), 3'ss of exon 20
lower sequence: Vv13s0158g00140.t01 (Vitis vinifera), 3'ss of exon 20
gtaattttaaattgcaccaaaagaattatgaatttgcctgtgtttattttaatatgggtcgtaatagaaatcttgaactcatcatatttgttgagctatttgcttgcgttgactgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACATCAGACGCCCTTGGAGGTTCACGTGCAAATCCAGCTAGGAAGCGGGAGAT
                   | |   |||| || | | |  | ||| | ||| | |   || |  |||  | |||| | || | | |    |||| ||   | ||  | |  | |   ||||  || |||| |||  | ||  |||| |||||||| || |||||||| || ||||| ||||| ||||||||||||||||| ||||| | ||||||||| ||
-------------ttttttatacttttattaaatgggcaatatttgtattattgtta-tcatc-tagtta-cttgcattcttgaaa---attgaccttgctcct--cttctatttctccagCCCAGCAAAGGCCAGTAGTTGCAACATTGACAAGACTGTTCAATGAAACGTCAGAGGCCCTGGGAGGTTCACGTGCAAACCCAGCCAAGAAGCGGGAAAT
















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|19935111|gb|BQ080141.1|BQ080141
EST:     TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTG                         GGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
genomic: TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTGgtaattttaa ... actgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
EST: gi|192300468|gb|FG991480.1|FG991480
EST:     TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTG                         GGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
genomic: TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTGgtaattttaa ... actgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
EST: gi|23735479|gb|BU766023.1|BU766023
EST:     TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTG                         GGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
genomic: TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTGgtaattttaa ... actgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
EST: gi|208330437|gb|GE132270.1|GE132270
EST:     TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTG                         GGCATCAAATG
genomic: TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTGgtaattttaa ... actgtgccagGGCATCAAATG
EST: gi|26047639|gb|CA784361.1|CA784361
EST:     TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTG                         GGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
genomic: TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTGgtaattttaa ... actgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
EST: gi|208143919|gb|GD941550.1|GD941550
EST:     TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTG                         GGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
genomic: TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTGgtaattttaa ... actgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
EST: gi|17963163|gb|BM269915.1|BM269915
EST:     TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTG                         GGCATCAAATGCCTATTGTCACAACTTTGACA
genomic: TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTGgtaattttaa ... actgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACA
EST: gi|23728086|gb|BU762089.1|BU762089
EST:     TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTG                         GGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
genomic: TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTGgtaattttaa ... actgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
EST: gi|21256102|gb|BQ452990.1|BQ452990
EST:     TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTG                         GGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
genomic: TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTGgtaattttaa ... actgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
EST: gi|193488737|gb|FK454502.1|FK454502
EST:     TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTG                         GGCGTCAAATG
genomic: TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTGgtaattttaa ... actgtgccagGGCATCAAATG
EST: gi|9820517|gb|BE556027.1|BE556027
EST:     TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTG                         GGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
genomic: TCCAACTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTGgtaattttaa ... actgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatcttgaactcatcatatttgttgagctatttgcttgcgttgactgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACATCAGACGCCCTTGGAGGTTCACGTGCAAATCCAGCTAGGAAGCGGGAGAT
                                        cgttgac  putative branch site (score: 4)
              atcatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattttaaattgcaccaaaagaattatgaatttgcctgtgtttattttaatatgggtcgtaatagaaatcttgaactcatcatatttgttgagctatttgcttgcgttgactgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACATCAGACGCCCTTGGAGGTTCACGTGCAAATCCAGCTAGGAAGCGGGAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT