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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttaataataccttttaacactttatagttcttttattggtttgagtaatttccatccaatataatgactgtttgcctttctctttcttttatattagGTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTGATATCATCAACTTTCTTGAAGGGTGTAATTTGACTCTGGAGGATGTTAA

Basic information

species Glycine max
transcript GLYMA19G18340.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G18340.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0040g02910.t01 (Vitis vinifera), 3'ss of exon 1
attttaataataccttttaacac--tttata-gttcttttattggtttgagtaatttccatccaatataatgactgtttgcctttctctttcttttatattagGTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTGATATCATCAACTTTCTTGAAGGGTGTAATTTGACTCTGGAGGATGTTAA
||   ||| |||     | |     || ||| || | | ||     || |  | | | | |   |||||   ||   ||  || ||| | ||| | | || |||||||   ||||| |   ||  |||  ||   ||| |  |  |||  ||||||||  ||||||| |||||||| ||||||||||||||  |||| |||||
atccaaatgatatggaatgattgcattcatatgtgcatgtagactattcaccattgttcttttgatata--tacatattaactgtctttctctctga-atcagGTTTGGTCTATGGGAGATTGTCTGGGATTACAAAACACACATTGAGGACTGATATTCTCAACTTGCTTGAAGGATGTAATTTGACTCTCCAGGACGTTAA
















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|298172811|gb|HO019795.1|HO019795
EST:     TTTGAATTCAACACCCCCTCCTCCTCCGTTCTTTGAGACTGACCATTCAG                         GTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTG
genomic: TTTGAATTCAACACCCCCTCCTCCTCCGTTCTTTGAGACTGACCATTCAGgtactacctt ... tttatattagGTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTG
EST: gi|298163981|gb|HO013626.1|HO013626
EST:     TTTGAATTCAACACCCCCTCCTCCTCCGTTCTTTGAGACTGACCATTCAG                         GTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTG
genomic: TTTGAATTCAACACCCCCTCCTCCTCCGTTCTTTGAGACTGACCATTCAGgtactacctt ... tttatattagGTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTG
EST: gi|9203906|gb|BE330130.1|BE330130
EST:     TTTGAATTCAACACCCCCTCCTCCTCCGTTCTTTGAGACTGACCATTCAG                         GTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTG
genomic: TTTGAATTCAACACCCCCTCCTCCTCCGTTCTTTGAGACTGACCATTCAGgtactacctt ... tttatattagGTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTG
EST: gi|298166366|gb|HO008603.1|HO008603
EST:     TTTGAATTCAACACCCCCTCCTCCTCCGTTCTTTGAGACTGACCATTCAG                         GTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTG
genomic: TTTGAATTCAACACCCCCTCCTCCTCCGTTCTTTGAGACTGACCATTCAGgtactacctt ... tttatattagGTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTG
EST: gi|24135884|gb|BU926394.1|BU926394
EST:     TTTGAATTCAACACCCCCTCCTCCTCCGTTCTTTGAGACTGACCATTCAG                         GTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTG
genomic: TTTGAATTCAACACCCCCTCCTCCTCCGTTCTTTGAGACTGACCATTCAGgtactacctt ... tttatattagGTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTG
EST: gi|9564251|gb|BE473760.1|BE473760
EST:     TTTGAATTCAACACCCCCTCCTCCTCCGTTCTTTGAGACTGACCATTCAG                         GTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTG
genomic: TTTGAATTCAACACCCCCTCCTCCTCCGTTCTTTGAGACTGACCATTCAGgtactacctt ... tttatattagGTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTG
EST: gi|151409938|gb|EV279746.1|EV279746
EST:     TTTGAATTCAACACCCCCTCCTCCTCCGTTCTTTGAGACTGACCATTCAG                         GTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTG
genomic: TTTGAATTCAACACCCCCTCCTCCTCCGTTCTTTGAGACTGACCATTCAGgtactacctt ... tttatattagGTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTG
EST: gi|9204922|gb|BE331146.1|BE331146
EST:     ACACCCCCTCCTCCTCCGTTCTTTGAGACTGACCATTCAG                         GTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTG
genomic: ACACCCCCTCCTCCTCCGTTCTTTGAGACTGACCATTCAGgtactacctt ... tttatattagGTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtaatttccatccaatataatgactgtttgcctttctctttcttttatattagGTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTGATATCATCAACTTTCTTGAAGGGTGTAATTTGACTCTGGAGGATGTTAA
                         ctgtttgcctttctct  CT-rich tract
                                      tctttcttttatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttaataataccttttaacactttatagttcttttattggtttgagtaatttccatccaatataatgactgtttgcctttctctttcttttatattagGTTTGACATATGGTAATCTGCTTGGTGTTCGTAAATATGCGCTGAAAACTGATATCATCAACTTTCTTGAAGGGTGTAATTTGACTCTGGAGGATGTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - -tggtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tccatcc