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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggaacaaaataattagtatttatattagcctgtataagttaattcagtggttttggcatgacttttgcagtattttatgccctaattatttcaacttcctttcagTGGTATGAGAAATTTACTGAAGTTGATGAGGTTATACCTGTTAGTGCCAAATATGGTCAGGGGGTTGAAGATGTCAAGGACTGGATACTGTCAAAGCTTC

Basic information

species Glycine max
transcript GLYMA16G24870.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G24870.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G66470.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------------------------------gttggaacaaaat---aattagtatttatattagcctgtataagttaattcagtggttttggcatgacttttgcagtattttatgccc--taattatttcaacttcctttcagTGGTATGAGAAATTTACTGAAGTTGATGAGGTTATACCTGTTAGTGCCAAATATGGTCAGGGGGTTGAAGATGTCAAGGACTGGATACTGTCAAAGCTTC
                                                                    | |||  || |   | |        ||  |   || || |  | |  |||    ||   |      | ||||  | || | |||    ||  |  | ||||| |||| ||||||||||| |||||||| || |||||||| ||||||||||| ||||| || ||||| || ||  | || |||||||| || |||||| | || || ||||
gtgagtatgctgtcgttgctatccttgaaccttggtaatactgtcctgttattaaaatcccaccattctagaatgaacttgcagtggtggaagatgcttcactataaacttgagatcaagatttggagtcatggtattgctatgttctttgcttaatagatgctgcaact-ccttgcagTGGTATGAAAAATTTACGGATGTTGATGAAGTTATACCTGTAAGTGCAAAGTATGGACATGGAATAGAGGATGTCAAAGAGTGGATATTATCCAAACTTC

upper sequence: GLYMA16G24870.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0023g02120.t01 (Vitis vinifera), 3'ss of exon 4
gttggaacaaaataattagtatttatattagcctgtataagttaattcagtggttttggcatgact-tttgcagtattttatgccctaattatttcaacttcctttcagTGGTATGAGAAATTTACTGAAGTTGATGAGGTTATACCTGTTAGTGCCAAATATGGTCAGGGGGTTGAAGATGTCAAGGACTGGATACTGTCAAAGCTTC
      ||  |    ||| ||  |  ||||  || |     |||||   |  ||  |   ||   |  ||  |    ||||| |   |    | |||  |||||||||||||||||||||||| |  || ||||||||||| ||||| || |||||||| |||||||| || || || ||||||||||| |||||| ||||||| ||||
------acgcatatgttattagat-catta--ctatgcttcttaatcatggtgtgctaaaattcttactttgaactgtttattctgaatgagtatcattttcctttcagTGGTATGAGAAATTCATAGATGTTGATGAGGTCATACCAGTGAGTGCCAAGTATGGTCAAGGAGTAGATGATGTCAAGGATTGGATATTGTCAAAACTTC
















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|58018987|gb|CX705729.1|CX705729
EST:     TAAACAAGAAGGACCTTGTTAAACCTGGTGAACTTGCAAAGAAACTTGAG                         TGGTATGAGAAATTTACTGAAGTTGATGAGGTTATACCTGTTAGTGCCAAA
genomic: TAAACAAGAAGGACCTTGTTAAACCTGGTGAACTTGCAAAGAAACTTGAGgttggaacaa ... ttcctttcagTGGTATGAGAAATTTACTGAAGTTGATGAGGTTATACCTGTTAGTGCCAAA
EST: gi|58019195|gb|CX705937.1|CX705937
EST:     TAAACAAGAAGGACCTTGTTAAACCTGGTGAACTTGCAAAGAAACTTGAG                         TGGTATGAGAAATTTACTGAAGTTGATGAGGTTATACCTGTTAGTGCCAAA
genomic: TAAACAAGAAGGACCTTGTTAAACCTGGTGAACTTGCAAAGAAACTTGAGgttggaacaa ... ttcctttcagTGGTATGAGAAATTTACTGAAGTTGATGAGGTTATACCTGTTAGTGCCAAA
EST: gi|9258756|gb|BE346903.1|BE346903
EST:     TAAACAAGAAGGACCTTGTTAAACCTGGTGAACTTGCAAAGAAACTTGAG                         TGGTATGAGAAATTTACTGAAGTTGATGAGGTTATACCTGTTAGTGCCAAA
genomic: TAAACAAGAAGGACCTTGTTAAACCTGGTGAACTTGCAAAGAAACTTGAGgttggaacaa ... ttcctttcagTGGTATGAGAAATTTACTGAAGTTGATGAGGTTATACCTGTTAGTGCCAAA
EST: gi|214007313|gb|DB985849.1|DB985849
EST:     TAAACCTGGTGAACTTGCAAAGAAACTTGAG                         TGGTATGAGAAATTTACTGAAGTTGATGAGGTTATACCTGTTAGTGCCAAA
genomic: TAAACCTGGTGAACTTGCAAAGAAACTTGAGgttggaacaa ... ttcctttcagTGGTATGAGAAATTTACTGAAGTTGATGAGGTTATACCTGTTAGTGCCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggcatgacttttgcagtattttatgccctaattatttcaacttcctttcagTGGTATGAGAAATTTACTGAAGTTGATGAGGTTATACCTGTTAGTGCCAAATATGGTCAGGGGGTTGAAGATGTCAAGGACTGGATACTGTCAAAGCTTC
                             ccctaat  putative branch site (score: 3)
                                      tttcaacttcctttc  putative PPT
                                taattatttcaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggaacaaaataattagtatttatattagcctgtataagttaattcagtggttttggcatgacttttgcagtattttatgccctaattatttcaacttcctttcagTGGTATGAGAAATTTACTGAAGTTGATGAGGTTATACCTGTTAGTGCCAAATATGGTCAGGGGGTTGAAGATGTCAAGGACTGGATACTGTCAAAGCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG