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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctcttttattttactttatttaatgcttccatttacctgcacctgattcttttccttgtatgttattgtagTCAGCGAGCTGTTAAAACTGCATTGTGGTGTAACTTTCTTGTTTTTTCACTCAAGTTTGGAGTATGGTTAGCTTCCTCTAGTCATGTTATGTTAGCTGAA

Basic information

species Glycine max
transcript GLYMA08G23740.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G23740.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g23180.1 (Oryza sativa), 3'ss of exon 2
---------------------gtctcttttattttactttattta-atgctt--ccatttacctgcacctgattcttttccttgt---atgttattgtagTCAGCGAGCTGTTAAAACTGCATTGTGGTGTAACTTTCTTGTTTTTTCACTCAAGTTTGGAGTATGGTTAGCTTCCTCTAGTCATGTTATGTTAGCTGAA
                      ||  |     |||   || || | | ||||  | |||    |     | ||  |  | ||  |   |||| ||   || || ||||| ||||| || ||| |||||||||| |||||||| |||||  | |||||||| |||||| |  |  | ||||||||||||||| ||||||| 
gtccaatattacgattagttaatcattacatatttggattgttcacaagcttacctattacattttgtttcatgttgatgctaatggaatgtgatctcagCCATCGAGCGGTTAACACAGCACTGTGGTGTAATTTTCTTGTCTTTTCGTTGAAGTTTGGTGTATGGCTTTCAACATCTAGTCATGTTATGCTAGCTGAG

upper sequence: GLYMA08G23740.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0054g00220.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------gtctcttttattttactttatttaatgcttccatttacctgcacctgattcttttccttgtatgtt-attgtagTCAGCGAGCTGTTAAAACTGCATTGTGGTGTAACTTTCTTGTTTTTTCACTCAAGTTTGGAGTATGGTTAGCTTCCTCTAGTCATGTTATGTTAGCTGAA
                          |    ||   |   |||||     ||    || |||   |   | |   | | | |||   ||||| ||| ||| || ||||| || | ||||||||| ||||||||||| || || ||||| ||||||||||| || |||||| |  ||||||| ||||||||||| ||||||
tgagccttttttgcaattagggaccagaaatttagctcccacttttcaccatctgaccttttttgttttcttttgtttctgcctaacatgtttattctagCCAACGAGCAGTCAGAACTGCATTATGGTGTAACTTCCTCGTCTTTTCTCTCAAGTTTGGGGTCTGGTTAACAACCTCTAGCCATGTTATGTTGGCTGAA
















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|192300735|gb|FG991117.1|FG991117
EST:     ACCAGGGCTAAGCCAGCAACCACCAACATTGAATTCAACGATCACCACAG                         TCAGCGAGCTGTTAAAACTGCATTGTGGTGTAACTTTCTTGTTTTTTCACT
genomic: ACCAGGGCTAAGCCAGCAACCACCAACATTGAATTCAACGATCACCACAGgtctctttta ... gttattgtagTCAGCGAGCTGTTAAAACTGCATTGTGGTGTAACTTTCTTGTTTTTTCACT
EST: gi|19347131|gb|BM892011.1|BM892011
EST:     ACCAGGGCTAAGCCAGCAACCACCAACATTGAATTCAACGATCACCACAG                         TCAGCGAGCTGTTAAAACTGCATTGTGGTGTAACTTTCTTGTTTTTTCACT
genomic: ACCAGGGCTAAGCCAGCAACCACCAACATTGAATTCAACGATCACCACAGgtctctttta ... gttattgtagTCAGCGAGCTGTTAAAACTGCATTGTGGTGTAACTTTCTTGTTTTTTCACT
EST: gi|151393656|gb|EV263531.1|EV263531
EST:     ACCAGGGCTAAGCCAGCAACCGCCAACATTGAATTCAACGATCACCACAG                         TCAGCGAGCTGTTAAAACTGCATTGTGGTGTAACTTTCTTGTTTTTTCACT
genomic: ACCAGGGCTAAGCCAGCAACCACCAACATTGAATTCAACGATCACCACAGgtctctttta ... gttattgtagTCAGCGAGCTGTTAAAACTGCATTGTGGTGTAACTTTCTTGTTTTTTCACT
EST: gi|208089109|gb|GD887000.1|GD887000
EST:     ACCAGGGCTAAGCCAGCAACCACCAACATTGAATTCAACGATCACCACAG                         TCAGCGAGCTGTTAAAACTGCATTGTGGTGTAACTTTCTTGTTTTTTCACT
genomic: ACCAGGGCTAAGCCAGCAACCACCAACATTGAATTCAACGATCACCACAGgtctctttta ... gttattgtagTCAGCGAGCTGTTAAAACTGCATTGTGGTGTAACTTTCTTGTTTTTTCACT
EST: gi|208039647|gb|GD838459.1|GD838459
EST:     ACCAGGGCTAAGCCAGCAACCACCAACATTGAATTCAACGATCACCACAG                         TCAGCGAGCTGCTAAAACTGCATTGTGGTGTAACTTTCTTGTTTTCTCACT
genomic: ACCAGGGCTAAGCCAGCAACCACCAACATTGAATTCAACGATCACCACAGgtctctttta ... gttattgtagTCAGCGAGCTGTTAAAACTGCATTGTGGTGTAACTTTCTTGTTTTTTCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttaatgcttccatttacctgcacctgattcttttccttgtatgttattgtagTCAGCGAGCTGTTAAAACTGCATTGTGGTGTAACTTTCTTGTTTTTTCACTCAAGTTTGGAGTATGGTTAGCTTCCTCTAGTCATGTTATGTTAGCTGAA
                        acctgat  putative branch site (score: 4)
                                          tatgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctcttttattttactttatttaatgcttccatttacctgcacctgattcttttccttgtatgttattgtagTCAGCGAGCTGTTAAAACTGCATTGTGGTGTAACTTTCTTGTTTTTTCACTCAAGTTTGGAGTATGGTTAGCTTCCTCTAGTCATGTTATGTTAGCTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA