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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttttcatcctaaaagatagattgaagttgctgcttgcatatgatatgccttgacttttttgcctttgattttaattattatccctctcattcattagGTTCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGAG

Basic information

species Glycine max
transcript GLYMA17G14240.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os08g41460.8 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------------------------------------tttttttcatcctaaaagatagattgaagttgctgcttgca-tatgatatgccttgactt--ttttgcctttgattttaattattatccctctcattcattagGTTCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGAG
                                                                                        |  ||||   | |  | ||   ||     ||| |  | ||| | |  | |   |  |||   |  ||  |||   | ||||   ||    ||   ||||  || ||||||||||| |||||| |||| || ||||||||||||||||| || |||
gtgagaatcatatgacatgatgtcagagatacattttttttttgcattacgccatgtttaatatattttttcttgactagatttatggtcatttttcacttcgatgaagaatcattattgtttttggcagttttgtttatgtgtactaaatactgtgtttatatctaatc--tagatttcgtcttcac-agATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG

upper sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g64020.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------------------------------------------tttttttcatcctaaaagatagattgaagttg--ctgcttgcatatgatatgcctt------gacttt-tttgcctttgattttaattattatccctctcattcatt-agGTTCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGAG-------------------------------------------------
                                                                                |||| |   | |       | | | | |||  ||| ||||     ||    | |      ||||||  ||   ||||       | |||     |  ||| |||| |||||||||||| |||||||  ||||||| |||||||||| | || | | ||                                                   
gtgagttcttttcatctcactcttgcttccttccaatatacctagctagtatgaaataaatattggactgtcagtataccttttactgtccattgtcctggtgggatttgaactggttgcgacgaattcatcctttatcagactttacttatgtttgtcacctctaatttcgatttgcatgcatttagGTTCTTCTTCATCGATGAGTTGACTGGCTTTGAGATCA-ACATATTCCAGGTAAATTCTTTTTCCTTTCTTCCAATTAATTATTCGACTGACTATTTGACA

upper sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g64020.2 (Oryza sativa), 3'ss of exon 4
------------------------------------------------------------------------------tttttttcatcctaaaagatagattgaagttg--ctgcttgcatatgatatgcctt------gacttt-tttgcctttgattttaattattatccctctcattcatt-agGTTCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGAG
                                                                                |||| |   | |       | | | | |||  ||| ||||     ||    | |      ||||||  ||   ||||       | |||     |  ||| |||| |||||||||||| |||||||  ||||||| |||||||||| | || | | ||  
gtgagttcttttcatctcactcttgcttccttccaatatacctagctagtatgaaataaatattggactgtcagtataccttttactgtccattgtcctggtgggatttgaactggttgcgacgaattcatcctttatcagactttacttatgtttgtcacctctaatttcgatttgcatgcatttagGTTCTTCTTCATCGATGAGTTGACTGGCTTTGAGATCA-ACATATTCCAG--

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|193499357|gb|FK462104.1|FK462104
EST:     TTGAAGATGTTCCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATT                         GTTCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGA
genomic: TTGAAGATGTTCCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATTgtaagtagtt ... cattcattagGTTCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGA
EST: gi|9258401|gb|BE346548.1|BE346548
EST:     TTGAAGATGTTCCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATT                         GTTCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGA
genomic: TTGAAGATGTTCCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATTgtaagtagtt ... cattcattagGTTCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGA
EST: gi|9259613|gb|BE347760.1|BE347760
EST:     TTGAAGATGTTCCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATT                         GTTCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGA
genomic: TTGAAGATGTTCCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATTgtaagtagtt ... cattcattagGTTCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGA
EST: gi|192317109|gb|FK007862.1|FK007862
EST:     GCTGAACGTCCCGGCTACTGGGATTGCATTAGGATT                         GTTCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGA
genomic: GCTGAACGTCCCGGCTACTGTGATTGCATTAGGATTgtaagtagtt ... cattcattagGTTCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgccttgacttttttgcctttgattttaattattatccctctcattcattagGTTCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGAG
                          ttttaat  putative branch site (score: 3)
                                   ttatccctctcattc  putative PPT
            ttttttgcctttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttttcatcctaaaagatagattgaagttgctgcttgcatatgatatgccttgacttttttgcctttgattttaattattatccctctcattcattagGTTCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - -aaaagata
- - - - - - - - - - - - - - - - - gcttgca
- - - - - - - - - - - - - - - - - - - - - - - tatgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccctct