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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTGCAAGCACTTCTCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactctttcttttgtgtagttgtgtctctactcttgtgaaaagtttcttcttatatcctttatgtgtggaactgccaaagcttaatatattgaaga...

Basic information

species Glycine max
transcript GLYMA06G17470.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G17470.3 (Glycine max), 5'ss of exon 3
lower sequence: Vv17s0000g00610.t01 (Vitis vinifera), 5'ss of exon 3
GAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTGCAAGCACTTCTCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactctttctt--ttgtgtagttgtgtctctactcttgtgaaaagtttcttcttatatcctttatgtgtggaactgccaaagcttaatatattgaaga
|||||| ||||| ||||||||||| ||||| |||||||| |||||  | |||||||| ||||| ||||||||||||||||| || |||||||| || |||||||   |   |  |  |  |       | ||||     || |   |   || || |  | |   |||  |  | | ||| | | | | | |  |||     
GAGCCCTGCACTTACTCTGAAGACAGCACTCCTTTCTGTACAAGCCTTGCTCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttgcttctagtcttcctacattatctccttatttattttagtcttattttcttgttaattaaattagcagctgtctatggtcattccattatc--

upper sequence: GLYMA06G17470.3 (Glycine max), 5'ss of exon 3
lower sequence: PP1S16_326V6.2 (Physcomitrella patens), 5'ss of exon 6
GAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTGCAAGCACTTCTCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactctttcttttgtgtagttgtgtctctactcttgtgaaaagtttcttc-------ttatatcctttatgtgtggaactgccaaagcttaatatattgaaga------------------------------------------------------------------
||| ||||| || ||||| || ||||| || || ||  | || || ||| | ||  | ||  |||||||||||||||||||||| || ||||||||||||||   | ||      ||| ||     | |      |||||  | |   ||||||       || || | | |   | |     |  ||| |   ||||   | ||                                                                    
GAGTCCAGCTCTGACTCTCAAAACTGCCCTCCTCTCCCTTCAGGCTCTTTTATCAACACCAGAGCCTGATGATCCTCAAGATGCTGTTGTGGCACAGCAGgttgaattcccctcattgagtgtacattttgtctttcttgcaatacccttcttcgcaaaaattctaccatgtcattctcatcttatcaatgacaaatactctcaacctagacaagggctcttttgatctctacccttattcacatatgcgtggcatttctcttgtgtttgcag
















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|8402902|gb|BE058536.1|BE058536
EST:     TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|17152827|gb|BM142760.1|BM142760
EST:     CTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: CTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|4397642|gb|AI496639.1|AI496639
EST:     TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         T
genomic: TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcag-
EST: gi|4397642|gb|AI496639.1|AI496639
EST:     TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         T
genomic: TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcag-
EST: gi|151403796|gb|EV273606.1|EV273606
EST:     TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|7028702|gb|AW458485.1|AW458485
EST:     TCTCTGCTACTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAG
genomic: TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|15813074|gb|BI785349.1|BI785349
EST:     TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|298177912|gb|HO021937.1|HO021937
EST:     TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCT
genomic: TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCT
EST: gi|298189934|gb|HO038337.1|HO038337
EST:     TCTCTGCTCCTCAGCCTGATGATCCTCAGGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|298176063|gb|HO015468.1|HO015468
EST:     TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|298189987|gb|HO032108.1|HO032108
EST:     TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|254313570|gb|GR831199.1|GR831199
EST:     TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|298180493|gb|HO022046.1|HO022046
EST:     TCTCTGCTCCTCAGCCTGATGATCCTCAAGACGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGA
genomic: TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGA
EST: gi|58022999|gb|CX709740.1|CX709740
EST:     TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTGCAAGCACTTCTCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactctttcttttgtgtagttgtgtctctactcttgtgaaaagtttcttcttatatcctttatgtgtggaactgccaaagcttaatatattgaaga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG