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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGAATCCTGTTTGGAATCAAACATTTGACTTTGTTGTTGAGGATGGATTACATGATATGCTAATTGTTGAAGTTTGGGACCACGACACATTCGGAAAGgtaaacaattgtagacgtacttagattgcctttttctaatgtcttgatgactttcagtcaaatggcattgaagtttaaatactaattatgtgggaaatga...

Basic information

species Glycine max
transcript GLYMA17G11800.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G11800.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os04g55220.1 (Oryza sativa), 5'ss of exon 12
CTTGAATCCTGTTTGGAATCAAACATTTGACTTTGTTGTTGAGGATGGATTACATGATATGCTAATTGTTGAAGTTTGGGACCACGACACATTCGGAAAGgtaaa--caattgtagacgtacttagattgcctttttctaatgtcttgatgactttcagtca-----aatggc-attgaagtttaaatactaattatgtgggaaatga
||||||||| |||||||| ||||| ||||| |||||||| || ||||| |||||||||||||| ||  | ||||| |  || || || || ||  | |  ||||   |||||| ||   |  |   ||| |  |   | | || |||| | |  | ||| |       ||  | | |||     |   ||| | |||||       | 
CTTGAATCCAGTTTGGAACCAAACTTTTGATTTTGTTGTCGAAGATGGTTTACATGATATGCTTATGTTGGAAGTATATGATCATGATACTTTTAGTAGAgtaagttcaattgaagtttttatctcattac--tggacgagtggcttgttcaactgcagacgtttgtgataacgactgacaccaaggcactgaatatgtttctgtag-

upper sequence: GLYMA17G11800.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G071163_T01 (Zea mays), 5'ss of exon 12
CTTGAATCCTGTTTGGAATCAAACATTTGACTTTGTTGTTGAGGATGGATTACATGATATGCTAATTGTTGAAGTTTGGGACCACGACACATTCGGAAAGgtaaacaattgtagacgtacttagattgcctttttctaatgtcttgatgactttcagtcaaatggcattgaagtttaaatactaattatgtgggaaatga
|||||| || || ||||||||||| ||||| ||||| ||||| ||||| |||||||| ||||| ||  | ||||| |  || || ||||| ||| | |  ||||       |  |||     || || | | ||  ||     |   |   ||   | ||| ||  | || |   |||        ||||       |  
CTTGAACCCAGTATGGAATCAAACTTTTGATTTTGTCGTTGAAGATGGCTTACATGACATGCTTATGTTGGAAGTATATGATCATGACACTTTCCGTAGAgtaagt-----tcaacggg---agctttcatattcttaccagttgagtagttt---gccaactgcaaatgtaaggtaaccgtcggatatgctttccgtag

upper sequence: GLYMA17G11800.1 (Glycine max), 5'ss of exon 11
lower sequence: AT1G05500.1 (Arabidopsis thaliana), 5'ss of exon 12
CTTGAATCCTGTTTGGAATCAAACATTTGACTTTGTTGTTGAGGATGGATTACATGATATGCTAATTGTTGAAGTTTGGGACCACGACACATTCGGAAAGgtaaac---aattgtagacgtacttagattgcctttttctaatgtcttgatgacttt--cagtcaaatggcattgaagttta----aatactaattatgtgggaaatga-------------------------------------------
|||||| || || ||||| || || ||||| ||||| ||||| || || ||||||||||||||| |  ||||||| |||||||||||||| || |||||||||||    ||  | |     |||   |||   |  || | || |||   | | |    ||     |||   ||   ||||     | || | ||| ||| || | ||                                            
CTTGAACCCGGTATGGAACCAGACTTTTGATTTTGTAGTTGAAGACGGGTTACATGATATGCTAGTCCTTGAAGTCTGGGACCACGACACCTTTGGAAAGgtaaaaccaaaccgcaacaacactgttatttgatggttattat-tctgcgtcattgcaccaaatggatgtttttctcgtttggtttattatttattgtgttggcattgggcattggaaaaatgaaacattgtggctttacttttgtggacag

upper sequence: GLYMA17G11800.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv11s0118g00230.t01 (Vitis vinifera), 5'ss of exon 11
CTTGAATCCTGTTTGGAATCAAACATTTGACTTTGTTGTTGAGGATGGATTACATGATATGCTAATTGTTGAAGTTTGGGACCACGACACATTCGGAAAGgtaaacaattgtagacgtacttagat-tgcctttttctaatgtcttgatgactttcagtcaaatggcattgaagtttaaatactaattatgtgggaaatga
||||||||| |||||||||||||| |||||||||||||||||||||||||| ||||||||||| ||| | ||||| |||||||| |||||||| || |||||||| ||   | |  ||  |||  | ||  ||||||   |    | || |  |  | | || ||||    |   |||| |  |   |  |    | |  |
CTTGAATCCAGTTTGGAATCAAACTTTTGACTTTGTTGTTGAGGATGGATTGCATGATATGCTGATTCTGGAAGTCTGGGACCATGACACATTTGGGAAGgtaaataaacct-gttgtttttatctatgtgtttttcatttactattataagatctaataaactggctcgaacaattaagtgttgcatgagaaatagaaaa

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|208284453|gb|GE086387.1|GE086387
EST:     TACATGATATGCTAATTGTTGAAGTTTGGGACCACGACACATTCGGAAAG                         GACTATATGGGCAGATGCATATTGACGCTTACCAGGGTAATACTGGAAGGG
genomic: TACATGATATGCTAATTGTTGAAGTTTGGGACCACGACACATTCGGAAAGgtaaacaatt ... atgcatgcagGACTATATGGGCAGATGCATATTGACGCTTACCAGGGTAATACTGGAAGGG
EST: gi|6913840|gb|AW395370.1|AW395370
EST:     TACATGATATGCTAATTGTTGAAGTTTGGGACCACGACACATTCGGAAAG                         GACTATATGGGCAGATGCATATTGACGCTTACCAGGGTAATACTGGAAGGG
genomic: TACATGATATGCTAATTGTTGAAGTTTGGGACCACGACACATTCGGAAAGgtaaacaatt ... atgcatgcagGACTATATGGGCAGATGCATATTGACGCTTACCAGGGTAATACTGGAAGGG
EST: gi|20813758|gb|BQ298236.1|BQ298236
EST:     TACATGATATGCTAATTGTTGAAGTTTGGGACCACGACACATTCGGAAAG                         GACTATATGGGCAGATGCATATTGACGCTTACCAGGGTAATACTG
genomic: TACATGATATGCTAATTGTTGAAGTTTGGGACCACGACACATTCGGAAAGgtaaacaatt ... atgcatgcagGACTATATGGGCAGATGCATATTGACGCTTACCAGGGTAATACTG
EST: gi|254342026|gb|GR853163.1|GR853163
EST:     TACATGATATGCTAATTGTTGAAGTTTGGGACCACGACACATTCGGAAAG                         GACTATATGGGCAGATGCATATTGACGCTTACCAGGGTAATACTGGAAAGG
genomic: TACATGATATGCTAATTGTTGAAGTTTGGGACCACGACACATTCGGAAAGgtaaacaatt ... atgcatgcagGACTATATGGGCAGATGCATATTGACGCTTACCAGGGTAATACTGGAA-GG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGAATCCTGTTTGGAATCAAACATTTGACTTTGTTGTTGAGGATGGATTACATGATATGCTAATTGTTGAAGTTTGGGACCACGACACATTCGGAAAGgtaaacaattgtagacgtacttagattgcctttttctaatgtcttgatgactttcagtcaaatggcattgaagtttaaatactaattatgtgggaaatga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG