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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGTCATTTTATGgtactttcatgtacacactgaacctatatgcttaattgtaccttgccacttgattctaatttagttttgcatatgcttgcag

Basic information

species Glycine max
transcript GLYMA02G43930.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G43930.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 7
GTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGTCATTTTATGgtactt--tcatgtacacactgaacctatatgcttaattgtaccttgccacttgattctaatt-tagttttg-catatgcttgcag-------------
|| || || || || ||  || |||||||||| ||||||||||| ||||| || ||||| ||||| ||||| ||||| || || || || ||||| |||||||  |    | ||  |  ||| ||||   | ||| |||||   ||  |  || ||  | ||| ||| |||  ||| |  || |               
GTGGAAGGGACAATTCAACAGCTATTTGAAGGTCATCATATGAATTATATTGAGTGCATTAATGTTGACTACAAATCTACAAGGAAAGAATCATTCTATGgtaggtgacaaggtgaaatctggaccttgtttctttattgt-ttttatctattcatcatgattgtagatttatcatgtattttcgtaactcttttctag

upper sequence: GLYMA02G43930.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 7
GTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGTCATTTTATGgtactttcatgtacacactgaacctatatgcttaattgtaccttgccacttgattctaatttagttttgcatatgcttgcag
|| || ||||| ||  |  | ||||||||||| || || || ||||||||||| ||||| ||||| || |||||||| |  ||||| || || ||||||||||   |  | | |||| ||||| |  |   | | || ||  ||    |||  |  |  | ||   |||||           
GTGGAAGGAACAATTGAACAATTATTTGAAGGCCACCACATAAACTATATCGAGTGCATTAATGTTGATTATAAATCTAACAGAAAAGAATCCTTTTATGgtaagct--ttttcacattgaacattcagtatcatttttaatttagtgcttactcatgttataacattgcag----------

upper sequence: GLYMA02G43930.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 5'ss of exon 7
GTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGTCATTTTATGgtactttcatgtacacactgaacctatatgcttaattgtaccttgccacttgattctaatttagttttgcatatgcttgcag
|| ||||| ||||||||| |||||||||||||||| ||||||||||| || |||||||||||||||||||| ||||| || || ||||||||||||||||||||||   | || |          | |||| | |||     |      || |||  ||  ||  || |  | || | ||||
GTGGAGGGCACTATACAGCAGTTATTTGAAGGGCACCATATGAACTACATTGAATGCATCAATGTGGACTACAAATCTACAAGGAAGGAGTCATTTTATGgtacttattt-tatatttatggttgaaatgcctgatttagtgtctgtttttcattgcaaaataaatt-gtttgtg-tggcag

upper sequence: GLYMA02G43930.1 (Glycine max), 5'ss of exon 7
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 5'ss of exon 7
GTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGTCATTTTATGgtactttcatgtacacactgaacctatatgcttaattgt-accttgccacttgattctaatttagttttgcatatgcttgcag--------------------
|| ||||| || || ||| |  | || ||||||||||| |||||||| || || ||||||||||| || |||||||||||  | || ||||| || ||||||||    ||| |     ||||  || | ||   || |  || ||| || |  |   | |||   | ||   | |  ||| |                     
GTCGAGGGCACAATCCAGCAACTGTTCGAAGGGCATCACATGAACTACATAGAGTGCATCAATGTTGATTATAAATCAACACGGAAAGAGTCTTTCTATGgtacgactatgca---gttgaagttagaagcaggatggagactttgacaatcaagaatgattctttattttgtttcattgaacatctgtcttagaaagaggag

upper sequence: GLYMA02G43930.1 (Glycine max), 5'ss of exon 7
lower sequence: PP1S104_2V6.1 (Physcomitrella patens), 5'ss of exon 7
GTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGTCATTTTATGgtactttcatgtacac---actgaaccta----tatgcttaattgtaccttgccacttgattc----taatttagttttgcatatgcttgcag-----------------------------------------------
|| ||||| || ||||| ||  | |||||||| ||||||||||| |||||||||||||||||||| || | ||| || ||| | |||||||| | |||||||||  |  |    ||   | |||  |||    | | |  |       || | ||  ||  |     |  |   | ||||   || ||| |                                                 
GTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGTCCTATTATGgtacacttcttctgacttgattgactctaatgttgtcccgagacaacactgggcatgtggcttatcatggtcgggctttgttgat-cttccgtacgctgctagatttcactttaataatatgtgaagtaaacgttggcag

upper sequence: GLYMA02G43930.1 (Glycine max), 5'ss of exon 7
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 5'ss of exon 7
GTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGTCATTTTATGgtactttcatgtacacactgaacctatatgcttaattgtaccttgccacttgattctaatttagttttgcatatgct-tgcag-------------------
|||||||| || || ||  |  | |||||||| |||||||||||||| || || || |||||||| ||||| || |||||  | || |||||||||||||||||  |     |    |||         |  |    | | |||   |  ||||  ||||||| |     |||   | | ||                    
GTTGAGGGCACAATTCAACAACTGTTTGAAGGTCATCATATGAACTACATAGAGTGTATCAATGTTGACTACAAGTCAACACGCAAAGAGTCATTTTATGgtacggtttcacagtttctgtttgagatagggtgg--ggatcttcgtatgtgatcttaatttattacgtaataaattattcattgaccgttgtctgagttga

upper sequence: GLYMA02G43930.1 (Glycine max), 5'ss of exon 7
lower sequence: EFJ18164 (Selaginella moellendorffii), 5'ss of exon 5
GTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGTCATTTTATGgtactttcatgtacacactgaacctatatgcttaattgtaccttgccacttgattctaatttagttttgcatatgcttgcag
||||| || || |||||| || | || ||||| || |||||||| ||||| |||||||||||||||||||| || || ||| ||||||| || |||||||||   ||  || |    | | |  |  | ||  |||  |      ||  | || |   |                       
GTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCACCATATGAATTATATTGAATGCATCAATGTGGACTACAAGTCCACTCGAAAGGAATCTTTTTATGgtttgtttctgcattttcgggaatttcaggc--aatattgttaacccgttggaataacag----------------------

upper sequence: GLYMA02G43930.1 (Glycine max), 5'ss of exon 7
lower sequence: EFJ19227 (Selaginella moellendorffii), 5'ss of exon 7
GTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGTCATTTTATGgtactttcatgtacacactgaacctatatgctta-attgtaccttgccacttgattctaatttagttttgcatatgcttgcag
||||| ||||| || ||  || | ||||| || |||||||||||||| |||||||||||||| || || || ||||| ||  | || ||||||||||||||||  || || |  |   |   |     | || | |  ||   || |                                    
GTTGAAGGAACGATTCAACAGCTTTTTGAGGGTCATCATATGAACTACATCGAATGCATCAACGTCGATTACAAATCTACGCGGAAAGAGTCATTTTATGgtatgttgatattgag--tagtctgggcttctcacaacgtgtgttacag----------------------------------

upper sequence: GLYMA02G43930.1 (Glycine max), 5'ss of exon 7
lower sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 5
GTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGTCATTTTATGgtactttcatgtacacactgaacctatatgcttaattgtaccttgccacttgattctaatttagttttgcatatgcttgcag
||||| || || |||||| || | || ||||| ||||||||||| ||||| ||||||||||||||||||||||| || ||| ||||||| || |||||||||   ||  || |    | | |  |  | ||  |||  |      ||  | || |   |                       
GTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAATCTTTTTATGgtttgtttctgcattttcgggaattgcaggc--aatattgttaacccgttggaataacag----------------------

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|254342408|gb|GR858570.1|GR858570
EST:     CGAATGCATCAATGTTGACTATAAATCAACTAGAAAGGAGTCATTTTATG                         ACCTTCAGCTTGATGTGAAGGGCTGTCCTGATGTTTATGCTTCCTTTGACA
genomic: CGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGTCATTTTATGgtactttcat ... atgcttgcagACCTTCAGCTTGATGTGAAAGGCTGTCCTGATGTTTATGCTTCCTTTGACA
EST: gi|120496383|gb|EH224550.1|EH224550
EST:     CGAATGCATCAATGTTGACTATAAATCAACTAGAAAGGAGTCATTTTATG                         ACCTTCAGCTTGATGTGAAGGGATGTCCTGATGTTTATGCTTCCTTTGACA
genomic: CGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGTCATTTTATGgtactttcat ... atgcttgcagACCTTCAGCTTGATGTGAAAGGCTGTCCTGATGTTTATGCTTCCTTTGACA
EST: gi|254342407|gb|GR858569.1|GR858569
EST:     CGAATGCATCAATGTTGACTATAAATCAACTAGAAAGGAGTCATTTTATG                         ACCTTCAGCTTGATGTGAAGGGCTGTCCTGATGTTTATGCTTCCTTTGACA
genomic: CGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGTCATTTTATGgtactttcat ... atgcttgcagACCTTCAGCTTGATGTGAAAGGCTGTCCTGATGTTTATGCTTCCTTTGACA
EST: gi|209717383|gb|BW659059.1|BW659059
EST:     CGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGTCATTTTATG                         ACCTTCAGCTTGATGTGAAGGGCTGTCCTGATGTTTATGCTTCCTTTGACA
genomic: CGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGTCATTTTATGgtactttcat ... atgcttgcagACCTTCAGCTTGATGTGAAAGGCTGTCCTGATGTTTATGCTTCCTTTGACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGTCATTTTATGgtactttcatgtacacactgaacctatatgcttaattgtaccttgccacttgattctaatttagttttgcatatgcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG