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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGTGTGGTGGGACTATGTCACTGATTTTCAAATTAGATGCCCCATGAAGGAGAAGAAGTACAATAAGGAATGTGCAAATGCTGTTATTAAATCACTGGgtaaataaatcaccatcgcacgctatttttatcttacagcatggctgatgatgactttactattacgtttgttcgatatctgcag

Basic information

species Glycine max
transcript GLYMA01G45380.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G45380.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os10g20630.1 (Oryza sativa), 5'ss of exon 2
TGGGTGTGGTGGGACTATGTCACTGATTTTCAAATTAGATGCCCCATGAAGGAGAAGAAGTACAATAAGGAATGTGCAAATGCTGTTATTAAATCACTGGgtaaataaatc----accatcgcacgctatttttatcttacagcatggctgatgatgact-ttactattacgttt----gttcgatatctgcag------
||| | |||||||| ||||| ||||||||||| || || ||||| |||||||| || ||||| || ||| |||||||| |  |||| || |||||||| |||   |   ||          |     |   |||   | |    | |  ||||  |     |||||  |||||       || ||  | || |       
TGGATCTGGTGGGATTATGTAACTGATTTTCACATAAGGTGCCCAATGAAGGACAAAAAGTATAACAAGAAATGTGCAGAAACTGTCATCAAATCACTAGgttggttcttcttttgtttctgagactttcctttgcataatgataagcatgattgtagtaattacttgtacgtacttaaattggacgtttgaaatatgcc

upper sequence: GLYMA01G45380.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G303631_T01 (Zea mays), 5'ss of exon 2
TGGGTGTGGTGGGACTATGTCACTGATTTTCAAATTAGATGCCCCATGAAGGAGAAGAAGTACAATAAGGAATGTGCAAATGCTGTTATTAAATCACTGGgta-aataaatcaccatcgcacgctatttttatcttacagcatggctgatgatgactttactattacgtttgttcgatatctgcag---------------
||||| |||||||| ||||| ||||||||||| || || || || |||||||||||||||||||||||  |||||||| |  |||| || |||||||| |||    |   |   | |  | ||||   || |   | || ||| |   ||      | ||  |  | ||||||  | | |   ||                
TGGGTCTGGTGGGATTATGTGACTGATTTTCACATAAGGTGTCCAATGAAGGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccgttttctttcctcgcttacttaagaatcca-cattgtatatatattttgtaaaaacatgtttgtaagtttttaacatgcttggcacccactt

upper sequence: GLYMA01G45380.1 (Glycine max), 5'ss of exon 2
lower sequence: AT2G14720.1 (Arabidopsis thaliana), 5'ss of exon 2
TGGGTGTGGTGGGACTATGTCACTGATTTTCAAATTAGATGCCCCATGAAGGAGAAGAAGTACAATAAGGAATGTGCAAATGCTGTTATTAAATCACTGGgtaaataaatcaccatcgcacgctatttttatcttacagcatggctgatgatgactttactattacgtttgttcgatatctgcag------
||||| |||||||| ||||| |||||||| || || ||||| || ||||||||||| || ||||| || || |||||  |  |||| || ||||| || ||| | |   ||  | |  || | | |   ||  | | || |  ||   |  ||     |  |   | | | ||| || | ||         
TGGGTCTGGTGGGATTATGTTACTGATTTCCAGATCAGATGTCCAATGAAGGAGAAAAAATACAACAAAGATTGTGCTGAGTCTGTAATCAAATCTCTTGgtgagtgtttcttc-ttaca-ggtctcgatagttgaaagaaaagcaatttttgggagaatgaggtcatattttctatgtatgtccctacag

upper sequence: GLYMA01G45380.1 (Glycine max), 5'ss of exon 2
lower sequence: AT2G14740.2 (Arabidopsis thaliana), 5'ss of exon 2
TGGGTGTGGTGGGACTATGTCACTGATTTTCAAATTAGATGCCCCATGAAGGAGAAGAAGTACAATAAGGAATGTGCAAATGCTGTTATTAAATCACTGGgtaaataaatcaccatcgcacgctatttttatctt-acagcatggctgatgatga--ctttactattacgtttgttcgatatctgcag
||||| |||||||| ||||| |||||||| || || ||||| ||||||||||||||||| ||||||||||| |||||  || | ||||| ||||| || ||| | |   |  |  |   | || | ||  |     |||   | |  ||  ||||  | |   || || || | | |           
TGGGTCTGGTGGGATTATGTTACTGATTTCCAGATCAGATGTCCCATGAAGGAGAAGAAATACAATAAGGAGTGTGCTGATTCCGTTATCAAATCTCTTGgtgagtgtgt--ctgttatatgcaaattaaagaaagacaattttggggagaatgatgcatagttactatgtctttacag---------

upper sequence: GLYMA01G45380.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv03s0091g00740.t01 (Vitis vinifera), 5'ss of exon 2
TGGGTGTGGTGGGACTATGTCACTGATTTTCAAATTAGATGCCCCATGAAGGAGAAGAAGTACAATAAGGAATGTGCAAATGCTGTTATTAAATCACTGGgtaaataaatcaccatcgcacgctatttttatc----ttacagcatggctgatgatgactttactattacgtttgttcgatatctgcag
|||||||||||||||||||| |||||||||||||||||||| ||||||| | |||| || ||||| |||||||||||  |  |||| ||   ||| || |||||||||   | | | |||  || |  || |     |  |||      |||| |  | |||  |||| |   |||| | | |   |||
TGGGTGTGGTGGGACTATGTGACTGATTTTCAAATTAGATGTCCCATGAGGAAGAAAAAATACAACAAGGAATGTGCTGAAACTGTCATCGCATCTCTAGgtaaataatatatccttgcatcctctgattgtaaggataccagtcatattgattaataattttttatttctaatgttggttctgcacag

upper sequence: GLYMA01G45380.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ06539 (Selaginella moellendorffii), 5'ss of exon 2
TGGGTGTGGTGGGACTATGTCACTGATTTTCAAATTAGATGCCCCATGAAGGAGAAGAAGTACAATAAGGAATGTGCAAATGCTGTTATTAAATCACTGGgtaaataaatcaccatcgcacgctatttttatcttacagcatggctgatgatgactttactattacgtttgttcgatatctgcag
||||||||||||||||| || || || ||||| || || || || |||||||| |||||||| || ||||| |||||  | |  ||  | || ||  || |||| |         | |||  |  |||   | |  | || |  || |  |||| |||  | | |                    
TGGGTGTGGTGGGACTACGTGACCGACTTTCAGATCAGGTGTCCGATGAAGGATAAGAAGTATAACAAGGATTGTGCCGAGGAAGTCTTGAAGTCGTTGCgtaagt------tttttgcatacattttccttttcgcggc-tcacttac-atgagtttcatttcag-------------------

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|6724788|gb|AW309187.1|AW309187
EST:     GGAGAAGAAGTACAATAAGGAATGTGCAAATGCTGTTATTAAATCACTGG                         GTCTCAATACGGAAAAGATTGAAAAGTGCATGGGAGATCCAGACGCCGATA
genomic: GGAGAAGAAGTACAATAAGGAATGTGCAAATGCTGTTATTAAATCACTGGgtaaataaat ... atatctgcagGTCTCAATACGGAAAAGATTGAAAAGTGCATGGGAGATCCAGACGCCGATA
EST: gi|193548893|gb|FK508364.1|FK508364
EST:     ACAATAAGGAATGTGCAAATGCTGTTATTAAATCACTGG                         GTCTCAATACGGAAAAGATTGAAAAGTGCATGGGAGATCCAGACGCCGATA
genomic: ACAATAAGGAATGTGCAAATGCTGTTATTAAATCACTGGgtaaataaat ... atatctgcagGTCTCAATACGGAAAAGATTGAAAAGTGCATGGGAGATCCAGACGCCGATA
EST: gi|193513745|gb|FK468675.1|FK468675
EST:     TACAATAAGGAATGTGCAAATGCTGTTATTAAATCACTGG                         GTCTCAATACGGAAAAGATTGAAAAGTGCATGGGAGATCCAGACGCCGATA
genomic: TACAATAAGGAATGTGCAAATGCTGTTATTAAATCACTGGgtaaataaat ... atatctgcagGTCTCAATACGGAAAAGATTGAAAAGTGCATGGGAGATCCAGACGCCGATA
EST: gi|193610199|gb|FK565763.1|FK565763
EST:     TACAATAAGGAATGTGCAAATGCTGTTATTAAATCACTGG                         GTCTCAATACGGAAAAGATTGAAAAGTGCATGGGAGATCCAGACGCCGATA
genomic: TACAATAAGGAATGTGCAAATGCTGTTATTAAATCACTGGgtaaataaat ... atatctgcagGTCTCAATACGGAAAAGATTGAAAAGTGCATGGGAGATCCAGACGCCGATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGTGTGGTGGGACTATGTCACTGATTTTCAAATTAGATGCCCCATGAAGGAGAAGAAGTACAATAAGGAATGTGCAAATGCTGTTATTAAATCACTGGgtaaataaatcaccatcgcacgctatttttatcttacagcatggctgatgatgactttactattacgtttgttcgatatctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT