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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtatatcatttatacaagataaatctgaataatctagtaggattatgacattgtttattcattttgtagGAACATGTTGAAGGGTATCATGAATTGTCTGCAAAGACAAAAATATTCTTTTCCACAGCAGTTGCAAAATGGGATGCGGATTTCTATGTCAAAGTGGATG

Basic information

species Glycine max
transcript GLYMA13G02420.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G02420.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g27950.1 (Oryza sativa), 3'ss of exon 6
-----------------------------------------------------gtaatgtatatcatttataca--agataaatctgaataatctagtag-gattatgacattgt--ttattcattt-tgtagGAACATGTTGAAGGGTATCATGAATTGTCTGCAAAGACAAAAATATTCTTTTCCACAGCAGTTGCAAAATGGGATGCGGATTTCTATGTCAAAGTGGATG
                                                       ||   | |||  || |||      |    ||| |     || ||  | ||||     ||     |  ||| | ||||||| ||||||||||||||||| ||  | ||||||||||| || |||||||||||||| || || |||  ||||||||| |||||||||||||| |||||||
gtatggtgacatccaccaaaagtagaagcacatcattctttacctatttctgttaaaccaaaatctgttttactgtgattggggctgtagtccatactaatgtttattctgctgcaaccacacatgtatgtagGACCATGTTGAAGGGTATCACGAGCTATCTGCAAAGACCAAGATATTCTTTTCCACTGCTGTGGCATTATGGGATGCTGATTTCTATGTCAAGGTGGATG

upper sequence: GLYMA13G02420.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 6
------------gtaatgtatatca----tttatacaagataaatctgaataatctagtaggattatgacat-tgtttattcattttgt-agGAACATGTTGAAGGGTATCATGAATTGTCTGCAAAGACAAAAATATTCTTTTCCACAGCAGTTGCAAAATGGGATGCGGATTTCTATGTCAAAGTGGATG
             |  ||  | |||    |||  ||| | |     ||||  | | | |   ||| |  ||| |||| |||  ||     |||| ||||| ||||||||||||||| | || || |||||||| || ||||| || ||||||||||  |  |||||||| || || ||||| || || ||||
gtaagtaatgctttcctgcctttcaaagctttgaacatgctttccttgaaccagc-actgacattttaccatgtgttcatttgttcaaccagGACCATGTAGAAGGGTATCATGAACTCTCAGCTAAGACAAAGATTTTCTTCTCTACAGCAGTTGGTATTTGGGATGCTGACTTTTATGTGAAGGTTGATG

upper sequence: GLYMA13G02420.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ20056 (Selaginella moellendorffii), 3'ss of exon 7
gtaatgtatatcatttatacaagataaatctgaataatctagtaggattatgacattgtttattcattttgtagGAACATGTTGAAGGGTATCATGAATTGTCTGCAAAGACAAAAATATTCTTTTCCACAGCAGTTGCAAAATGGGATGCGGATTTCTATGTCAAAGTGGATG
                        ||||| ||    ||   ||  ||   | || || |   ||| || ||||||| ||||||||||| ||||  || |||||||| || || ||||| | |||||||||||| || |||||||||||||| || || || |||||||| ||||
-----------------------gtaaatttgctccat--ggtgagacgtttac-ttataatttcgttctgtagGACCATGTTGAAGGCTATCTCGAGTTGTCTGCCAAAACCAAAATCTACTTTTCCACAGCTGTGGCAAAATGGGATGCCGACTTTTACGTCAAAGTAGATG

upper sequence: GLYMA13G02420.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ30358 (Selaginella moellendorffii), 3'ss of exon 6
gtaatgtatatcatttatacaagataaatctgaataatctagtaggattatgacattgtttattcatt--ttgtagGAACATGTTGAAGGGTATCATGAATTGTCTGCAAAGACAAAAATATTCTTTTCCACAGCAGTTGCAAAATGGGATGCGGATTTCTATGTCAAAGTGGATG
|||||  | |   ||| ||     |   |||    ||| || |   |    |    |  || |    |      |||| ||| ||||||| ||    ||  |||| ||||| || || || | |||||| ||||| ||||| |||||||||||||| ||||| |||||||| || |
gtaatagaaacgctttctatgtctttcctcttt-caatgtactgaaacgtagtttctccttgtctgctggcgcaagGACCATATTGAAGGCTACATGGAGCTGTCGGCAAAAACGAAGATCTACTTTTCTACAGCTGTTGCTAAATGGGATGCGGAATTCTACGTCAAAGTCGACG

upper sequence: GLYMA13G02420.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ28470 (Selaginella moellendorffii), 3'ss of exon 6
gtaatgtatatcatttatacaagataaatctgaataatctagtaggattatgacattgtttattcatt--ttgtagGAACATGTTGAAGGGTATCATGAATTGTCTGCAAAGACAAAAATATTCTTTTCCACAGCAGTTGCAAAATGGGATGCGGATTTCTATGTCAAAGTGGATG
|||||  | |   ||| ||     |   |||    ||| || |   |    |    |  || |    |      |||| ||| ||||||| ||    ||  |||| ||||| || || || | |||||| ||||| ||||| |||||||||||||| ||||| |||||||| || |
gtaatagaaacgctttctatgtctttcctcttt-caatgtactgaaacgtagtttctccttgtctgctggcgcaagGACCATATTGAAGGCTACATGGAGCTGTCCGCAAAAACGAAGATCTACTTTTCTACAGCTGTTGCTAAATGGGATGCGGAATTCTACGTCAAAGTCGACG

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|151401991|gb|EV271804.1|EV271804
EST:     ATCGAGCTATTGATTCAGAAGAAGCCCAGCACAAAGACTTCCTTCGCCTG                         GAACATGTTGAAGGGTATCAAGAATTGTCTGCAAAGACAAAAATATTCTTT
genomic: ATCGAGCTATTGATTCAGAAGAAGCCCAGCACAAAGACTTCCTTCGCCTGgtaatgtata ... cattttgtagGAACATGTTGAAGGGTATCATGAATTGTCTGCAAAGACAAAAATATTCTTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagataaatctgaataatctagtaggattatgacattgtttattcattttgtagGAACATGTTGAAGGGTATCATGAATTGTCTGCAAAGACAAAAATATTCTTTTCCACAGCAGTTGCAAAATGGGATGCGGATTTCTATGTCAAAGTGGATG
                                           ttcatttt  CT-rich tract
                                   attgtttattcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtatatcatttatacaagataaatctgaataatctagtaggattatgacattgtttattcattttgtagGAACATGTTGAAGGGTATCATGAATTGTCTGCAAAGACAAAAATATTCTTTTCCACAGCAGTTGCAAAATGGGATGCGGATTTCTATGTCAAAGTGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA