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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGGgtgagagaacagaatactagatttacttgctctatgtttgtacgttctaccggtttttttctaatataagtttgtatag

Basic information

species Glycine max
transcript GLYMA10G36210.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G36210.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os01g65330.2 (Oryza sativa), 5'ss of exon 10
-------------------------------------------------------AGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGGgtgagagaacagaatactagatttacttgctctatgtttgtacgttctaccggtttttttctaatataagt-ttgtatag-----
                                                        ||||| ||||| ||||| ||||||||||| ||||| ||||||||||  |    ||   |  |  | || |    | ||   | |      |||   |||||  |  |  ||   | || | |       
ATATATATGAGCTTTGTTTTGTGTGTTCCTGAATCTGATAATTTAAATAATACAGGGCTCACCATGGTTTTGGTTGGGTTGGAGAGTGGGCAAATACAGGgttggtatccaacttcatccagttgcaacatataaagtggctaaaactaagagttttgatgcatgatgtttattatctgatgcag

upper sequence: GLYMA10G36210.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os01g65330.1 (Oryza sativa), 5'ss of exon 11
AGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGGgtgagagaacagaatactagatttacttgctctatgtttgtacgttctaccggtttttttctaatataagt-ttgtatag-----
 ||||| ||||| ||||| ||||||||||| ||||| ||||||||||  |    ||   |  |  | || |    | ||   | |      |||   |||||  |  |  ||   | || | |       
GGCTCACCATGGTTTTGGTTGGGTTGGAGAGTGGGCAAATACAGGgttggtatccaacttcatccagttgcaacatataaagtggctaaaactaagagttttgatgcatgatgtttattatctgatgcag

upper sequence: GLYMA10G36210.1 (Glycine max), 5'ss of exon 14
lower sequence: AT1G34320.1 (Arabidopsis thaliana), 5'ss of exon 12
AGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGGgtgag-----agaacagaat-actagatttacttgctctatgtttgtacgttctaccg-gtttttttctaa-tataagtttgtatag----------
||| |||||||| ||||||||||||||||||||||| | | | |||| ||     |  |||   | | |   | |   |||| | | | | | |   | || |  || ||| |||| | | || || |  |           
AGCGCATCATGGTTTTGGATGGGTTGGAGAATGGGCAAGTTCCGGgtaagccctgactacaagctgattctctctttgtgctgtgtatatatgcagacaactgcattctttactaaatgttagattatgcaaaataactcag

upper sequence: GLYMA10G36210.1 (Glycine max), 5'ss of exon 14
lower sequence: Vv18s0076g00260.t01 (Vitis vinifera), 5'ss of exon 11
AGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGGgtgaga--gaacagaatactagatttactt--gctctatgtttgtacgttctaccggttttttt----ctaatataagt-ttgtatag-------------------------------------------------
|||||||||||||||||| |||||||| |||||||| ||||| |||| ||   |||  || |  |   ||| |||  | | |||  || |     |||  | |  |  |    ||| |   | | || | ||                                                  
AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGGgtaaggttgaaatgattggtgcttttcctttagttttataattattataactattgctgctgctactgctactgctactattatttatccatcttataggccctttgcgattcatgaaaattttctgataccttcag

upper sequence: GLYMA10G36210.1 (Glycine max), 5'ss of exon 14
lower sequence: PP1S54_228V6.1 (Physcomitrella patens), 5'ss of exon 11
AGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGGgtgagagaacagaatactagatttac-ttgctctatgtttgtacgttctacc----ggtttttttctaatataagtttgtatag----------------
    |||||||||||||||||||||||||| ||||| ||| | |||| ||   |||      |   ||| | ||  ||| |     ||        |    | |   | |||| ||  | ||| |  ||                
GAAGCATCATGGCTTTGGATGGGTTGGAGAGTGGGCGAATGCTGGgtaagttgacactcctttctgtttgcgttcttctgtaacgttattcctggacttgagttgcatctctattaggattttctgaagcgactatattccaagt

upper sequence: GLYMA10G36210.1 (Glycine max), 5'ss of exon 14
lower sequence: PP1S15_33V6.1 (Physcomitrella patens), 5'ss of exon 12
AGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGGgtgagagaacagaatactagatttacttgctcta------tgtttgtacgttcta--ccggtttt--tttctaatataagtttgtatag-----------
    || ||||||||||||||||| ||||| ||||| ||| |||||| ||| |||| |  |||    || |  ||| ||       |||  |       |    |  ||    || || | |||   | |  ||           
GAAGCACCATGGCTTTGGATGGGTCGGAGAGTGGGCGAATGCAGGgtaagaaaacacatcactttcctttcacgctgtaatggaacgttgatgtccctcaatttgagttcgacttttattgtaatactctgaagcgattgtgttc

upper sequence: GLYMA10G36210.1 (Glycine max), 5'ss of exon 14
lower sequence: EFJ24079 (Selaginella moellendorffii), 5'ss of exon 10
AGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGGgtgagagaacagaatactagatttacttgctctatgtttgtacgttctaccggtttttttctaatataagtttgtatag
||||||||| || |||||||||||||| |||||||| ||| | |||||||       | | |    ||   ||  |||  ||||      || || | | ||  |||                 
AGCTCATCACGGATTTGGATGGGTTGGCGAATGGGCAAATTCTGGgtgagt------atttcgttgttagtttcttcttcgttt-----ctcaactgttcttcatcttcag-------------

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|15662904|gb|BI700275.1|BI700275
EST:     AGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGG                         GTCTGAGTTCAACCGAAAACCTGCCGGCCAGACCGACTTGTTGAAAATTGA
genomic: AGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGGgtgagagaac ... gtttgtatagGTCTGAGTTCAACCGAAAACCTGCCGGCCAGACCGACTTGTTGAAAATTGA
EST: gi|120490977|gb|EH219144.1|EH219144
EST:     AGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGG                         GTCTGAGTTCAACCGAAAACCTGCCGGCCAGACCGACTTGTTGAAAATTGA
genomic: AGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGGgtgagagaac ... gtttgtatagGTCTGAGTTCAACCGAAAACCTGCCGGCCAGACCGACTTGTTGAAAATTGA
EST: gi|207759243|gb|GD734386.1|GD734386
EST:     AGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGG                         GTCTGAGTTCAACCGAAAACCTGCCGGCCAGACCGACT
genomic: AGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGGgtgagagaac ... gtttgtatagGTCTGAGTTCAACCGAAAACCTGCCGGCCAGACCGACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGGgtgagagaacagaatactagatttacttgctctatgtttgtacgttctaccggtttttttctaatataagtttgtatag

- - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - TGGAGA
- - - - - - - - - - - -  GGAGAA