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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccaagcttatgcctgatagtttcttggcaaaagttgtacctgtgtttttattcaatcatttatttattcggttttctaagggtagagcatgtcttttggatctaggattgatatttcaatcctagtcccggcattttagttggtgttgatcacgattgttttgttaaacttgtgtttttttagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCTAAAGTGACGAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGACAAAGTCAAGA

Basic information

species Glycine max
transcript GLYMA20G33910.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 3
gtaaccaagcttatgcctgatagtttcttggcaaaagttgtacctgtgtttttattcaatcatttatttattcggttttctaagggtagagcatgtcttttggatctaggattgatatttcaatcctagtcccggcattttagttggtgttgatcacgattgttttgttaaacttgtgtttttttagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCTAAAGTGACGAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGACAAAGTCAAGA
                                                                                        |||  ||  ||||   | |   || ||| ||| |       |   || | ||    |  ||   |  | | |    |   || |  | ||||     |||| || | ||| |||||||||||||| ||||| || |||||||| || || |||||||| || ||||| ||||||||||||||||   |||  || ||||
---------------------------------------------------------------------------------gttatgtgagattgcttttttagttttttatggatctttaacagtacattttgggagtta---tcatgcaaacaatgttgagctcaatataactatgttgc---agGGACGCACTGTTGTTATTGAGCAAAGCTTTGGTGCTCCTAAAGTTACAAAGGATGGAGTTACTGTTGCCAAGAGCATTGAATTCAGTAACAGGGTTAAGA

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 3
gtaaccaagcttatgcctgatagtttcttggcaaaagttgtacctgtgtttttattcaatcatttatttattcggttttctaagggtagagcatgtcttttggatctaggattgatatttcaatcctagtcccggcattttagttggtgttgatcacgattgttttgttaaacttgtgt-ttttttagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCTAAAGTGACGAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGACAAAGTCAAGA
                                                                                     | | ||  ||| | ||||  |||  | |  |  |    |  |  |  | |  |  |   | |||||  |  |     ||    | ||| ||| | || |  |||| || ||||||||||||||||| || | |||  |||| ||||| || || || || || || ||||| ||||||||||| |||||||| | ||||||||
------------------------------------------------------------------------------------agcacag--tgtttgttgggcctacaactttttatgtttttattttgtcagagtgctgtgttgtgttatttgcag--attggacttaacgtgtctattatgcagGGACGCAATGTGGTTATTGAGCAGAGCTATGGTTCACCGAAAGTCACAAAGGACGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAGTCAAGA

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 2
gtaaccaagcttatgcctgatagtttcttggcaaaagttgtacctgtgtttttattcaatcatttatttattcggttttctaagggtagagcatgtcttttggatctaggattgatatttcaatcctagtcccggcat-tttagttggtgttgatcacgattgttttgttaaacttgtgtttttttagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCTAAAGTGACGAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGACAAAGTCAAGA
                                                                          |   ||   |  || |  ||  |||   ||| |  | || |    ||  |  |||| | |     ||||||| || |||  |  || | | |||     | ||  ||| |  ||||||| |||||||||||||||||||| ||||| ||||| ||||| || || ||||| || || || || |||||||||||||| ||||| | ||| ||||
--------------------------------------------------------------------------gcactcactgattataatattgctt---gatgt--gctttac---tctgttgtagtactgttgcatttagtttgttttgtacttgaatttattg-----cctgc-tttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGA

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 2
gtaaccaagcttatgcctgatagtttcttggcaaaagttgtacctgtgtttttattcaatcatttatttattcggttttctaagggtagagcatgtcttttggatctaggattgatatttcaatcctagtcccggcattttagttggtgttgatcacgattgttttgttaaacttgtgtttttttagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCTAAAGTGACGAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGACAAAGTCAAGA
                                                                            |  || |    |    ||    ||||| |    | || |  ||    |  || |   | | |  | ||| || |||  |  ||   | | |     ||| |||      ||||||| |||||||||||||||||||| || || ||||| ||||| || || ||||| || || ||||| |||||||||||||| ||||| | ||| ||||
--------------------------------------------------------------------------actcactgattcca----atactgtttggttt---gttttactttgttgtaatactgttgccttagttgtttgttttgtacttgaacttatcgcctgccttctgt------agGGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGA

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaccaagcttatgcctgatagtttcttggcaaaagttgtacctgtgtttttattcaatcatttattta--ttcggttttctaagggtagagcatgtcttttggatctaggattgatatttcaatcctagtcccggcattttagttggtgttgatcacgattgttttgttaaacttgtgtttttttagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCTAAAGTGACGAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGACAAAGTCAAGA
                                       ||||   | || || | ||    || ||||   || |   |  |  ||  ||||  |   |  |     |  ||||  |   | |    | |   | | ||   | |||||  | |       || ||| |   | || |  ||||  |||| |||||||| || |||||||||||||  || || ||||||||||| |||||||| || || ||||| || || ||||| ||||| |||||| | ||||
---------------------------------------gtactctttttcttctacacattttgatttgatttggacatgatttggccagaggttccttccttagcatgtgatt--tgggtgaccggttgattctgtatcgaatttggt-ctaagactttctgctttatgtga-ttctaattttgaagGGACGTAATGTTGTGATTGAGCAAAGTTGGGGTGCTCCTAAAGTGACAAAAGATGGTGTTACTGTTGCCAAAAGTATTGAGTTCAAAGACAAAATTAAGA

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaaccaagcttatgcctgatagtttcttggcaaaagttgtacctgtgtttttattcaatcatttatttattcggttttctaagggtagagcatgtcttttggatctaggattgatatttcaatcctagtcccggcattttagttggtg--ttgatcacgat--tgttttgttaaacttgtgtttttttagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCTAAAGTGACGAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGACAAAGTCAAGA
||||||       |||    | | || |  | |    |    || |   |    |  |||  ||  | |  | | |||    ||    ||| || |   || ||  |||  | |   ||| |      |    |  |   |||||   |  || |     ||   ||   |||   ||    ||     |||| || | |||  | || ||||||  ||||||| | ||||||||||| || ||||| || || ||||| || |||||||||||||||||||   | ||||
gtaacctgctgcctgctattttgcttttcagtagggatcaatcccgaact---gtctaattcttggtattctagcttt----agatccgag-attttactttgacttagagtcgtagttttaggg--ggatttgataacatagtttacgaattaactgtaatgtcgtgacgttgtgctctctttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGA

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|209725419|gb|BW658281.1|BW658281
EST:     AGGGTGTCGAAGAGCTCGCTGATGCCGTTAAAGTAACAATGGGCCCTAAG                         GGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCTAAAGTGACGAAA
genomic: AGGGTGTCGAAGAGCTCGCTGATGCCGTTAAAGTAACAATGGGCCCTAAGgtaaccaagc ... gtttttttagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCTAAAGTGACGAAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggcattttagttggtgttgatcacgattgttttgttaaacttgtgtttttttagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCTAAAGTGACGAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGACAAAGTCAAGA
               tgttgat  putative branch site (score: 4)
                                            tgttttttt  putative PPT
                          attgttttgttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccaagcttatgcctgatagtttcttggcaaaagttgtacctgtgtttttattcaatcatttatttattcggttttctaagggtagagcatgtcttttggatctaggattgatatttcaatcctagtcccggcattttagttggtgttgatcacgattgttttgttaaacttgtgtttttttagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCTAAAGTGACGAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGACAAAGTCAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA