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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgactttagttcattttggataagtggttaacacagtatttgtattgcattcaaatacattgtcggcctaacctaattacacaaccaaactctgcagCTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAA

Basic information

species Glycine max
transcript GLYMA20G04870.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G04870.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g38800.1 (Oryza sativa), 3'ss of exon 6
---------gtgagtgactttagttcattttggataagtggttaacacagtatttg-tattgcattcaaatacattgtcggcctaacctaat---------tacacaaccaaactctgcagCTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAA
         |||            |  ||||   | | |||||    | |   |   | |||  || |||  | || |   | | || |||          |   |  | |    |  ||||| ||  | ||||| |||||||| |||||  | || ||||||||||||||||||  | ||||||||||||| ||||||||||||||||| 
gttagtcttgtgttccttccccactttttttatcttattggttctttctgagctcaatgttgacttaaaaatctttttttacatgacttaaaatctattaatgttcttcaatgtccaacagCTCTTTCTACTTCGAGCTGCTGGATTTCTGCTGCCATGCTATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAG

upper sequence: GLYMA20G04870.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g24650.3 (Oryza sativa), 3'ss of exon 7
gtgagtgactttagttcattttggataagtggttaacacagtatttgtattgcattcaaatacattgtcggcctaacctaattacacaaccaaactctgcagCTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAA
||||||||    | | |  |||   ||  |||||| ||  || |||||  | |||    ||     || ||       || | |  |      |||   ||||||||  |  | ||||||||||| |||||  |||| | |||||| |||||||||||| | ||||| ||||| |||||  ||||  |||| 
gtgagtgaaag-aatgctctttaactatctggttatcattgt-tttgttgtacatcatcattagaagttgg-------tattgatgctctattacttgacagCTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG

upper sequence: GLYMA20G04870.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G303431_T01 (Zea mays), 3'ss of exon 6
gtgagtgactttagttcattttggataagtggttaacacagtatttgta-ttgcattcaaatacattgtcggcctaacctaattacacaaccaaactctgcagCTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAA
                     ||  | ||  || | |     ||||||| ||| ||   |   |  |   |   |  |    |       | |  |||||||||||||  ||||||| |||||||| |||||  | || ||||| |||||||| |||  | ||||||||||||| ||||| ||||||||||| 
--------------------gtgagtgagatgt-agcctttcatttgtacttggatgttag--cggtccagatattgctctgtcctgactcgaccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG

upper sequence: GLYMA20G04870.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G113619_T04 (Zea mays), 3'ss of exon 8
gtgagtgactttagttcattttggataagtggttaacacagtatttgtattgcattcaaatacattgtcggcctaacctaattacacaaccaaactctgcagCTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAA
|| |||||  | |   ||| ||| | ||         | | | || | | || ||   || || ||||     |||  |  ||   |||   ||      |||||||  || | |||||||||||||| ||  | || | ||| ||||||||||||||||||||||| ||||| |||||  |||| ||||| 
gtaagtgaaataa--ccatcttgaaaaa--------tatattgttggcaatgtataataacac-ttgtttttttaa--tggtt-tgcaattgaa------agCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG

upper sequence: GLYMA20G04870.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G02960.2 (Arabidopsis thaliana), 3'ss of exon 6
-----gtgagtgactttagttcattttggataagtggttaacacagtatttgtattgcattcaaat-acattgtcggcctaacctaattacacaaccaaactctgcagCTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAA
      | | |||   |  ||| ||||   |   |  || |     | | |   ||||||| || |   |    |   | | |  ||||     |      | |  ||||| || |||| || |||||||| |||||| | || |||||||||||||||||||| ||||||||| | || |||||  |||| ||||| 
gtaagctcattgaagcttcttccttttttctttttcttttattttttgtctcagttgcatttaagttgtaacaccaaacca-caaaattgtctgattcttattt-tagCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG

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|13791400|gb|BG653991.1|BG653991
EST:     TTTCTGTCACAGATTCTGACGCTGAAGATGATCCATCCACTTTTTTCTCT                         CTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCT
genomic: TTTCTGTCACAGATTCTGACGCTGAAGATGATCCATCCACTTTTTTCTCTgtgagtgact ... aactctgcagCTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCT
EST: gi|163918182|gb|EH039898.1|EH039898
EST:     TTTCTGTCACAGATTCTGACGCTGAAGATGATCCATCCACTTTTTTCTCT                         CTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCT
genomic: TTTCTGTCACAGATTCTGACGCTGAAGATGATCCATCCACTTTTTTCTCTgtgagtgact ... aactctgcagCTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCT
EST: gi|33390538|gb|CA853733.1|CA853733
EST:     TTTCTGTCACAGATTCTGACGCTGAAGATGATCCATCCACTTTTTTCTCT                         CTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCT
genomic: TTTCTGTCACAGATTCTGACGCTGAAGATGATCCATCCACTTTTTTCTCTgtgagtgact ... aactctgcagCTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCT
EST: gi|254336158|gb|GR841483.1|GR841483
EST:     TTTCTGTCACAGATTCTGACGCTGAAGATGATCCATCCACTTTTTTCTCT                         CTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCT
genomic: TTTCTGTCACAGATTCTGACGCTGAAGATGATCCATCCACTTTTTTCTCTgtgagtgact ... aactctgcagCTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCT
EST: gi|15664135|gb|BI701506.1|BI701506
EST:     TTTCTGTCACAGATTCTGACGCTGAAGATGATCCATCCACTTTTTTCTCT                         CTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCT
genomic: TTTCTGTCACAGATTCTGACGCTGAAGATGATCCATCCACTTTTTTCTCTgtgagtgact ... aactctgcagCTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCT
EST: gi|19348890|gb|BM893422.1|BM893422
EST:     TTTCTGTCACAGATTCTGACGCTGAAGATGATCCATCCACTTTTTTCTCT                         CTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCT
genomic: TTTCTGTCACAGATTCTGACGCTGAAGATGATCCATCCACTTTTTTCTCTgtgagtgact ... aactctgcagCTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCT
EST: gi|15203904|gb|BI426672.1|BI426672
EST:     TTTCTGTCACAGATTCTGACGCTGAAGATGATCCATCCACTTTTTTCTCT                         CTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCT
genomic: TTTCTGTCACAGATTCTGACGCTGAAGATGATCCATCCACTTTTTTCTCTgtgagtgact ... aactctgcagCTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgcattcaaatacattgtcggcctaacctaattacacaaccaaactctgcagCTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAA
      attcaaata  TA-rich tract