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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatcattctttaaaatattttctcatatgctccttccttttcatgttaagctctttctttgttatagctgataattttcacgtacagAGAGGCTCTCAATGTGCCTGGATGTGAAGCTATCCACTTAACGGAAATTCAGTCAAGCATTGAGTGTGACACTTTTATGCCTCCAGTTGATTTCACTATA

Basic information

species Glycine max
transcript GLYMA06G01280.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 2
---------------gtacatcattctttaaaatattttctcatatgctccttccttttcatgttaagctctttctttgttatagctgataattttcacgtacagAGAGGCTCTCAATGTGCCTGGATGTGAAGCTATCCACTTAACGGAAATTCAGTCAAGCATTGAGTGTGACACTTTTATGCCTCCAGTTGATTTCACTATA
                | |   |   | ||  || |    |    || | ||   |  ||    | | |||| |     || || |||  || |||||| |  || ||  |||| ||||  |||  |||||| ||  |||| ||||| || |||||||||||||||||||||||||| ||||| |||||  |||| ||  |  | 
gtgagctgttaacttttgccaaagcatctagtatgtaaattgtgttgtttctgtatactccacctcaactctattcacctt-tatctgtaaaatttcac-tgtagGGAATCTCTTAATGGACCTTCATGTGAGGCAGTCCATTTAACTGACATTCAGTCAAGCATTGAGTGTGACACCTTTATTCCTCCGATTGACTTATCGGTG

upper sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 1
-----gtac-atcattctttaaaatattttctcatatgc---tccttccttttcatgttaagctctttctttgttat-----agctgataattttcacgtacagAGAGGCTCTCAATGTGCCTGGATGTGAAGCTATCCACTTAACGGAAATTCAGTCAAGCATTGAGTGTGACACTTTTATGCCTCCAGTTGATTTCACTATA
      ||  |  |   ||| ||| |   | | |||      | ||     | || || |   | |  |  || |||            ||| ||    |  |||||   | | ||||  |||| |||||| ||||||||  | || || ||||||||||||||||||||||| ||||| || ||||||||||| ||  |  | 
gtgagttattagtaccttttgaaacaacatattatacatgtatgctgttgctgcacgtaactgtgtcgcaatgctattcacccttctgcaatatttttatgtagAGAATATTTGAATGGACCTGCATGTGAGGCTATCCATCTGACTGATATTCAGTCAAGCATTGAGTGTGATACTTTCATCCCTCCAGTTGACTTTTCAGTG

upper sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G005990_T01 (Zea mays), 3'ss of exon 2
---gtacatcattctttaaaatattttctcatatgctccttcctttt---catgttaagctctttctttgttatag-----ctgataattttcacgtacagAGAGGCTCTCAATGTGCCTGGATGTGAAGCTATCCACTTAACGGAAATTCAGTCAAGCATTGAGTGTGACACTTTTATGCCTCCAGTTGATTTCACTATA
       || |   |||  || |   | |  ||      |||  ||    ||||| | | | || |  || |||            ||| ||   ||  |||||   ||| || |  |||| |||||| ||||||||  |||| || |||||||| |||||||||||||||||||| || ||||| ||||| ||| |  | 
gtgagttattaccttttggaacaacatattgtacatgtattctgttgctgcatgtcatg-tgttgcaatgctattcacccttctggaatatttttgtgtagAGAATATCTTAAAGGACCTGCATGTGAGGCTATCCATCTAACTGACATTCAGTCGAGCATTGAGTGTGACACTTTCATCCCTCCGGTTGACTTCTCAGTG

upper sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G072608_T01 (Zea mays), 3'ss of exon 1
---gtacatcattctttaaaatattttctcatatgctccttcctttt---catgttaagctctttctttgttatag-----ctgataattttcacgtacagAGAGGCTCTCAATGTGCCTGGATGTGAAGCTATCCACTTAACGGAAATTCAGTCAAGCATTGAGTGTGACACTTTTATGCCTCCAGTTGATTTCACTATA
       || |   |||  || |   | |  ||      |||  ||    ||||| | | | || |  || |||            ||| ||    |  |||||   ||| || |  |||| |||||| ||||||||  |||| || |||||||| ||||||||||||| |||||| || ||||| ||||| ||| |  | 
gtgagttattaccttttggaacaacatattgtacatgtattctgttgctgcatgtcatg-tgttgcaatgctattcacccttctggaatatttttctgtagAGAATATCTTAAAGGACCTGCATGTGAGGCTATCCATCTAACTGACATTCAGTCGAGCATTGAGTGTGTCACTTTCATCCCTCCGGTTGACTTCTCAGTG

upper sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 3
gtacatcattctttaaaatattttctcatatgctccttccttttcatgttaagctctttctttgttatagctgataattttcacg-tacagAGAGGCTCTCAATGTGCCTGGATGTGAAGCTATCCACTTAACGGAAATTCAGTCAAGCATTGAGTGTGACACTTTTATGCCTCCAGTTGATTTCACTATA
                  | | | ||    || || || || |   |    |||| |||| || ||  || |||| || ||  |  ||||| || ||||||||||  ||||||||||| ||||||||| | || |||||| || ||||| | || ||||||||||| || ||| |  |||||| |    ||
-----------------gtgtgtactttgttgatcattgctgtat-taaggagctttttcgttctttcagttgattatcttttcaatacagGGAAGCTCTCAATGCACCTGGATGTGATGCTATCCACATTACAGAAATTGAGACAAGCTTCGAATGTGACACTTTCATCCCTGCTATTGATTCCTTGGTA

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|10846876|gb|BF069675.1|BF069675
EST:     TCTCTGTCAATTGAGAAAGTTTTTGTTATAGGGGGTGGTCAGATATTTAG                         AGAGGCTCTCAATGTGCCTGGATGTGAAGCTATCCACTTAACGGAAATTCA
genomic: TCTCTGTCAATTGAGAAAGTTTTTGTTATAGGGGGTGGTCAGATATTTAGgtacatcatt ... tcacgtacagAGAGGCTCTCAATGTGCCTGGATGTGAAGCTATCCACTTAACGGAAATTCA
EST: gi|308098411|gb|HO760152.1|HO760152
EST:     TCTCTGTCAATTGAGAAAGTTTTTGTTATAGGGGGTGGTCAGATATTTAG                         AGAGGCTCTCAATGTGCCTGGATGTGAAGCTATCCACTTAACGGAAATTCA
genomic: TCTCTGTCAATTGAGAAAGTTTTTGTTATAGGGGGTGGTCAGATATTTAGgtacatcatt ... tcacgtacagAGAGGCTCTCAATGTGCCTGGATGTGAAGCTATCCACTTAACGGAAATTCA
EST: gi|151397669|gb|EV267542.1|EV267542
EST:     TCTCTGTCAATTGAGAAAGTTTTTGTTATAGGGGGTGGTCAGATATTTAG                         AGAGGCTCTCAATGTGCCTGGATGTGAAGCTATCCACTTAACGGAAATTCA
genomic: TCTCTGTCAATTGAGAAAGTTTTTGTTATAGGGGGTGGTCAGATATTTAGgtacatcatt ... tcacgtacagAGAGGCTCTCAATGTGCCTGGATGTGAAGCTATCCACTTAACGGAAATTCA
EST: gi|21637920|gb|BM108075.1|BM108075
EST:     TCTCTGTCAATTGAGAAAGTTTTTGTTATAGGGGGTGGTCAGATATTTAG                         AGAGGCTCTCAATGTGCCTGGATGTGAAGCTATCCACTTAACGGAAATTCA
genomic: TCTCTGTCAATTGAGAAAGTTTTTGTTATAGGGGGTGGTCAGATATTTAGgtacatcatt ... tcacgtacagAGAGGCTCTCAATGTGCCTGGATGTGAAGCTATCCACTTAACGGAAATTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttccttttcatgttaagctctttctttgttatagctgataattttcacgtacagAGAGGCTCTCAATGTGCCTGGATGTGAAGCTATCCACTTAACGGAAATTCAGTCAAGCATTGAGTGTGACACTTTTATGCCTCCAGTTGATTTCACTATA
                                 agctgat  putative branch site (score: 4)
                                          ttttcac  putative PPT
                                    tgataatttt  TA-rich tract