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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatctttctttaaaatattttgttcttcatccgctccttccttttcatgttaagctctttctttgttatagctgataattttcatgtacagAGAGGCTCTCAATGCGCCTGGATGTGAAGCTATCCACTTAACAGAAATTCAGTCAAGTATTGAGTGTGACACTTTTATGCCTCCAGTTGATTTCACTATG

Basic information

species Glycine max
transcript GLYMA04G01240.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 2
-------gtacatctttctttaaaatattttgttcttcatccgc-tccttccttttcatgtta----agctctttctttgttatagctgataattttcatgtacagAGAGGCTCTCAATGCGCCTGGATGTGAAGCTATCCACTTAACAGAAATTCAGTCAAGTATTGAGTGTGACACTTTTATGCCTCCAGTTGATTTCACTATG
       ||  | ||||    |||  || | ||   | |   |  |  || || |  |    |    | |||| |     || || |||  || |||||  |  || ||  |||| ||||  |||  |||||| ||  |||| ||||| || ||||||||||| |||||||||||||| ||||| |||||  |||| ||  |  ||
gtgagctgt-taacttttgccaaagcatctagtatgtaaattgtgttgtttctgtatactccacctcaactctattcacctt-tatctgtaaaatttcac-tgtagGGAATCTCTTAATGGACCTTCATGTGAGGCAGTCCATTTAACTGACATTCAGTCAAGCATTGAGTGTGACACCTTTATTCCTCCGATTGACTTATCGGTG

upper sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 1
-----------gtacatctttctttaaaatattttgttcttcatccgctccttccttttcatgttaagctctttctttgttatagctgataattttcatgtacagAGAGGCTCTCAATGCGCCTGGATGTGAAGCTATCCACTTAACAGAAATTCAGTCAAGTATTGAGTGTGACACTTTTATGCCTCCAGTTGATTTCACTATG
           |||| | ||     || ||||| |     |   | | | || |   |   |||   ||  |    ||       |||  ||| ||  | |  |||||   | | ||||  |||| |||||| ||||||||  | || || ||||||||||| ||||||||||| ||||| || ||||||||||| ||  |  ||
gtgagttattagtaccttttgaaacaacatattatacatgtatgctgttgctgcacgtaactgtgtcgcaatgctattcacccttctg-caatatttttatgtagAGAATATTTGAATGGACCTGCATGTGAGGCTATCCATCTGACTGATATTCAGTCAAGCATTGAGTGTGATACTTTCATCCCTCCAGTTGACTTTTCAGTG

upper sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G005990_T01 (Zea mays), 3'ss of exon 2
-----gtac-atctttctttaaaatattttgttc-ttcatccgctccttccttttcatgttaagctctttctttgttatagctgataattttcatgtacagAGAGGCTCTCAATGCGCCTGGATGTGAAGCTATCCACTTAACAGAAATTCAGTCAAGTATTGAGTGTGACACTTTTATGCCTCCAGTTGATTTCACTATG
      ||  | ||||    | || || |||| | |  || |  |   | | | ||||||   ||  |    ||       |||  ||| ||  |||  |||||   ||| || |  |||| |||||| ||||||||  |||| || |||||||| || ||||||||||||||||| || ||||| ||||| ||| |  ||
gtgagttattaccttttggaacaacatattgtacatgtattctgttgctgcatgtcatgtgttgcaatgctattcacccttctgg-aatatttttgtgtagAGAATATCTTAAAGGACCTGCATGTGAGGCTATCCATCTAACTGACATTCAGTCGAGCATTGAGTGTGACACTTTCATCCCTCCGGTTGACTTCTCAGTG

upper sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 3
gtacatctttctttaaaatattttgttcttcatccgctccttccttttcatgttaagctctttctttgttatagctgataattttcatg-tacagAGAGGCTCTCAATGCGCCTGGATGTGAAGCTATCCACTTAACAGAAATTCAGTCAAGTATTGAGTGTGACACTTTTATGCCTCCAGTTGATTTCACTATG
                     | ||| |||  |       | |  | | | |   |||| |||| || ||  || |||| || ||     ||||| || ||||||||||| ||||||||||| ||||||||| | ||||||||| || ||||  | || ||||||||||| || ||| |  |||||| |    | 
--------------------gtgtgtactttgttgatcattgctgtattaag--gagctttttcgttctttcagttgattatcttttcaatacagGGAAGCTCTCAATGCACCTGGATGTGATGCTATCCACATTACAGAAATTGAGACAAGCTTCGAATGTGACACTTTCATCCCTGCTATTGATTCCTTGGTA

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|193433108|gb|FK395760.1|FK395760
EST:     TCTCTGTCAATTGAGAAAGTATTTGTTATAGGAGGTGGTCAGATATTTAG                         AGAGGCTCTCAATGCGCCTGGATGTGAAGCTATCCACTTAACAGAAATTCA
genomic: TCTCTGTCAATTGAGAAAGTATTTGTTATAGGAGGTGGTCAGATATTTAGgtacatcttt ... tcatgtacagAGAGGCTCTCAATGCGCCTGGATGTGAAGCTATCCACTTAACAGAAATTCA
EST: gi|193426489|gb|FK386618.1|FK386618
EST:     TCTCTGTCAATTGAGAAAGTATTTGTTATAGGAGGTGGTCAGATATTTAG                         AGAGGCTCTCAATGCGCCTGGATGTGAAGCTATCCACTTAACAGAAATTCA
genomic: TCTCTGTCAATTGAGAAAGTATTTGTTATAGGAGGTGGTCAGATATTTAGgtacatcttt ... tcatgtacagAGAGGCTCTCAATGCGCCTGGATGTGAAGCTATCCACTTAACAGAAATTCA
EST: gi|193322903|gb|FK288761.1|FK288761
EST:     TCTCTGTCAATTGAGAAAGTATTTGTTATAGGAGGTGGTCAGATATTTAG                         AGAGGCTCTCAATGCGCCTGGATGTGAAGCTATCCACTTAACAGAAATTCA
genomic: TCTCTGTCAATTGAGAAAGTATTTGTTATAGGAGGTGGTCAGATATTTAGgtacatcttt ... tcatgtacagAGAGGCTCTCAATGCGCCTGGATGTGAAGCTATCCACTTAACAGAAATTCA
EST: gi|193430827|gb|FK396461.1|FK396461
EST:     TCTCTGTCAATTGAGAAAGTATTTGTTATAGGAGGTGGTCAGATATTTAG                         AGAGGCTCTCAATGCGCCTGGATGTGAAGCTATCCACTTAACAGAAATTCA
genomic: TCTCTGTCAATTGAGAAAGTATTTGTTATAGGAGGTGGTCAGATATTTAGgtacatcttt ... tcatgtacagAGAGGCTCTCAATGCGCCTGGATGTGAAGCTATCCACTTAACAGAAATTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttccttttcatgttaagctctttctttgttatagctgataattttcatgtacagAGAGGCTCTCAATGCGCCTGGATGTGAAGCTATCCACTTAACAGAAATTCAGTCAAGTATTGAGTGTGACACTTTTATGCCTCCAGTTGATTTCACTATG
                                 agctgat  putative branch site (score: 4)
                                          ttttcat  putative PPT
                                      ataattttcatgta  TA-rich tract