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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcaattttaaactttattttaatttccaattcattgttcactctgtgtgtgttagtatctcatctcgtcattgtaatttgtaatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGA

Basic information

species Glycine max
transcript GLYMA15G10370.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 9
gtttgcaattttaaactttattttaatttccaattcattgttcactctgtgtgtgttagtatctcatctcgtcattgtaatttgtaatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGA
|||||   |||  |  || ||  | | |       ||   || |  ||   | |    ||||   |    |  | || ||     ||   ||||||| || || || || || || ||||| || || || || ||||| ||| | |||||| |||| ||||||||||| |||||||| |||||||| |
gtttgttgtttctagattaataattactgtagtgccaaattttatact---tctacctgtatggaa----gataatgcaa---acaaaattacagTACACTATTGAGGAAAAGGTGATTGAGAGAGCATATAAGAAGCTAGCATTGGATGCTTTGGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAA

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 12
gtttgcaattttaaactttattttaatttccaattcattgttcactctgtgtgtgttagtatctcatctcgtcattgtaatttgtaatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGA
                 ||| | |  |  |||  |   | |  | |  |  ||   | | |   | |    | ||| |   |||   |  | ||| || | || || |  ||||||||||| || || ||||| ||| | ||||||||||||||||| |||||||||||| ||||||| || ||||| |
----------------gttactcttgtacccatgtg--tatgaagtaagaatgacctgg-agaacttgaactaattctgcattggtcttatgcagAATGCTATTGAGGCTAAAGTCATTGAGAGAGCTTACAAGAAGTTGGCACTTGATGCTCTGGTTATTCAGCAAGGGAGATTGGCAGAACAGAAAA

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 12
gtttgcaattttaaactttattttaatttccaattcattgttcactctgtgtgtgttagtatctcatctcgtcattgtaatttgtaatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGA
        |  |   || |   | |||||| | || |       |  || | |  |||  || | ||   ||    ||  |||||     |||||| | | || || |||||||| |||||||| || ||||| ||| | ||||||||||||||||| ||||| |||||| ||||||| || ||||| |
------gttggtctcctctccgtgaatttcaagttaa--aacagccatgagaggtttaaaat-taattatgt----gttgtttgtt----tacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 12
gtttgcaattttaaactttattttaatttccaattcattgttcactctgtgtgtgttagtatctcatctcgtcattgtaatttgtaatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGA
                                 |  |  | | |||   ||||||||| |   |       || ||     || |  |  | |||||||| || |||||||||||||||||| | || ||||||||||||||||| |||||| ||||||| || || || ||| | || || ||||   
--------------------------------gtaaaaggatgact---tgtgtgttatttctttgctgactcgtt-----ttctgtttct-cagTATACTATTGAAGAGAAAGTCATTGAACGCGCGTACAAAAAGCTTGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCCGAACAGAGAG

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 12
gtttgcaattttaaactttattttaatttccaattcattgttcactctgtgtgtgttagtatctcatctcgtcattgtaatttgtaatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGA
                                 |  |  | | |||   ||||||||| |   |       || ||     || |  |  | |||||||| || |||||||||||||||||| | || ||||||||||||||||| |||||| ||||||| || || || ||| | ||||| ||||   
--------------------------------gtaaaaggatgact---tgtgtgttatttctttgctgactcgtt-----ttctgtttct-cagTATACTATTGAAGAGAAAGTCATTGAACGCGCGTACAAAAAGCTTGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCTGAACAGAGAG

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|6069767|gb|AW099383.1|AW099383
EST:     ATAGGATTGGTCAGAAGAAAGAAGTTCAAGTTCTGCGATGTTGTACTGAG                         TATACAATAGAAGAGAAAGTCATTGTAAGGGGCCTACAANA-GCTTGCACT
genomic: ATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAGgtttgcaatt ... aatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGG-CCTACAAAAAGCTTGCACT
EST: gi|193688000|gb|FK628315.1|FK628315
EST:     ATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAG                         TATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTT
genomic: ATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAGgtttgcaatt ... aatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTT
EST: gi|193487791|gb|FK452772.1|FK452772
EST:     AAAAGAAAGAAGTTCAAG-TTTCCGTTTTTGTACTGAG                         TATACAATAGAAGAGAAAGTCATTGAAAGGGCCT-CAAAAAGCTTGCACTT
genomic: AAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAGgtttgcaatt ... aatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcactctgtgtgtgttagtatctcatctcgtcattgtaatttgtaatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGA
                                 attgtaatttgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcaattttaaactttattttaatttccaattcattgttcactctgtgtgtgttagtatctcatctcgtcattgtaatttgtaatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG