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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccattactcgtctatcattatattcttcttaccttctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC

Basic information

species Glycine max
transcript GLYMA07G05390.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 4
ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccattactcgtcta---tcattatattcttcttacctt--ctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
      ||  || |   || |      |  ||| || | |  ||| |  |    | || ||| |     |||| ||| || | ||  |   | || | | | ||||| || || ||  | |||||||||||||| ||||| ||||| ||||||||||| ||||| || || |||||||||||||||||||| |||||  |||| |
-----ctgtgttgtattatttgataggtctgcatttgtaagctgtaggagtttattcttgtcaaagaatattacatttttgtaactgtgcttcataatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC

upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g64670.1 (Oryza sativa), 3'ss of exon 3
ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccattactcgtctatcattatattcttcttaccttctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
     ||   |  |||||   ||    |   || |   |  |   |||    ||     ||  | | || |   | | |   ||     ||  ||  |||||||||||||| |||||||| ||||| ||||| || || ||||| || ||||||||  |||| || || |||||||| |||||||| |||||  | || |
-----gtctgtaatcaaacactgtatttatacactcacg--tcagggaccatatgctctgtggaacttttttaccatttgggctc----ttgttgtacagGTTGATCGGGTCTTGTACTCGTCAGTGGTTTACCCCCACAACTACGGCTTCATCCCTCGAACGCTCTGCGAAGACAACGATCCAATGGATGTTCTAGTGC

upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G104918_T03 (Zea mays), 3'ss of exon 4
ttcttgtggattctcaaatcttgacccttcgcaattctg-acttgtgga-tgccattactcg-tctatcattatattcttcttaccttc-taattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
    ||||     | |  | |           | |||||  ||  || | ||  ||   |   | | |  || | |  |||| |||||    |  | | | ||||||||||| ||  | |||||||||||||| || ||||| || ||||||||||| ||||| ||||| |||||||||||||| ||||| ||||| ||||| |
----tgtgttacataatttgtcaggatgattgagttctgtgctgatgaaatgtaatagtttaatttgtttttctttctttctaacctttgctacaatttgacagGTTGATCGAGTCCTTTACTCATCAGTTGTATACCCTCACAATTATGGTTTCATTCCAAGGACTCTTTGTGAAGACAATGACCCAATGGATGTGTTGGTCC

upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G061928_T02 (Zea mays), 3'ss of exon 4
ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtgga--tgccattactcg-tctatcattatattcttcttacct-tctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
 |||  |  ||  ||   | |    |     || | ||||  ||  ||  ||  ||   |   | |  | || | |  |||| || | |   |  | | |  |||||||||| ||  |||||||||||||||| || ||||| || ||||||||| | ||||| ||||| |||||||||||||| ||||| ||||| || || |
-tctgttacataatc---tgtcaggctgattcagtcctgaactgatgaaatgtaatggtttaatttgactttctttcgttctgacatgtgctacaatttgatagGTTGATCGAGTCCTGTACTCATCAGTTGTATACCCTCACAATTATGGTTTCGTTCCAAGGACTCTTTGTGAAGACAATGACCCAATGGATGTGTTAGTCC

upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 3
ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccattactcgtctatcattatattcttcttaccttctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
                  |  ||   |||| |||       |||||     | || ||  |  |   || |  |    | || ||  | || ||  ||||||||| ||| | |||||||| || ||||||||||| || || || || ||||||||| | ||  ||||||||||||| |||||  |||||||| | || |
-----------------gtaatgtgacttcccaa----agattgtgatcttcttttctt-ttaactgttctgatgga-tgacattgaatttgatc-tcagGTTGACCGGATCTTGTACTCCTCCGTTGTTTATCCACACAATTACGGATTCATCCCACGGACATTGTGTGAAGACAACGATCCTCTTGATGTCCTTGTCC

upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 4
ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccattactcgtctatcattatattcttcttaccttctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
             | | ||    ||       | || | |  | || |||   ||  |     |  || |   ||  |     |      |     ||||||||||||  || | |||||||||||||| || ||||| |||||||||||  | ||  | ||  |||||||||||||||| || ||||||||||| ||  
------------gttagatgagaacaaagtttatttttta--tatgaatggttttcttatagcaaaatcaatctcaacaagtttgaattctctcattcagGTTGATCGTATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTTGTTCCTCGCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCA

upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------------------------------------ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccattactcgtctatcattatattcttcttaccttctaa--ttaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
                                                                       |     | |||    |  | ||    ||||    || | |  | || ||||| | |   |   ||    || || ||  ||   | |||  | ||||  ||||| || || || || || ||||| || || ||||||||||||||||| ||||| ||  | || || |||||||||||||||||| | ||||| ||  | |
gtaagactgaaccctgaagtgctttaatttccagacatttttccacatgatttggatatttgagcaccaaatcaccattgatggagatctgttttttcttccattttgttatgtatgcatgccttcatatg---atgggaatgttttttctattgtttaacatcaatgcccagGTCGACCGTGTCTTATATTCATCTGTGGTGTATCCTCATAACTATGGATTCATTCCCCGTACCCTATGTGAAGACAATGATCCACTGGATGTTTTAATCC

upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
-----ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccatta-ctcgtctatcattatattcttcttaccttctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
     |  |||    |    || |||  ||  |      |||  |  |      ||  ||  || | ||   |  |        | | |||    | | |  ||||||||||||  | ||||||||||||||||| ||||| || || ||||| ||||| ||| | ||||| ||||| ||  | ||||| ||||||||  | ||  
gtacgtcattgccagtgactaactctaaacgatcttgtcttcatatcttcacgagctgttggcttggct-caaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA

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|254344222|gb|GR851025.1|GR851025
EST:     AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG                         GTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTC
genomic: AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAGgtatgaacca ... taatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTC
EST: gi|17400209|gb|BM176991.1|BM176991
EST:     AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG                         GTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTC
genomic: AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAGgtatgaacca ... taatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTC
EST: gi|254315134|gb|GR830127.1|GR830127
EST:     AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG                         GTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTC
genomic: AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAGgtatgaacca ... taatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTC
EST: gi|254344223|gb|GR851026.1|GR851026
EST:     AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG                         GTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTC
genomic: AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAGgtatgaacca ... taatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTC
EST: gi|18040990|gb|BM309284.1|BM309284
EST:     AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG                         GTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTC
genomic: AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAGgtatgaacca ... taatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTC
EST: gi|48574801|gb|CO036084.1|CO036084
EST:     AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG                         GTTGATCGGGTTTTGTAC
genomic: AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAGgtatgaacca ... taatggtcagGTTGATCGGGTTTTGTAC
EST: gi|209698574|gb|BW652427.1|BW652427
EST:     AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG                         GTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTC
genomic: AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAGgtatgaacca ... taatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTC
EST: gi|151399288|gb|EV269159.1|EV269159
EST:     AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG                         GTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTC
genomic: AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAGgtatgaacca ... taatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatgccattactcgtctatcattatattcttcttaccttctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
                 tatcattatattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccattactcgtctatcattatattcttcttaccttctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA