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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattaatggttatcagaaatattgaagttctgatgtacttattttgatggttacttgtgactgaggtctttgttggttatgtttgttaacttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAAGAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCA

Basic information

species Glycine max
transcript GLYMA13G05700.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 9
ttattaatggttatcagaaatattgaagttctgatgtacttattttgatggttacttgtgactgaggtctttgttggttatgtttgttaacttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAAGAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCA
   ||    | | | |  |    | | ||||| || || | | |||  |  |||   || |      |   | |||  | | ||| ||      | | |||||||||| || ||||| |||||||| ||||| || ||||||||||| |||||  |||||||||| ||||||||||||||||| ||||||||||| ||||
--gttttatgctgttacta----taaggttcttatttattcactttatttattataagttatcctaattcat-ttgtctgtatttatt------taacagTCTCGAGCACATCCACGAGAAATAATAACTGAAGTTCTTAAAGCTCTGCAAGAGCTAAATGTTTGCTGGAAGAAGATTGGACATTATAACATGAAATGCA

upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 3'ss of exon 9
ttattaatggttatcagaaatattgaagttctgatgtacttattttgatggttacttgtgactgaggtctttgttggt-tatgtttgttaacttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAAGAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCA
             ||    ||   || |||||  | |||| | |    | || ||     |||||  | | || ||   ||| |   ||| |     | |||||||||| || || || || ||||||| ||||||||| || || ||  |||| |||||||| || |||||||||| |||||| || |||||||||||||
------------gtcttgcat---gatgttctcttttact-actacttttgtgacac---actgaaatttgtgctgacgtatatcacttatcc---aacagTCTCGAGCTCAGCCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTGAAGACTTAAATGTCTGCTGGAAGAAGAATGGACAGTACAACATGAAGTGCA

upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 9
ttattaatggttatcagaaatattgaagttctgatgtacttattttgatggttacttgtgactgaggtctttgttggttatgtttgttaacttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAAGAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCA
                     ||  || ||||  |   ||        |  ||| ||   | ||   |  |  ||   ||| | | ||   ||||| ||||||||||| || |||   ||||||||| |||| || || |||||||| ||||||||||||||||  ||||| ||||| || |||||||||||||||||||
------------------gtaatctaatttctagtaacctccaccattttattatttt--attgcttttctcattcaatatttct-ttgttttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAAGAATTAAATGTTTACTGGAAAAAGATAGGTCACTATAACATGAAGTGCA

upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G077278_T01 (Zea mays), 3'ss of exon 9
ttattaatggttatcagaaatattgaagttctgatgtacttattttgatg-gttacttg--tgactgaggtctttgttggttatgtttgttaacttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAAGAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCA
                    || |    || | | |||| | || ||||| ||| | ||  | | |  |   |  | |   | | | ||| |   | | | |||||||||| || ||||| |||||||| | ||| || ||||||||||| |||||| | |||||||  ||||| |||||||||||||| |||||||| ||||
-------------------gtaattttcttgttaagtacatcttatgatgtgtttcatgaattattccgaattccgattcatttatctgtaattgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAAGAACTGAATGTTTACTGGAAAAAGATTGGACACTACAACATGAAATGCA

upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 8
ttattaatggttatcagaaatattgaagttctgatgtacttattttgatggttacttgtgactgaggtctttgttggttatgtttgttaacttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAAGAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCA
                    ||||| | | ||| |    ||| |||      |   | || |  ||  |||   | | | | |   |||||     | ||||||| ||||| || ||||||||||||  ||||||| | ||||| || ||||||||||| ||  | |||||||||| ||| ||||| ||| |||| ||||
-------------------gtattgga-tactgttcattttacttta----ctttgtatggcctagcacttgtattgatgtatcacttaacc---aacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAAGAATTAAACGTCAGATGGAAGAAGAATGGGCACTACAACGTGAAATGCA

upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 9
ttattaatggttatcagaaatattgaagttctgatgtacttattttgatggttacttgtgactgaggtctttgttggttatgtttgttaacttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAAGAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCA
         ||| | | |  |  || | || || | ||   | ||      ||  |  |   || | |   | |||      |||| |  |     | ||||||| || || || |||||||||||||| || ||||| ||||| || ||||| || ||||| |||||||||||||| || ||||| |||||||||||||
---------gttttgatattttctgtatttatggtataaagacttcagcttttgat-atatatgtgattaatattgtaacaatttgatcgc-----acagTCTCGGGCTCATCCCCGTGAAATAATGACGGAAGTCCTGAAAGCCCTGCAAGATTTGAATGTATGTTGGAAGAAGATAGGGCACTACAACATGAAGTGCA

upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 9
-----------------------------------ttattaatggttatcagaaatattgaagttctgatgtacttattttgatggttacttgtgactgaggtctttgttggttatgtt----tgttaacttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAAGAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCA
                                     || ||   || | |     |   |   || ||| |   || | |  ||  |     |  |  |  ||  |  |  || ||||    ||||   |||  | ||||||  || || || |||||||| |||| ||| ||  | |||||||| |||||| | ||||| ||||||||||||||||| ||||| |||||||| ||  
gtttgttcctgattactgattctttttgttcctcaccataaagtcttctgaatgcaacacacaatcagatatctgtactctt-tgcctctacatagccaaa-tcgataatcattctgttaccttgttgttttg-aacagTCTCATGCGCATCCTCGTGAAATCATGAATGAAGTTTTGAAAGCTCTTCAAGAACTCAATGTGTGTTGGAAGAAGATTGGTCACTACAACATGAAATGTC

upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 9
--ttattaatg-gttatcagaaatattgaagttctgatgtacttattttgatggtt-acttgtgactgaggtctt-tgttggttatgtttgttaacttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAAGAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCA
  | || ||    ||||    ||| ||     | |||| ||  | || |  || ||  ||| | |   | |  |  || |  |  | |    |||||| ||| ||||||||||||| ||  |  | ||||||||||| || || ||||||||||||||| | ||||| |||||||| |||||||| || || |||||||| ||||
gctcatcaaaatattatttacaatctt----ctttgat-tatatcttatactgttttgcttataagaaaagaataatgattatcttttcaactaacttttgacagTCTCGAGCCCAGCCTAGACAGATAATGACTGAAGTTCTCAAAGCTCTACAAGAACTGAATGTGTGTTGGAAAAAGATTGGGCATTACAACATGAAATGCA

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|208047764|gb|GD843965.1|GD843965
EST:     GAATGCGGCAACAGTTCCCTGTTGAGAGAAAATGGGCCCTTGGGCTCCAG                         TCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAA
genomic: GAATGCGGCAACAGTTCCCTGTTGAGAGAAAATGGGCCCTTGGGCTTCAGgtgcagtgtt ... cttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAA
EST: gi|8403580|gb|BE059214.1|BE059214
EST:     GAATGCGGCAACAGTTCCCTGTTGAGAGAAAATGGGCCCTTGGGCTTCAG                         TCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAA
genomic: GAATGCGGCAACAGTTCCCTGTTGAGAGAAAATGGGCCCTTGGGCTTCAGgtgcagtgtt ... cttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAA
EST: gi|208218482|gb|GE020490.1|GE020490
EST:     GAATGCGGCAACAGTTCCCTGTTGAGAGAAAATGGGCCCTTGGGCTTCAG                         TCTCGAAGACCCAACCACGTGAAAT
genomic: GAATGCGGCAACAGTTCCCTGTTGAGAGAAAATGGGCCCTTGGGCTTCAGgtgcagtgtt ... cttgtgatagTCTCGA-G-CCCAACCACGTGAAAT
EST: gi|193534371|gb|FK493390.1|FK493390
EST:     CCTGTTGAGAGAAAATGGGCCC-TGGGCTTCAG                         TCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAA
genomic: CCTGTTGAGAGAAAATGGGCCCTTGGGCTTCAGgtgcagtgtt ... cttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAA
EST: gi|208194268|gb|GD992437.1|GD992437
EST:     GGGCCCTTGGGCTTCAG                         TCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAA
genomic: GGGCCCTTGGGCTTCAGgtgcagtgtt ... cttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAA
EST: gi|22540977|gb|BU090820.1|BU090820
EST:     GAATGCGGCAACAGTTCCCTGTTGAGAGAAAATGGGCCCTTGGGCTTCAG                         TCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAA
genomic: GAATGCGGCAACAGTTCCCTGTTGAGAGAAAATGGGCCCTTGGGCTTCAGgtgcagtgtt ... cttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAA
EST: gi|7234476|gb|AW569813.1|AW569813
EST:     GAATGCGGCAACAGTTCCCTGTTGAGAGAAAATGGGCCCTTGGGCTTCAG                         TCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAA
genomic: GAATGCGGCAACAGTTCCCTGTTGAGAGAAAATGGGCCCTTGGGCTTCAGgtgcagtgtt ... cttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAA
EST: gi|208219813|gb|GE018937.1|GE018937
EST:     GAATGCGGCAACAGTTCCCTGTTGAGAGAAAATGGGCCCTTGGGCTTCAG                         TCTCGAGCCCAACCACGTGAAAT
genomic: GAATGCGGCAACAGTTCCCTGTTGAGAGAAAATGGGCCCTTGGGCTTCAGgtgcagtgtt ... cttgtgatagTCTCGAGCCCAACCACGTGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatggttacttgtgactgaggtctttgttggttatgtttgttaacttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAAGAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCA
                                       tgttaac  putative branch site (score: 2)
                                ttatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattaatggttatcagaaatattgaagttctgatgtacttattttgatggttacttgtgactgaggtctttgttggttatgtttgttaacttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAAGAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG