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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttattacaatgttttttttttttttggtcttgatatccgggttacgttgtctatttatgattctgagttgtctgtttttttttttaaacattgtcagAGGGGCTTTGATCAACAATGGCTGTCATTAACATTCTCTAAGGCTATATTTCTTGGAAATGGTCTTGTTGCTATTTTGTCTGGGCTGTTTGGAAATGTAC

Basic information

species Glycine max
transcript GLYMA04G41090.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 3
ttcttattacaatgttttttttttttttg-gtcttgatatccgggttacgttgtc-tatttatgattctgagttgtctgtttttttttttaaacattgt-cagAGGGGCTTTGATCAACAATGGCTGTCATTAACATTCTCTAAGGCTATATTTCTTGGAAATGGTCTTGTTGCTATTTTGTCTGGGCTGTTTGGAAATGTAC
    ||  | | || ||   |  ||   |     |  ||| |   |    | |   |     ||||| |  |||| |   |     | |       ||| ||||| || ||||| | ||| ||| ||||  |||||||||| ||||||||||||||||||||||| || ||||| ||  |  ||||||| |||| |||| | |
--tctacgaaactgattaactagttacagcaatcttttattcaaatcttttgggaattcccttgattatctgttgac-actgcaaatctaccttgctgtacagAGAGGATTTGACCCACAGTGGTTGTCGATAACATTCTCCAAGGCTATATTTCTTGGAAATGGCCTAGTTGCGATCATCGCTGGGCTATTTGCAAATCTGC

upper sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g02380.2 (Oryza sativa), 3'ss of exon 3
--ttcttatt-acaatgttttttttttttttggtcttgatatccgggttacgttgtctatttatgattctgagttgtctgtttttttttttaaacattgtcagAGGGGCTTTGATCAACAATGGCTGTCATTAACATTCTCTAAGGCTATATTTCTTGGAAATGGTCTTGTTGCTATTTTGTCTGGGCTGTTTGGAAATGTAC
  || |  ||  |||  || |    | | ||    |  || ||     | |||| || |||| | | | | |  | |    ||    |||    | ||  ||||| || ||||||  ||||||||||||  | |||||||| ||||||||||||||||| ||||| || || || ||| | || ||||| |||| |||  | |
ccttgtcgtttgcaaacttctccaatgtattacagtcaatttcttatctgcgttatcaatttttcactgtaaagtttaaccttggcatttc---ctttcacagAGAGGTTTTGATTCACAATGGCTGTCGATCACATTCTCCAAGGCTATATTTCTTGGCAATGGCCTGGTCGCAATTGTATCCGGGCTATTTGCAAACCTGC

upper sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G067638_T01 (Zea mays), 3'ss of exon 3
ttcttattacaatgttttttttttttttggtcttgatatccgggttacgttgtctatttatgattctg--agttgtctgtttttttttttaaacattgt-cagAGGGGCTTTGATCAACAATGGCTGTCATTAACATTCTCTAAGGCTATATTTCTTGGAAATGGTCTTGTTGCTATTTTGTCTGGGCTGTTTGGAAATGTAC
   |  ||   || ||| |  |  |   |   |||||  |   |||   |  |    || || |  ||       |  |   ||||      | ||||| ||||  || ||||||| ||||||| ||||  |||||||||| ||||||||||||||||| |||||||| || || ||| |  |||| || |||| |||| | |
---tcttttttatttttctaatgataaagccattgatggctttgttttctcattcccttttgttcttgctgacaatgggcaattttacactgatattgtacagAAAGGATTTGATCCACAATGGTTGTCGATAACATTCTCCAAGGCTATATTTCTTGGCAATGGTCTAGTGGCCATTGTTGCTGGCCTATTTGCAAATTTTC

upper sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 3
ttcttattacaatgttttttttttttttggtcttgatatccgggttac---gttgtcta--tttatgattctgagttgtctgtttttttttttaaacattgt-cagAGGGGCTTTGATCAACAATGGCTGTCATTAACATTCTCTAAGGCTATATTTCTTGGAAATGGTCTTGTTGCTATTTTGTCTGGGCTGTTTGGAAATGTAC
        | || |  ||  | |  ||   |     ||   ||| ||    ||||| |   ||| | ||  |  ||||  | || || | ||      |||| |||||||| ||||| ||||| ||||||||| | |||||||||||||| ||||||||||| ||||||||  |||| ||| |||||||  |||||||||||||||
------aaaaaaagccttcgtgtggttaacttcaagtagttgggatataatgttgtgttgttttgttatattatgttggttcttattgtgttccttgcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTTCTTGGCAATGGTCTAATTGCCATTCTGTCTGGATTGTTTGGAAATGTAC

upper sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 3
-----ttcttattacaatgttttttttttttttggtcttgatatccgggttacgttgtctattt--atgattctgagttgtctgtttttttttttaaacattgtcagAGGGGCTTTGATCAACAATGGCTGTCATTAACATTCTCTAAGGCTATATTTCTTGGAAATGGTCTTGTTGCTATTTTGTCTGGGCTGTTTGGAAATGTAC
      ||| | |    |   |   |  | |    |  | || || |  ||||  |||||||||  |||||| | |        | ||     |||| |  || |||||||||||||| ||||| ||| ||||  | ||||| || ||||| ||||||||||| ||||| |||||||||||| | |||||| ||||||||||| |||
accccctctaaatcttgtcaataactgatgtagaattcttatttcagaattac-ctgtctattttgatgattgtaa-----taatattccaccttaatctgtg-cagAGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTTCTTGGCAATGGCCTTGTTGCTATTCTCTCTGGGTTGTTTGGAAATCTAC

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|193450488|gb|FK412076.1|FK412076
EST:     CACTTCTGTTTTCAGCATTTGAATCATGGCTTGTTGCCGAGCACTTCAAG                         AGGGGCTTTGATCAACAATGGCTGTCATTAACATTCTCTAAGGCTATATTT
genomic: CACTTCTGTTTTCAGCATTTGAATCATGGCTTGTTGCCGAGCACTTCAAGgtgaggaata ... acattgtcagAGGGGCTTTGATCAACAATGGCTGTCATTAACATTCTCTAAGGCTATATTT
EST: gi|6718954|gb|AW306601.1|AW306601
EST:     CACTTCTGTTTTCAGCATTTGAATCATGGCTTGTTGCCGAGCACTTCAAG                         AGGGGCTTTGATCAACAATGGCTGTCATTAACATTCTCTA
genomic: CACTTCTGTTTTCAGCATTTGAATCATGGCTTGTTGCCGAGCACTTCAAGgtgaggaata ... acattgtcagAGGGGCTTTGATCAACAATGGCTGTCATTAACATTCTCTA
EST: gi|208193531|gb|GD991604.1|GD991604
EST:     CACTTCTGTTTTCAGCATTTGAATCATGGCTTGTTGCCGAGCACTTCAAG                         AGGGGCTTTGATCAACAATGGCTGTCATTAACAATTACTACTAAAGGCTAT
genomic: CACTTCTGTTTTCAGCATTTGAATCATGGCTTGTTGCCGAGCACTTCAAGgtgaggaata ... acattgtcagAGGGGCTTTGATCAACAATGGCTGTCATTAACA-TT-CT-CTAA-GGCTAT
EST: gi|19345775|gb|BM890655.1|BM890655
EST:     CACTTCTGTTTTCAGCATTTGAATCATGGCTTGTTGCCGAGCACTTCAAG                         AGGGGCTTTGATCAACAATGGCTGTCATTAACATTCTCTAAGGCTATATTT
genomic: CACTTCTGTTTTCAGCATTTGAATCATGGCTTGTTGCCGAGCACTTCAAGgtgaggaata ... acattgtcagAGGGGCTTTGATCAACAATGGCTGTCATTAACATTCTCTAAGGCTATATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacgttgtctatttatgattctgagttgtctgtttttttttttaaacattgtcagAGGGGCTTTGATCAACAATGGCTGTCATTAACATTCTCTAAGGCTATATTTCTTGGAAATGGTCTTGTTGCTATTTTGTCTGGGCTGTTTGGAAATGTAC
                            tctgttttttttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttattacaatgttttttttttttttggtcttgatatccgggttacgttgtctatttatgattctgagttgtctgtttttttttttaaacattgtcagAGGGGCTTTGATCAACAATGGCTGTCATTAACATTCTCTAAGGCTATATTTCTTGGAAATGGTCTTGTTGCTATTTTGTCTGGGCTGTTTGGAAATGTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - -caatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gattctg