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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgtttatttcaccaattttcttgtggtaaatttcttacacttacatgttcttctaactatgcattcttcactgttctatgtaaaattctatttggcagATACGAAGTCATGCACAAAAGTATTTTCTTAAAGTTCAGAAGAATGGAACAAGTGAACATGTACCTCCTCCTCGGCCAAAGAGAAAAGCTGCTCGCCCAT

Basic information

species Glycine max
transcript GLYMA16G03640.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G03640.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0046g02260.t01 (Vitis vinifera), 3'ss of exon 2
-agtgtttatttcaccaattttct---tgtggtaaatttcttacacttacatgttcttctaactatgcattcttcactgttctatgtaaaattctatttggcagATACGAAGTCATGCACAAAAGTATTTTCTTAAAGTTCAGAAGAATGGAACAAGTGAACATGTACCTCCTCCTCGGCCAAAGAGAAAAGCTGCTCGCCCAT
 | | | ||    |||| | | |     ||||| |        | |    ||| |  | | | |     |  |    | |   ||   | |||    || ||||||||| || ||||| |||||||| ||| | || |||||||| ||||| |||||||||||||| |||||||||||||||||||| ||||| || |  ||||
taatttctaggcaaccattctgcagcacgtggttatgcatggtccccactatgcttgtatgattccctttcatatcttttcacatacgagatt----tttgcagATACGTAGCCATGCGCAAAAGTACTTTTTGAAGGTTCAGAAAAATGGTACAAGTGAACATGTGCCTCCTCCTCGGCCAAAGAGGAAAGCAGCCCATCCAT

upper sequence: GLYMA16G03640.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S198_135V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------------------------------------------------agtgtttat--ttcaccaatttt-----cttgtggtaaatt-tcttacacttacatgttctt-ctaactatgcattcttcac-tgttctatgtaaaattctatttg-gcagATACGAAGTCATGCACAAAAGTATTTTCTTAAAGTTCAGAAGAATGGAACAAGTGAACATGTACCTCCTCCTCGGCCAAAGAGAAAAGCTGCTCGCCCAT
                                                                                      ||| || ||  ||   || | |      | |||  | | || | || |  ||  | |||||| || |  |  |    ||||  || |     | |  ||   || | |||||| ||||| ||||||||||| |||||||| ||||||||||| ||  ||||  | || ||||| ||||| || || || ||  | ||  | ||||  ||||
gtacaatgacgttctcgctgattttcgcatggagagagaatctacgttcacattgttctagtcttgcgggttttagtgcacaaagcagttttcatgttttttcagtgtgtgagacatgttctcagttatttttccttttgaagttcttgcttatgaaacgaaattcatatgctgctctttatgttaatttcgtgcagATCCGAAGCCATGCACAAAAATATTTTCTGAAAGTTCAGAAAAACAGAACTGGCGAGCATGTTCCTCCACCACGTCCGAAACGCAAGTCCGCTCAACCAT

upper sequence: GLYMA16G03640.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S46_272V6.1 (Physcomitrella patens), 3'ss of exon 2
--agtgtttatttcaccaattttcttgtggtaaatttcttacacttacatgttcttctaactatgcattcttcactgttctatgtaaaattctatttggcagATACGAAGTCATGCACAAAAGTATTTTCTTAAAGTTCAGAAGAATGGAACAAGTGAACATGTACCTCCTCCTCGGCCAAAGAGAAAAGCTGCTCGCCCAT
  |  ||   |||   | |           |     | |   | | |  |  | |||| | | |   |   | | |  ||| |  ||     | ||  |||||| |||||||| || ||||| |||||| | ||||| ||||||||||||||  | |||||||| ||||| || || || ||  | ||  | ||||  ||||
ccaaggtcagtttatgcgaccaaaacaaacttggcctatagaagtgaattcattttcttattgtcggt--gttatttatctttaaaatccatttttatgcagATCCGAAGTCACGCTCAAAAATATTTTTTAAAAGTACAGAAGAATGGAACTGGGGAACATGTTCCTCCGCCACGACCGAAACGCAAGTCAGCTCAACCAT

upper sequence: GLYMA16G03640.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ36434 (Selaginella moellendorffii), 3'ss of exon 2
agtgtttatttcaccaattttcttgtggtaaatttcttacacttacatgttcttctaactatgcattc--ttcactgttctatgtaaaattctatttggcagATACGAAGTCATGCACAAAAGTATTTTCTTAAAGTTCAGAAGAATGGAACAAGTGAACATGTACCTCCTCCTCGGCCAAAGAGAAAAGCTGCTCGCCCAT
                           || || ||| |   |||   |  | ||||      | |||   |||  |  | | ||  || |||       |||||  |||||||||| || ||||||||| | ||||| ||||||||||||||  | ||||| || |||||||| ||||| ||| | ||| ||||||  ||||
---------------------------gtgaaattcctttgctttattcatgttcttcgcggggatttagttcgttagtgtgtgacaatttc-------cagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAGCGTAAATCTGCTCAACCAT

upper sequence: GLYMA16G03640.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ04991 (Selaginella moellendorffii), 3'ss of exon 2
agtgtttatttcaccaattttcttgtggtaaatttcttacacttacatgttcttctaactatgcattc--ttcactgttctatgtaaaattctatttggcagATACGAAGTCATGCACAAAAGTATTTTCTTAAAGTTCAGAAGAATGGAACAAGTGAACATGTACCTCCTCCTCGGCCAAAGAGAAAAGCTGCTCGCCCAT
                           || || ||| |   |||   |  | ||||      | |||   |||  |  | | ||  || |||       |||||  |||||||||| || ||||||||| | ||||| ||||||||||||||  | ||||| || |||||||| ||||| ||  | ||| ||||||  ||||
---------------------------gtgaaattcctttgctttattcatgttcttcgcggggatttagttcgttagtgtgtgacaatttc-------cagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAACGTAAATCTGCTCAACCAT

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|7691405|gb|AW759533.1|AW759533
EST:     GGGACTGGAAAAAGATTGAAGCATTTGTTGGTTCAAAAACAGTTATCCAG                         ATACGAAGTCATGCACAAAAGTATTTTCTTAAAGTTCAGAAGAATGGAACA
genomic: GGGACTGGAAAAAGATTGAAGCATTTGTTGGTTCAAAAACAGTTATCCAGgtatttataa ... tatttggcagATACGAAGTCATGCACAAAAGTATTTTCTTAAAGTTCAGAAGAATGGAACA
EST: gi|208047174|gb|GD845615.1|GD845615
EST:     GGGACTGGAAAAAGATTGAAGCATTTGTTGGTTCAAAAACCGTTATCCAG                         ATACGAAGTCATGCAACAAAAGTATTTTCTTAAAGTTCAGAAG
genomic: GGGACTGGAAAAAGATTGAAGCATTTGTTGGTTCAAAAACAGTTATCCAGgtatttataa ... tatttggcagATACGAAGTCATGCA-CAAAAGTATTTTCTTAAAGTTCAGAAG
EST: gi|7926397|gb|AW832423.1|AW832423
EST:     GGGACTGGAAAAAGATTGAAGCATTTGTTGGTTCAAAAACAGTTATCCAG                         ATACGAAGTCATGCACAAAAGTATTTTCTTAAAGTTCAGAAGAATGGAACA
genomic: GGGACTGGAAAAAGATTGAAGCATTTGTTGGTTCAAAAACAGTTATCCAGgtatttataa ... tatttggcagATACGAAGTCATGCACAAAAGTATTTTCTTAAAGTTCAGAAGAATGGAACA
EST: gi|207795863|gb|GD764102.1|GD764102
EST:     GGGACTGGAAAAAGATTGAAGCATTTGTTGGTTCAAAAACAGTTATCCAG                         ATACGAAGTCATGCACAGAAGTATTTTCTTAAAGTTCAGAAGAAGGGAACA
genomic: GGGACTGGAAAAAGATTGAAGCATTTGTTGGTTCAAAAACAGTTATCCAGgtatttataa ... tatttggcagATACGAAGTCATGCACAAAAGTATTTTCTTAAAGTTCAGAAGAATGGAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgttcttctaactatgcattcttcactgttctatgtaaaattctatttggcagATACGAAGTCATGCACAAAAGTATTTTCTTAAAGTTCAGAAGAATGGAACAAGTGAACATGTACCTCCTCCTCGGCCAAAGAGAAAAGCTGCTCGCCCAT
       ttctaac  putative branch site (score: 1)
                                          ttctattt  putative PPT
                                 tatgtaaaattctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgtttatttcaccaattttcttgtggtaaatttcttacacttacatgttcttctaactatgcattcttcactgttctatgtaaaattctatttggcagATACGAAGTCATGCACAAAAGTATTTTCTTAAAGTTCAGAAGAATGGAACAAGTGAACATGTACCTCCTCCTCGGCCAAAGAGAAAAGCTGCTCGCCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - tcaccaa
- - - - - - - - - - tcttgtg
- - - - - - - - - - - - - - - - - -cttacac
- - - - - - - - - - - - - - - - - - - - - - -catgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatgca