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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctattgagagttgaatgcaatatttgtatatttaatggaacacaagaagaaagtgaaagtggaagcatgtcattgattttagtgatgatcaaacttgcagTCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGATTAGAGAGGCAGCTGCGTTATTTAGGCTGCTCAAGTCATTGGAATGATT

Basic information

species Glycine max
transcript GLYMA10G00610.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G00610.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv07s0130g00310.t01 (Vitis vinifera), 3'ss of exon 11
ctattgagagttgaatgcaatatttgtatatttaatg--gaacacaagaagaaagtgaaagtggaagcatgtcattgattttagtgatgatcaaacttgcagTCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGATTAGAGAGGCAGCTGCGTTATTTAGGCTGCTCAAGTCATTGGAATGATT
  |   || | |         ||  ||||||  || |  ||| ||||     |||  | |||    ||   |  || || |||    ||        ||||||  ||||||| ||||||||||||||||| || || |||||||| ||| ||||||| || || ||||   |||||||||| || ||  | |||||||  | 
gcaccaagtgattggaattgcatg-gtatatgcaaggatgaatacaatttacaag-aatagtttttgctgattctttatgttatgattgtggttgggtgcagTTCAAGATCTTTTCATTGAAGTTCAAGCCTTCTGTATCGAGTTCTCAAGGATTAGGGAAGCTGCTGGACTATTTAGGCTTCTTAAAACTTTGGAATCTTG

upper sequence: GLYMA10G00610.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ16277 (Selaginella moellendorffii), 3'ss of exon 6
ctattgagagttgaatgcaatatttgtatatttaatggaacacaagaagaaagtgaaagtggaagcatgtcattgattttagtgatgatcaaacttgcagTCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGATTAGAGAGGCAGCTGCGTTATTTAGGCTGCTCAAGTCATTGGAATGATT
                                ||| | || |||         |   | ||    | |  | ||  |||  ||| ||       |  ||||  | ||||| || || |||||||||||||| |||||||||||||| || || |||||||| || |   | || ||||||||||||||| ||||||    
-------------------------------gtaacgaaaaacatttttc---tcttactgaggacttaacgttagttt--gtggtg-------taacagTTCACGATCTGTTTATCGAAGTTCAAGCGTTCTGCATCGAGTTTTCCCGCATCAGAGAGGCCGCGGGCCTTTTCAGGCTGCTCAAGTCACTGGAATAG--
















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|208282132|gb|GE076814.1|GE076814
EST:     ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATG                         TCAAAGATCTCTTCATTGAAGTTCAAG
genomic: ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATGgtgagtttac ... aaacttgcagTCAAAGATCTCTTCATTGAAGTTCAAG
EST: gi|31474652|gb|CD416680.1|CD416680
EST:     ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATG                         TCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
genomic: ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATGgtgagtttac ... aaacttgcagTCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
EST: gi|10232329|gb|BE801217.1|BE801217
EST:     ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATG                         TCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
genomic: ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATGgtgagtttac ... aaacttgcagTCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
EST: gi|16344608|gb|BI970203.1|BI970203
EST:     ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATG                         TCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
genomic: ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATGgtgagtttac ... aaacttgcagTCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
EST: gi|26057582|gb|CA800496.1|CA800496
EST:     ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATG                         TCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
genomic: ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATGgtgagtttac ... aaacttgcagTCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
EST: gi|214009017|gb|DB987096.1|DB987096
EST:     ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATG                         TCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
genomic: ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATGgtgagtttac ... aaacttgcagTCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
EST: gi|31458111|gb|CD400139.1|CD400139
EST:     ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATG                         TCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
genomic: ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATGgtgagtttac ... aaacttgcagTCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
EST: gi|14008705|gb|BG725309.1|BG725309
EST:     ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATG                         TCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
genomic: ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATGgtgagtttac ... aaacttgcagTCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
EST: gi|10710646|gb|BF010364.1|BF010364
EST:     ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATG                         TCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
genomic: ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATGgtgagtttac ... aaacttgcagTCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
EST: gi|23053081|gb|BU577572.1|BU577572
EST:     ACTTGTCTGTGTTTTTCTGCAAATTCTCATTCGGAACAACATTATTAATG                         TCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
genomic: ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATGgtgagtttac ... aaacttgcagTCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
EST: gi|151393880|gb|EV263751.1|EV263751
EST:     ACTTGTTTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATG                         TCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
genomic: ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATGgtgagtttac ... aaacttgcagTCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
EST: gi|9900317|gb|BE609285.1|BE609285
EST:     ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATG                         TCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
genomic: ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATGgtgagtttac ... aaacttgcagTCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
EST: gi|208204197|gb|GE007436.1|GE007436
EST:     TTCTGCAAAGCCTCATTCGGAACAACATTATTAATG                         TCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA
genomic: TTCTGCAAAGCCTCATTCGGAACAACATTATTAATGgtgagtttac ... aaacttgcagTCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagaaagtgaaagtggaagcatgtcattgattttagtgatgatcaaacttgcagTCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGATTAGAGAGGCAGCTGCGTTATTTAGGCTGCTCAAGTCATTGGAATGATT
                         cattgat  putative branch site (score: 4)
                          attgatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctattgagagttgaatgcaatatttgtatatttaatggaacacaagaagaaagtgaaagtggaagcatgtcattgattttagtgatgatcaaacttgcagTCAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGGATTAGAGAGGCAGCTGCGTTATTTAGGCTGCTCAAGTCATTGGAATGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - gaatgca
- - - - - - - - - - - - - - - - - - - - - -aagaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgat