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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctattgagagttgaatgtaattttgtatatttactggcacacaagaagaaagtgaaaatggctacatgtcactgattttagtgatgatcccaacttgcagTTAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGTATTAGAGAGGCAGCTGCGTTATTTAGGCTGCTCAAGTCATTGGAATGATT

Basic information

species Glycine max
transcript GLYMA02G00750.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G00750.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv07s0130g00310.t01 (Vitis vinifera), 3'ss of exon 11
ctattgagagttgaatgtaattttgta-tatttactggcacacaagaagaaagtgaaaatggctacatgtcactgattttagtgatgatcccaact---tgcagTTAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGTATTAGAGAGGCAGCTGCGTTATTTAGGCTGCTCAAGTCATTGGAATGATT
        |  ||| || ||||   |  ||| | |  | |   |   |       | ||| | |   ||    |  |||  || |||||      |   ||||||| ||||||| ||||||||||||||||| || || |||||||| ||| | ||||| || || ||||   |||||||||| || ||  | |||||||  | 
---gcaccaagtgattggaattgcatggtatatgcaaggatgaatacaatttacaagaatagtttt-tgctgattctttatgttatgattgtggttgggtgcagTTCAAGATCTTTTCATTGAAGTTCAAGCCTTCTGTATCGAGTTCTCAAGGATTAGGGAAGCTGCTGGACTATTTAGGCTTCTTAAAACTTTGGAATCTTG

upper sequence: GLYMA02G00750.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ16277 (Selaginella moellendorffii), 3'ss of exon 6
ctattgagagttgaatgtaattttgtatatttactggcacacaagaagaaagtgaaaatggctacatgtcactgat--tttagtgatgatcccaactt--gcagTTAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGTATTAGAGAGGCAGCTGCGTTATTTAGGCTGCTCAAGTCATTGGAATGATT
                                               | ||   ||||    |   | | |||||    |||  | |  |      |    ||||| | ||||| || || |||||||||||||| |||||||||||||| || || |||||||| || |   | || ||||||||||||||| ||||||    
-----------------------------------------------gtaacgaaaaacatttttctcttactgaggacttaacgttagtttgtggtgtaacagTTCACGATCTGTTTATCGAAGTTCAAGCGTTCTGCATCGAGTTTTCCCGCATCAGAGAGGCCGCGGGCCTTTTCAGGCTGCTCAAGTCACTGGAATAG--
















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|254328005|gb|GR834970.1|GR834970
EST:     ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAATATTATTAATG                         TTAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGTA
genomic: ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAATATTATTAATGgtgagtttac ... caacttgcagTTAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGTA
EST: gi|254328398|gb|GR835363.1|GR835363
EST:     ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAATATTATTAATG                         TTAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGTA
genomic: ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAATATTATTAATGgtgagtttac ... caacttgcagTTAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGTA
EST: gi|254328006|gb|GR834971.1|GR834971
EST:     ACTTGTCTGTGNNNNNNNGCAAAGCCTCATTCGGAACAATATTATTAATG                         TTAAAGATCTTTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGTA
genomic: ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAATATTATTAATGgtgagtttac ... caacttgcagTTAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGTA
EST: gi|214007170|gb|DB990497.1|DB990497
EST:     ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAATATTATTAATG                         TTAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGTA
genomic: ACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAATATTATTAATGgtgagtttac ... caacttgcagTTAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaaagtgaaaatggctacatgtcactgattttagtgatgatcccaacttgcagTTAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGTATTAGAGAGGCAGCTGCGTTATTTAGGCTGCTCAAGTCATTGGAATGATT
                        cactgat  putative branch site (score: 3)
                           tgatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctattgagagttgaatgtaattttgtatatttactggcacacaagaagaaagtgaaaatggctacatgtcactgattttagtgatgatcccaacttgcagTTAAAGATCTCTTCATTGAAGTTCAAGCGTTTTGCATCGAGTTTTCACGTATTAGAGAGGCAGCTGCGTTATTTAGGCTGCTCAAGTCATTGGAATGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - gaatgta
- - - - - - - - - - - - - - - ttactgg
- - - - - - - - - - - - - - - - - - -cacacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgat