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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttgtccctgtcattttatgttgatcattatttgaagaatgtcattttgtctcacttattatttaacaagattaaaatcttgtgactgcaatatggcagAGTATATTGCTGAAAGCAAGCCTCTTGGGGGTTTAATATTTTTGCTTCCCCGGATGTTCAGTTTTGAAAACAAAGATGGTATGGGAAGTAATCATCAAGA

Basic information

species Glycine max
transcript GLYMA11G18710.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G18710.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0080g00880.t01 (Vitis vinifera), 3'ss of exon 1
tcttgtccctgtcattttatgttgatca--ttatttgaagaatgtcattttgtctcacttattatttaacaagattaaaatcttgtgactgcaatatggcagAGTATATTGCTGAAAGCAAGCCTCTTGGGGGTTTAATATTTTTGCTTCCCCGGATGTTCAGTTTTGAAAACAAAGATGGTATGGGAAGTAATCATCAAGA
  |    || || |||  |  |  |||   ||   ||||   |      |||| | | ||||| | |||  ||  |  |   || || |  | |||| ||||| |||||| |  | |   ||||||| |||||| || ||||||||||||| |||||| | |||| |||||||| |||||  ||||| ||   | | |||  
-gtctaaccagttattcaacctgtatctgtttggctgaaatttaatgccttgt-tgatttattttctaattagtatctatctttatggcaaccatattgcagACTATATTACACAGAAACAGCCTCTGGGGGGTCTATTATTTTTGCTTCCTCGGATGATTAGTTCTGAAAACAGAGATGACATGGGGAGAGGTGACCAAAC
















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|209713102|gb|BW653809.1|BW653809
EST:     CACCGTCCTCCTCATACCGCTTCGTGAACTCAACATGTCTTTTGTCAAAG                         AGTATATTGCTGAAAGCAAGCCTCTTGGGGGTTTAATATTT
genomic: CACCGTCCTCCTCATACCGCTTCGTGAACTCAACATGTCTTTTGTCAAAGgttcttcttc ... aatatggcagAGTATATTGCTGAAAGCAAGCCTCTTGGGGGTTTAATATTT
EST: gi|19053254|gb|BM731921.1|BM731921
EST:     CACCGTCCTCCTCATACCGCTTCGTGAACTCAACATGTCTTTTGTCAAAG                         AGTATATTGCTGAAAGCAAGCCTCTTGGGGGTTTAATATTTTTGCTTCCCC
genomic: CACCGTCCTCCTCATACCGCTTCGTGAACTCAACATGTCTTTTGTCAAAGgttcttcttc ... aatatggcagAGTATATTGCTGAAAGCAAGCCTCTTGGGGGTTTAATATTTTTGCTTCCCC
EST: gi|6502320|gb|AW203693.1|AW203693
EST:     CACCGTCCTCCTCATACCGCTTCGTGAACTCAACATGTCTTTTGTCAAAG                         AGTATATTGCTGAAAGCAAGCCTCTTGGGGGTTTAATATTTTTGCTTCCCC
genomic: CACCGTCCTCCTCATACCGCTTCGTGAACTCAACATGTCTTTTGTCAAAGgttcttcttc ... aatatggcagAGTATATTGCTGAAAGCAAGCCTCTTGGGGGTTTAATATTTTTGCTTCCCC
EST: gi|15284923|gb|BI468814.1|BI468814
EST:     CACCGTCCTCCTCATACCGCTTCGTGAACTCAACATGTCTTTTGTCAAAG                         AGTATATTGCTGAAAGCAAGCCTCTTGGGGGTTTAATATTTTTGCTTCCCC
genomic: CACCGTCCTCCTCATACCGCTTCGTGAACTCAACATGTCTTTTGTCAAAGgttcttcttc ... aatatggcagAGTATATTGCTGAAAGCAAGCCTCTTGGGGGTTTAATATTTTTGCTTCCCC
EST: gi|209720188|gb|BW674526.1|BW674526
EST:     CACCGTCCTCCTCATACCGCTTCGTGAACTCAACATGTCTTTTGTCAAAG                         AGTATATTGCTGAAAGCAAGCCTCTTGGGGGTTTAATATTTTTGCTTCCCC
genomic: CACCGTCCTCCTCATACCGCTTCGTGAACTCAACATGTCTTTTGTCAAAGgttcttcttc ... aatatggcagAGTATATTGCTGAAAGCAAGCCTCTTGGGGGTTTAATATTTTTGCTTCCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtctcacttattatttaacaagattaaaatcttgtgactgcaatatggcagAGTATATTGCTGAAAGCAAGCCTCTTGGGGGTTTAATATTTTTGCTTCCCCGGATGTTCAGTTTTGAAAACAAAGATGGTATGGGAAGTAATCATCAAGA
                atttaac  putative branch site (score: 3)
         acttattatttaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttgtccctgtcattttatgttgatcattatttgaagaatgtcattttgtctcacttattatttaacaagattaaaatcttgtgactgcaatatggcagAGTATATTGCTGAAAGCAAGCCTCTTGGGGGTTTAATATTTTTGCTTCCCCGGATGTTCAGTTTTGAAAACAAAGATGGTATGGGAAGTAATCATCAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - ccctgtc
- - - - - - - - - -tgttgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgactgc