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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatttgcttgactggctggatttggtgtactttatacttttgctgatctatattgtgatcaaataaatggtacttatttcattgaatttttatttggcagTGAAGATGGAAGACTTAGCTGTGGTTATTCAAGTTTTAGGGGAAAGAGAGTGACAATGGAAGATTTTTATGATATTAAGACATTGAAGATTGGTGGCCAA

Basic information

species Glycine max
transcript GLYMA13G08090.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G08090.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g02570.t01 (Vitis vinifera), 3'ss of exon 2
gatttgctt-gactggctggatttggtg-tactttatacttttgctgatctatattgtgatcaa-ataaatggtacttatttcattgaatttttatttggcagTGAAGATGGAAGACTTAGCTGTGGTTATTCAAGTTTTAGGGGAAAGAGAGTGACAATGGAAGATTTTTATGATATTAAGACATTGAAGATTGGTGGCCAA
   |||||  || ||  |   |||| |  || |   ||| | |  |  | |  | |||| |||  || | |  ||  |  ||  ||   | | |  ||| ||||||||| |||| ||| |||||||| ||||||||||| |||||||||||||  |  ||||| ||||| |||||| | || |  |  ||||||| ||| |||
-tgttgctgagaatgtatatgtttgatactagtgactacctgtattagtatgaactgtggtcagcatcactcttatct--ttggtttcttgtctgattgacagTGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGCTAGCATGGAGGATTTCTATGATGTAAAAATGTCCAAGATTGATGGGCAA
















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|151411248|gb|EV281059.1|EV281059
EST:     ATGCCAGAGAAAGATGATGATGGTCGATTTGCTAGTGGAGGGTGGAAAAG                         TGAAGATGGAAGACTTAGCTGTGGTTATTCAAGTTTTAGGGGAAAGAGAGT
genomic: ATGCCAGAGAAAGATGATGATGGTCGATTTGCTAGTGGAGGGTGGAAAAGgtgaatatga ... tatttggcagTGAAGATGGAAGACTTAGCTGTGGTTATTCAAGTTTTAGGGGAAAGAGAGT
EST: gi|298196173|gb|HO044564.1|HO044564
EST:     GATGGTCGATTTGCTAGTGGAGGGTGGAAAAG                         TGAAGATGGAAGACTTAGCTGTGGTTATTCAAGTTTTAGGGGAAAGAGAGT
genomic: GATGGTCGATTTGCTAGTGGAGGGTGGAAAAGgtgaatatga ... tatttggcagTGAAGATGGAAGACTTAGCTGTGGTTATTCAAGTTTTAGGGGAAAGAGAGT
EST: gi|209700604|gb|BW670420.1|BW670420
EST:     ATGCCAGAGAAAGATGATGATGGTCGATTTGCTAGTGGAGGGTGGAAAAG                         --A---TGGAAGACTTAGCTGTGGTTATTCAAGTTTTAGGGGAAAGAGAGT
genomic: ATGCCAGAGAAAGATGATGATGGTCGATTTGCTAGTGGAGGGTGGAAAAGgtgaatatga ... tatttggcagTGAAGATGGAAGACTTAGCTGTGGTTATTCAAGTTTTAGGGGAAAGAGAGT
EST: gi|7640592|gb|AW734820.1|AW734820
EST:     ATGCCAGAGAAAGATGATGATGGTCGATTTGCTAGTGGAGGGTGGAAAAG                         TGAAGATGGAAGACTTAGCTGTGGTTATTCAAGTTTTAGGGGAAAGAGAGT
genomic: ATGCCAGAGAAAGATGATGATGGTCGATTTGCTAGTGGAGGGTGGAAAAGgtgaatatga ... tatttggcagTGAAGATGGAAGACTTAGCTGTGGTTATTCAAGTTTTAGGGGAAAGAGAGT
EST: gi|254313836|gb|GR831465.1|GR831465
EST:     ATGCCAGAGAAAGATGATGATGGTCGATTTGCTAGTGGAGGGTGGAAAAG                         TGAAGATGGAAGACTTAGCTGTGGTTATTCAAGTTTTAGGGGAAAGAGAGT
genomic: ATGCCAGAGAAAGATGATGATGGTCGATTTGCTAGTGGAGGGTGGAAAAGgtgaatatga ... tatttggcagTGAAGATGGAAGACTTAGCTGTGGTTATTCAAGTTTTAGGGGAAAGAGAGT
EST: gi|120531892|gb|EH260025.1|EH260025
EST:     ATGCCAGAGAAAGATGATGATGGTCGATTTGCTAGTGGAGGGTGGAAAAG                         TGAAGATGGAAGACTTAGCTGTGGTTATTCAAGTTTTAGGGGAAAGAGAGT
genomic: ATGCCAGAGAAAGATGATGATGGTCGATTTGCTAGTGGAGGGTGGAAAAGgtgaatatga ... tatttggcagTGAAGATGGAAGACTTAGCTGTGGTTATTCAAGTTTTAGGGGAAAGAGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctatattgtgatcaaataaatggtacttatttcattgaatttttatttggcagTGAAGATGGAAGACTTAGCTGTGGTTATTCAAGTTTTAGGGGAAAGAGAGTGACAATGGAAGATTTTTATGATATTAAGACATTGAAGATTGGTGGCCAA
 tgctgat  putative branch site (score: 3)
                                         tttttattt  putative PPT
               aaataaatggtactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatttgcttgactggctggatttggtgtactttatacttttgctgatctatattgtgatcaaataaatggtacttatttcattgaatttttatttggcagTGAAGATGGAAGACTTAGCTGTGGTTATTCAAGTTTTAGGGGAAAGAGAGTGACAATGGAAGATTTTTATGATATTAAGACATTGAAGATTGGTGGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - tgcttga
- - - - - - tggctgg
- - - - - - - - - - tttggtg
- - - - - - - - - - - - - - - - - - - - tgctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa