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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgactgccgagcgtccgaggatgtgttttcttatatttgatgatacctggttctttttttttttttttttttttaactcaattatacatgctttgccagGCGGATCTAAATCAAGCCATTTCGATGGTTTCATATTATGCTTCATCTTCAGAACCAGCTATGGTTCGTGGTAAAACTGTTTACATTCAGTATTCTAATA

Basic information

species Glycine max
transcript GLYMA09G37080.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 1
gtgact-gccgagcgtccgaggatgtgttttcttatatttgatgatacctggttctttttttttttttttttttttaactcaattatacatgctttgccagGCGGATCTAAATCAAGCCATTTCGATGGTTTCATATTATGCTTCATCTTCAGAACCAGCTATGGTTCGTGGTAAAACTGTTTACATTCAGTATTCTAATA
 ||| |   ||   ||   |  |||     |    | |    ||     ||  |   | || ||| ||  |   |||  | |   ||  |   |||  ||||| |||| ||| || || ||||| |||||||||||||||||||| ||||||||||| |||   |||||||| |||||||| || || ||||| || || |
ttgatttagcggaagtttcaa-atgaacagtgaactgtagactggacattgaattgctgttctttgttcctcacttatattataaatgtaccttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA

upper sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g25980.1 (Oryza sativa), 3'ss of exon 1
gtgactgccgagcgtccgaggatgtgttttcttatatttgatgatacctggttcttttt---ttttttttttttttttaactcaattatacatgctttgccagGCGGATCTAAATCAAGCCATTTCGATGGTTTCATATTATGCTTCATCTTCAGAACCAGCTATGGTTCGTGGTAAAACTGTTTACATTCAGTATTCTAATA
  ||      | | ||| |  |  | | || || | | |  | ||   |  ||  |  |   |  |     ||  ||   |  |   || | | |||||| || | ||  | |||||||| |||||||||||||| || | ||| |||||||| ||||||||     | || || ||||||||||||||||||||||| || |
--gaaactttatcttcctacaaattctattattgtttatacttatgttttatttgtaataaatgctgcgcattacttatgcaaagccattccttctttgc-agACTGACATTAATCAAGCTATTTCGATGGTTTCTTACTTTGCATCATCTTCGGAACCAGCGCAAATCCGAGGCAAAACTGTTTACATTCAGTATTCAAACA

upper sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G082174_T02 (Zea mays), 3'ss of exon 1
-gtgactgccgagcgtccgaggatgt--gttttcttatatttgatgatacctggttctttttttttttttttttttttaactcaattatacatgctttgccagGCGGATCTAAATCAAGCCATTTCGATGGTTTCATATTATGCTTCATCTTCAGAACCAGCTATGGTTCGTGGTAAAACTGTTTACATTCAGTATTCTAATA
  |   ||| || | | |     | |  ||||| |  |||| ||   | |||| ||  |   | || |||  | ||||  ||  |  || |    |||  ||||| |||| ||| || || ||||| ||||| || ||||||||||||||||||||||| |||   ||||||||||||||||| || || || ||||| || |
actatatgctgaacttgcagaccttttagttttgtattattcga-atttcctgcttagtcaatgttctttactgttttcccttcaacatgctcatttt--cagGCAGATCAAAACCAGGCAATTTCAATGGTGTCCTATTATGCTTCATCTTCAGAACCTGCTCAAGTTCGTGGTAAAACTGTATATATCCAATATTCAAACA

upper sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G082174_T03 (Zea mays), 3'ss of exon 1
gtgactgccgagcgtccgaggatgt--gttttcttatatttgatgatacctggttctttttttttttttttttttttaactcaattatacatgctttgccagGCGGATCTAAATCAAGCCATTTCGATGGTTTCATATTATGCTTCATCTTCAGAACCAGCTATGGTTCGTGGTAAAACTGTTTACATTCAGTATTCTAATA----
     ||| || | | |     | |  ||||| |  |||| ||   | |||| ||  |   | || |||  | ||||  ||  |  || |    |||  ||||| |||| ||| || || ||||| ||||| || ||||||||||||||||||||||| |||   ||||||||||||||||| || || || ||||| || |    
---tatgctgaacttgcagaccttttagttttgtattattcga-atttcctgcttagtcaatgttctttactgttttcccttcaacatgctcatttt--caggcagATCAAAACCAGGCAATTTCAATGGTGTCCTATTATGCTTCATCTTCAGAACCTGCTCAAGTTCGTGGTAAAACTGTATATATCCAATATTCAAACAGGCA

upper sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 1
-gtgactgccgagcgtccgaggatgt--gttttcttatatttgatgatacctggttctttttttttttttttttttttaactcaattatacatgctttgccagGCGGATCTAAATCAAGCCATTTCGATGGTTTCATATTATGCTTCATCTTCAGAACCAGCTATGGTTCGTGGTAAAACTGTTTACATTCAGTATTCTAATA
  ||  ||| |  | | |   | | |  ||| | |  |||| ||   | |||| ||  |   | ||  ||    || |  ||  |  || ||   |||  ||||| |||| ||| || || ||||| ||||| || ||||||||||||||||||||||| |||   ||||| ||||||||||| || || || ||||| || |
actgtatgctgcacttgcagagtttttagttctatattattcgaatct-cctgcttagtcagtgttccttacagttgtcccttcaacatgcacatttt--cagGCAGATCAAAACCAGGCAATTTCAATGGTGTCCTATTATGCTTCATCTTCAGAACCTGCTCAAGTTCGCGGTAAAACTGTCTATATCCAATATTCAAACA

upper sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0108g01030.t01 (Vitis vinifera), 3'ss of exon 1
gtgactgccgagcgtccgag--gatgtgttttcttatatttgatgatacctggttctttttttttttttttttttttaactcaattatacatgctttgccagGCGGATCTAAATCAAGCCATTTCGATGGTTTCATATTATGCTTCATCTTCAGAACCAGCTATGGTTCGTGGTAAAACTGTTTACATTCAGTATTCTAATA
 ||    |   |  |||| |    |   |||  ||  |  ||  | |  ||  |||| |||  |  |   | | |       ||   || ||   ||  |||  ||| || ||||| |||||||| |||||||||||||||||||||||||| ||||| ||   |||||||||||| ||||| || || || || ||||| |
-tggtgacttgg-atccgggttattaaatttatttcgagatgcagttttctttttctctttggtggtggctatatgctgacaaaaggtatatttctttgcagTTGGACCTTAATCAGGCCATTTCTATGGTTTCATATTATGCTTCATCTTCGGAACCTGCACAGGTTCGTGGTAAGACTGTGTATATCCAATACTCTAACA

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|208145487|gb|GD942664.1|GD942664
EST:     ACACCAAGTGCAATGTCGGCGCCAATCGCAACCAGGCTTTTGTCGAATTC                         GCGGATCTAAATCAAGCCATTTCGATGGTTTCATATTATGCT
genomic: ACACCAAGTGCAATGTCGGCGCCAATCGCAACCAGGCTTTTGTCGAATTCgtaagtacta ... gctttgccagGCGGATCTAAATCAAGCCATTTCGATGGTTTCATATTATGCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctggttctttttttttttttttttttttaactcaattatacatgctttgccagGCGGATCTAAATCAAGCCATTTCGATGGTTTCATATTATGCTTCATCTTCAGAACCAGCTATGGTTCGTGGTAAAACTGTTTACATTCAGTATTCTAATA
                          ttttaac  putative branch site (score: 2)
                                              ctttgcc  putative PPT
      ttcttttttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgactgccgagcgtccgaggatgtgttttcttatatttgatgatacctggttctttttttttttttttttttttaactcaattatacatgctttgccagGCGGATCTAAATCAAGCCATTTCGATGGTTTCATATTATGCTTCATCTTCAGAACCAGCTATGGTTCGTGGTAAAACTGTTTACATTCAGTATTCTAATA

-tgactgc
- - - - - - - - -gaggatg