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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttgcatgcacacctgctggatgattcaaccatgtatttgcttttggctattgaacagtttatcagattgctcatattttctggttctgaatttcagGTCAATCCTCAATTCTATGCATTTAGGTGGATTACTCTCCTGCTGACTCAGGAATTCAATTTTGCCGACAGCCTTCACATTTGGGATACTCTTTTAAGCG

Basic information

species Glycine max
transcript GLYMA05G28660.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G28660.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G068392_T01 (Zea mays), 3'ss of exon 7
--ttttttgcatgcacacctgctggatgattcaa--ccatgtatttgcttttggctattgaacagtttatcagattgctcatattttctggttctgaatttcagGTCAATCCTCAATTCTATGCATTTAGGTGGATTACTCTCCTGCTGACTCAGGAATTCAATTTTGCCGACAGCCTTCACATTTGGGATACTCTTTTAAGCG
    | |||     |  |||    || |||| ||     |  | | ||  || |  | ||  ||  ||  |  |    || ||       |||      | ||||| ||||| || ||||| ||||| || ||||| ||  | |||||||| ||||||||||| || ||||||| | ||||||| ||||| || || ||||| |
taagtcttgagaagaatcctag-agaggatttaaatttctaaactagcccttag--agtgt-catctttccgcaagcatcgtacccaactgttgctctctgcagGTTAATCCCCAGTTCTACGCATTCAGATGGATAACCTTACTGCTGACCCAGGAATTCAACTTCGCCGACACCATTCACATCTGGGACACACTATTAAGTG

upper sequence: GLYMA05G28660.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G04830.2 (Arabidopsis thaliana), 3'ss of exon 7
-ttttttgcatgcacacctgctggatgattcaaccatgtatttgcttttggctattgaacagtttatcagattg---ctcatattttctgg--ttctgaatttcagGTCAATCCTCAATTCTATGCATTTAGGTGGATTACTCTCCTGCTGACTCAGGAATTCAATTTTGCCGACAGCCTTCACATTTGGGATACTCTTTTAAGCG
    ||    || |  | || |     || ||   |  || |  |  | |   |||| |     | | ||||||   || | ||| | | |  |  |  ||| ||||| ||||| || |||||||||||||||||||| |||||||| || || || || || | |||    ||||| |||||||| |||||| | || |||||||
cagcttactttgtattcttgttctcctatcca-taacataataacagtgg---attggat--cctctgagattgagactgacattgtatagattctttgattacagGTAAATCCACAGTTCTATGCATTTAGGTGGATCACTCTCCTCCTAACACAAGAGTTTAGTTTCTTTGACAGTCTTCACATATGGGATGCACTCTTAAGCG

upper sequence: GLYMA05G28660.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G13730.2 (Arabidopsis thaliana), 3'ss of exon 7
ttttttgcatgcacacctgctggatgattcaaccatgtatttgcttt-tggctattgaacagtttatcagattgctcatatttt---ctggttctgaatttcagGTCAATCCTCAATTCTATGCATTTAGGTGGATTACTCTCCTGCTGACTCAGGAATTCAATTTTGCCGACAGCCTTCACATTTGGGATACTCTTTTAAGCG
     || |    | | | |   ||| || |    |  | || || | |  || || ||  |||  ||||  |  | | ||||    |  ||    | |||||| | || || |||||||||||||| || ||||| || |||||  ||||||| ||||||||||| |  || ||||||||||| ||||| || || |||||||
--aactgtaccatcgctttcaaaatgtttaagttttcaagtttctgtatttctgtttaaatgtt--tcagcattttgacatttgagacctgtgtcaattttcagATAAACCCGCAATTCTATGCATTCAGATGGATCACACTCCTATTGACTCAAGAATTCAATTTCGTGGAAAGCCTTCACATCTGGGACACACTCTTAAGCG

upper sequence: GLYMA05G28660.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 7
ttttttgcatgcacacctgctgga--tgattcaaccatgtatttgcttttggctattgaacagtttatcagattgctcatattttctggttctgaatttcagGTCAATCCTCAATTCTATGCATTTAGGTGGATTACTCTCCTGCTGACTCAGGAATTCAATTTTGCCGACAGCCTTCACATTTGGGATACTCTTTTAAGCG
   |  ||  ||| |  |  ||||  | | | ||  |  |  ||  |        |||  || | | ||||||  || ||  | | |  ||   |||  ||||||||||| ||||| ||||||||||| ||||| ||||||||  ||||||| || ||||||||||| |||||||||||||||||||| || ||| |||| |
-cataagctggcagatgt-ttggacttcagtgaattacatcatttttacccttggttggtcaatctctcagatgtctgatgctctatatttgcaaatggcagGTCAATCCCCAATTTTATGCATTTAGATGGATAACTCTCCTCTTGACTCAAGAGTTCAATTTTGCGGACAGCCTTCACATTTGGGACACACTTCTAAGTG

upper sequence: GLYMA05G28660.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S73_37V6.1 (Physcomitrella patens), 3'ss of exon 8
ttttttgcatgcacacctgctggatgattcaaccatgtatttgcttttggctattgaacagtttatcagattgctcat--attttctggttctgaatttcagGTCAATCCTCAATTCTATGCATTTAGGTGGATTACTCTCCTGCTGACTCAGGAATTCAATTTTGCCGACAGCCTTCACATTTGGGATACTCTTTTAAGCG
  |    |  | |  | |||||  |   ||      || ||| ||    | |  || | ||| ||  || |||   ||  | || || ||    |    ||||||||||||||||| ||||| || |||||||| |||||  |||| ||||| || ||||| || || |||    |||   |||||||| ||||| | ||| 
agtaagtcccgaagtcatgctgacttgctcttgggagtttttcctgcatgtttgtgtaaagtata--aggttggaaattgaattgcttgtgtgtatcgacagGTCAATCCTCAATTTTATGCTTTCAGGTGGATAACTCTATTGCTAACTCAAGAGTTCAACTTCGCTGACTCTATTCGTCTTTGGGATTCTCTTCTTAGCA

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|58022950|gb|CX709691.1|CX709691
EST:     TGAGAGAACATGATGAAGAGCTGTGGCGTCATCTTGAGGTTACTTCTAAG                         GTCAATCCTCAATTCTATGCATTTAGGTGGATTACTCTCCTGCTGACTCAG
genomic: TGAGAGAACATGATGAAGAGCTGTGGCGTCATCTTGAGGTTACTTCTAAGgtaagacagt ... tgaatttcagGTCAATCCTCAATTCTATGCATTTAGGTGGATTACTCTCCTGCTGACTCAG
EST: gi|6725878|gb|AW310277.1|AW310277
EST:     TGAGAGAACATGATGAAGAGCTGTGGCGTCATCTTGAGGTTACTTCTAAG                         GTCAATCCTCAATTCTATGCATTTAGGTGGATTACTCTCCTGCTGACTCAG
genomic: TGAGAGAACATGATGAAGAGCTGTGGCGTCATCTTGAGGTTACTTCTAAGgtaagacagt ... tgaatttcagGTCAATCCTCAATTCTATGCATTTAGGTGGATTACTCTCCTGCTGACTCAG
EST: gi|58016472|gb|CX703214.1|CX703214
EST:     TGAGAGAACATGATGAAGAGCTGTGGCGTCATCTTGAGGTTACTTCTAAG                         GTCAATCCTCAATTCTATGCATTTAGGTGGATTACTCTCCTGCTGACTCAG
genomic: TGAGAGAACATGATGAAGAGCTGTGGCGTCATCTTGAGGTTACTTCTAAGgtaagacagt ... tgaatttcagGTCAATCCTCAATTCTATGCATTTAGGTGGATTACTCTCCTGCTGACTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggctattgaacagtttatcagattgctcatattttctggttctgaatttcagGTCAATCCTCAATTCTATGCATTTAGGTGGATTACTCTCCTGCTGACTCAGGAATTCAATTTTGCCGACAGCCTTCACATTTGGGATACTCTTTTAAGCG
                             tcatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttttgcatgcacacctgctggatgattcaaccatgtatttgcttttggctattgaacagtttatcagattgctcatattttctggttctgaatttcagGTCAATCCTCAATTCTATGCATTTAGGTGGATTACTCTCCTGCTGACTCAGGAATTCAATTTTGCCGACAGCCTTCACATTTGGGATACTCTTTTAAGCG

- ttttgca
- - - - - gcacacc
- - - - - - - - -tgctgga
- - - - - - - - - - - - - - -caaccat
- - - - - - - - - - - - - - - - - - - - - - - - -gctattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctggtt