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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCGAGATCAGATCCACCAAGCAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAGgtaacgtataaacctttatgcccaacaatttgatcttagtatgtcattcattcagaggacaataatgcccacattgtttagatgtactgcccaagctgtt...

Basic information

species Glycine max
transcript GLYMA01G03930.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G03930.1 (Glycine max), 5'ss of exon 17
lower sequence: Vv19s0015g00470.t01 (Vitis vinifera), 5'ss of exon 18
GTGCGAGATCAGATCCACCAAGCAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAGgtaacgtataaacctttatgcccaacaatttgatcttagtatgtcattcattcagaggacaataatgcccaca-ttgttta-gatgtactgcccaagctgtt---
||  | |||||||| || ||||| || ||| | ||||||| ||||||||||||||| ||||| |||||||||||   || |  |||  | | ||  |  ||   || |   ||    |     ||  |      || ||  |  | || |||| || ||  | |  ||  | ||   
GTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTTGATACAACTGATAGAAAGATCCAGAAAAAGgt---gtgtttaccacttt-ccttatcatcaaatttccatactgaaaatgatcttatatgcttagtgatcgtacttatttaagaagtgtttcttaaa-tattaat

upper sequence: GLYMA01G03930.1 (Glycine max), 5'ss of exon 17
lower sequence: Vv01s0026g00340.t01 (Vitis vinifera), 5'ss of exon 18
GTGCGAGATCAGATCCACCAAGCAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAGgtaacgtataaacctttatgcccaacaatttgatcttagtatgtcattcat-tcagaggacaataatg--cccacattgtttagatgtactgcccaagctgtt-
||  | |||||||| || ||||| || ||| | |||||||  |||||||||||||| ||||| |||||||||||   || |  |||  | | | || ||     ||   |   ||  | | || | |     |  || ||  |  || |  || |||  |  |    ||  | || 
GTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTCGATACAACTGATAGAAAGATCCAGAAAAAGgt---gtgtttaccactttcctcatcatcgaaattccatactgaaaatgatcttaatatgctttagtgatcttacttatttaagacatgtttattaaa-tatta
















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|10237509|gb|BE806397.1|BE806397
EST:     CAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAG                         GTACGAGAAGCACAGTTAGCACAATACAACTTCATATTGGTTGTTGGGAGA
genomic: CAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAGgtaacgtata ... cattctgcagGTACGAGAAGCACAGTTAGCACAATACAACTTCATATTGGTTGTTGG-AGA
EST: gi|6666729|gb|AW278188.1|AW278188
EST:     CAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAG                         GTACGAGAAGCACAGTTAGCACAATACAACTTCATATTGGTTGTTGGAGAG
genomic: CAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAGgtaacgtata ... cattctgcagGTACGAGAAGCACAGTTAGCACAATACAACTTCATATTGGTTGTTGGAGAG
EST: gi|193587613|gb|FK542648.1|FK542648
EST:     CAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAG                         GTACGAGAAGCACAGTTAGCACAATACAACTTCATATTGGTTGT
genomic: CAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAGgtaacgtata ... cattctgcagGTACGAGAAGCACAGTTAGCACAATACAACTTCATATTGGTTGT
EST: gi|11687646|gb|BF595322.1|BF595322
EST:     CAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAG                         GTACGAGAAGCACAGTTAGCACAATACAACTTCATATTGGTTGTTGGAGAG
genomic: CAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAGgtaacgtata ... cattctgcagGTACGAGAAGCACAGTTAGCACAATACAACTTCATATTGGTTGTTGGAGAG
EST: gi|8402697|gb|BE058331.1|BE058331
EST:     CAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAG                         GTACGAGAAGCACAGTTAGCACAATACAACTTCATATTGGTTGTTGGAGAG
genomic: CAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAGgtaacgtata ... cattctgcagGTACGAGAAGCACAGTTAGCACAATACAACTTCATATTGGTTGTTGGAGAG
EST: gi|24136706|gb|BU927216.1|BU927216
EST:     CAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAACAAG                         GTACGAGAAGCACAGCTAGCCCAATACCACTTCCTATTG
genomic: CAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAGgtaacgtata ... cattctgcagGTACGAGAAGCACAGTTAGCACAATACAACTTCATATTG
EST: gi|193542339|gb|FK497529.1|FK497529
EST:     CAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAG                         GTACGAGAAGCACAGTTAGCACAATACAACTTCAT
genomic: CAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAGgtaacgtata ... cattctgcagGTACGAGAAGCACAGTTAGCACAATACAACTTCAT
EST: gi|207731298|gb|GD708955.1|GD708955
EST:     CAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAG                         GTACGAGAAGCACAGTTAGCACAATACAACTTCATATTGGTTGTTGGAGAG
genomic: CAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAGgtaacgtata ... cattctgcagGTACGAGAAGCACAGTTAGCACAATACAACTTCATATTGGTTGTTGGAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCGAGATCAGATCCACCAAGCAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAGgtaacgtataaacctttatgcccaacaatttgatcttagtatgtcattcattcagaggacaataatgcccacattgtttagatgtactgcccaagctgtt

- - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA