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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatgatttttttttgtcacctgttaacattggagcttggaagactatgttgccattaactttggaaatatgttttctgcagATATGCTGGATATTCATCATGCTTTCGTAAAGAAGCTGGATCTCATGGTCGAGACACTCTAGGAATATTCCGAGTCCACCAATTTGAGAAAGTGGAGCAG

Basic information

species Glycine max
transcript GLYMA20G37700.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G37700.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G27470.1 (Arabidopsis thaliana), 3'ss of exon 6
----------gtaatatgatttttttttgtcacctgttaaca-ttggagcttggaag-actatgttg--ccattaactttggaaatatgttttctgcagATATGCTGGATATTCATCATGCTTTCGTAAAGAAGCTGGATCTCATGGTCGAGACACTCTAGGAATATTCCGAGTCCACCAATTTGAGAAAGTGGAGCAG
            |   | |    |  | |   | |    ||| |||   |||  | | | |  |     ||   ||| ||    || | |||  | |||||||||||| || ||||| |||||| | |||||||| || || |||||  ||||||| || || || ||||| || ||||| ||||||||| | || |||
gtataaacaaacatagtaacacctactcgcagctttaagacaattgtttctttaatgtattgggaaaatccgccaacattatgtatttttttggtccagATATGCTGGTTACTCATCCTGCTTTAGAAAAGAAGCCGGTTCACATGGAAGAGACACCCTTGGTATTTTCCGTGTTCACCAGTTTGAGAAAATTGAACAG

upper sequence: GLYMA20G37700.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0128g00370.t01 (Vitis vinifera), 3'ss of exon 6
gtaatatgatttttttttgtcacctgttaacattggagcttggaagactatgttgccattaactttggaaatatgttttctgcagATATGCTGGATATTCATCATGCTTTCGTAAAGAAGCTGGATCTCATGGTCGAGACACTCTAGGAATATTCCGAGTCCACCAATTTGAGAAAGTGGAGCAG
    ||        || ||   ||| ||    |    |  |  |  |     | |   ||||  ||    | ||||||||  ||||||||||||||||||||| || ||||||||||| |||||||| |||||||| || ||||| |||||||||||||| ||||| ||||||||||||||||||
---gtaaacccaacttgtgaaccctatttgtctcacggtatctacaaaagaatggtggttaatatt----acatgttttcc-cagATATGCTGGATATTCATCTTGTTTTCGTAAAGAGGCTGGATCGCATGGTCGGGATACTCTGGGAATATTCCGAGTTCACCAGTTTGAGAAAGTGGAGCAG
















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|192299348|gb|FG988719.1|FG988719
EST:     ACCCTACCCAGCTACCATTAAG                         ATATGCTGGATATTCATCATGCTTTCGTAAAGAAGCTGGATCTCATGGTCG
genomic: ACCCTACCCAGCTACCATTAAGgtaatatgat ... ttttctgcagATATGCTGGATATTCATCATGCTTTCGTAAAGAAGCTGGATCTCATGGTCG
EST: gi|151396984|gb|EV266857.1|EV266857
EST:     TGTGCATATCATTTAGATGATTGGATCCACCCTATCCAGCTACCATTAAG                         ATATGCTGGATATTCATCATGCTTTCGTAAAGAAGCTGGATCTCATGGTCG
genomic: TGTGCATATCATTTAGATGATTGGATCCACCCTACCCAGCTACCATTAAGgtaatatgat ... ttttctgcagATATGCTGGATATTCATCATGCTTTCGTAAAGAAGCTGGATCTCATGGTCG
EST: gi|13788033|gb|BG650625.1|BG650625
EST:     TGTGCATATCATTTAGATGATTGGATCCACCCTACCCAGCTACCAATAAG                         ATATGCTGGATATTCATCATGCTTTCGTAAAGAAGCTGGATCTCATGGTCG
genomic: TGTGCATATCATTTAGATGATTGGATCCACCCTACCCAGCTACCATTAAGgtaatatgat ... ttttctgcagATATGCTGGATATTCATCATGCTTTCGTAAAGAAGCTGGATCTCATGGTCG
EST: gi|207735695|gb|GD712176.1|GD712176
EST:     TATCATTTAGATGATTGGATCCACCCTACCCAGCTACCAATAAG                         ATATGCTGGATATTCATCATGCTTTCGTAAAGAAGCTGGATCTCATGGTCG
genomic: TATCATTTAGATGATTGGATCCACCCTACCCAGCTACCATTAAGgtaatatgat ... ttttctgcagATATGCTGGATATTCATCATGCTTTCGTAAAGAAGCTGGATCTCATGGTCG
EST: gi|15814019|gb|BI786294.1|BI786294
EST:     TGTGCATATCATTTAGATGATTGGATCCACCCTACCCAGCTACCATTAAG                         ATATGCTGGATATTCATCATGCTTTCGTAAAGAAGCTGGATCTCATGGTCG
genomic: TGTGCATATCATTTAGATGATTGGATCCACCCTACCCAGCTACCATTAAGgtaatatgat ... ttttctgcagATATGCTGGATATTCATCATGCTTTCGTAAAGAAGCTGGATCTCATGGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattggagcttggaagactatgttgccattaactttggaaatatgttttctgcagATATGCTGGATATTCATCATGCTTTCGTAAAGAAGCTGGATCTCATGGTCGAGACACTCTAGGAATATTCCGAGTCCACCAATTTGAGAAAGTGGAGCAG
                          cattaac  putative branch site (score: 2)
                                           tgttttct  putative PPT
                                      aaatatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatgatttttttttgtcacctgttaacattggagcttggaagactatgttgccattaactttggaaatatgttttctgcagATATGCTGGATATTCATCATGCTTTCGTAAAGAAGCTGGATCTCATGGTCGAGACACTCTAGGAATATTCCGAGTCCACCAATTTGAGAAAGTGGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG