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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttctgaactcagtaatttttctagtactggtaaagatgttgcattttttttcttactttttaattgttgactatctgtgaacttcaaaataaatgtagGAGGATGCTGGGGAAATTTTGATATTGGGAAAGCATAATAAAGGGTGCCATTGTAAAAAATCTGGGTGCCTCAAGAAGTATTGTGAGTGCTTCCAAGCCA

Basic information

species Glycine max
transcript GLYMA08G04180.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G04180.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 3
------ttttctgaactcagtaattt-ttctagtactggtaaagatgttgcattttttttcttactttttaattgttgactatctgtgaacttcaaaataaatgtagGAGGATGCTGGGGAAATTTTGATATTGGGAAAGCATAATAAAGGGTGCCATTGTAAAAAATCTGGGTGCCTCAAGAAGTATTGTGAGTGCTTCCAAGCCA
      |||| || |  |  |  ||  || | ||||   | |  || |   ||||    |  ||   |     |  | | | |  ||   |    ||||      ||||||  ||||| ||  ||    || | || |||||||||||||||||||| || || || || || || ||||||||||| ||||||||||||||||| |
cgagtattttttggatgccatgtttcatttttgtacatctcattatctg--atttgccctgctatgatgcgtgtacttaatgttagt---ccctgaaattgcc--agGAGGCGGCTGGTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA

upper sequence: GLYMA08G04180.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g22670.1 (Oryza sativa), 3'ss of exon 4
ttttctgaactcagtaatttttctagtactggtaaagatgt-tgcattttttttcttactttttaattgttgactatctgtgaacttcaaaataaatgtagGAGGATGCTGGGGAAATTTTGATATTGGGAAAGCATAATAAAGGGTGCCATTGTAAAAAATCTGGGTGCCTCAAGAAGTATTGTGAGTGCTTCCAAGCCA
| || |||| |    || |  | | ||  ||||| |  | | | ||   || |  | |  |  || || |   |  |   | ||  | ||    |    |||| |||||||| | |        | |   ||||||||||||||| |||||||| || || || || || ||||||||||| ||||| ||||| ||||| |
tcttttgaattttcaaactcattttgt-ttggtagatttatatacaacattctcttcatgtgatatttttatgcatttgattaatcttaactgcacaccagGATGATGCTGGAGCACCAGCCTCACTTCCAAAGCATAATAAAGGTTGCCATTGCAAGAAGTCAGGATGTCTCAAGAAGTACTGTGAATGCTTTCAAGCAA

upper sequence: GLYMA08G04180.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G104246_T01 (Zea mays), 3'ss of exon 3
ttttctgaactcagtaatttttctagtactggtaaagatgttgcattttttttcttact-ttttaattgttgactatctgtgaacttcaaaataaatgtagGAGGATGCTGGGGAAATTTTGATATTGGGAAAGCATAATAAAGGGTGCCATTGTAAAAAATCTGGGTGCCTCAAGAAGTATTGTGAGTGCTTCCAAGCCA
  |    ||  | | |||| |   | || ||      || | |      || |  | ||    | |    || |  |   |  | | ||  | |    |||||||   || | ||  |     || | || ||||||||||||||||||||||| || || || || |||||||||||||| ||||||||||||||||| |
-ctatcaaatactgaaattatgtcattattgcatttaatttggaccaagttattgtgctgccatgacatgtggcattaattctagtccatgaaattgctagGAGGTGTCTAGTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGCCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA

upper sequence: GLYMA08G04180.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G059678_T01 (Zea mays), 3'ss of exon 3
ttttctgaactcagtaatttttctagtactggtaaagatgttg--cat-tttttttcttactttttaattgttgactatctgtgaacttcaaaataaatgtagGAGGATGCTGGGGAAATTTTGATATTGGGAAAGCATAATAAAGGGTGCCATTGTAAAAAATCTGGGTGCCTCAAGAAGTATTGTGAGTGCTTCCAAGCCA
       |   |||  ||| |   | || ||      || | |  ||| || || |  | | ||   |      | ||  | |   |    ||||      ||||||   || | ||  |     || | || ||||||||||||||||||||||| || || || || || ||||||||||| ||||||||||||||||| |
---atcaattacaggcattatatcattattgcatttcatttcggccatgttattgtgctgccttgacacgtcacattaattctagtccatgaaattttgccagGAGGTGCCTAGTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA

upper sequence: GLYMA08G04180.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S10_254V6.2 (Physcomitrella patens), 3'ss of exon 5
ttttctgaactca-gtaatttttctagtactggtaaagatgttgcattttttt---tcttactttttaatt--gttgact--atctgtgaact--tcaaa----ataaatgtagGAGGATGCTGGGGAAATTTTGATATTGGGAAAGCATAATAAAGGGTGCCATTGTAAAAAATCTGGGTGCCTCAAGAAGTATTGTGAGTGCTTCCAAGCCA
          ||| ||| ||| | ||||||     ||| |||| | ||||| |     || |   | |||   | | | |  || |  |||||  |  ||    || | || ||||||||||||| ||   |    |   ||| || || || ||||| || ||||| || ||||| |||||||||||||||||||| || ||||||||||| |
----------tcatgtattttctgtagtacc----aaggtgttccttttttatggacatttcccctcaatctgggtcagtggatttcggaactaatagaactttattattgcagGAGGATGCTGGAGAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA

upper sequence: GLYMA08G04180.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S9_436V6.1 (Physcomitrella patens), 3'ss of exon 5
ttttctgaactcagtaatttttctagtactggtaaagatgttgcattttttttcttacttt---ttaattgttgactat-ctgtgaacttcaaaataaatgtagGAGGATGCTGGGGAAATTTTGATATTGGGAAAGCATAATAAAGGGTGCCATTGTAAAAAATCTGGGTGCCTCAAGAAGTATTGTGAGTGCTTCCAAGCCA
     |   |    |  | |  | | |  |  |  | | ||| |||| |||||||||   |     | | |||||| |  |||    | ||    | | || ||||||||| ||| ||   |    |   ||| ||||| || ||||| ||||| |||||||| || |||||||||||||||||||| || |||||||||||||
---cgtattccttctgttgtaccaaattatattccata-gtttcattatttttcttaacctgggcgagtggttgacgaaactgatggcatcttggttattgcagGAGGATGTTGGAGAGCATCCTCTGGCGGGCAAGCACAACAAAGGATGCCACTGTAAAAAGTCGGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCCA

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|254330182|gb|GR839735.1|GR839735
EST:     CATTTAGGCCAAAAATAGCAAGTAGCCCTCATAGAACACGTGATATCAGG                         GAGGATGCTGGGGAAATTTTGATATTGGGAAAGCATAATAAAGGGTGCCAT
genomic: CATTTAGGCCAAAAATAGCAAGTAGCCCTCATAGAACACGTGATATCAGGgtatgtggtt ... ataaatgtagGAGGATGCTGGGGAAATTTTGATATTGGGAAAGCATAATAAAGGGTGCCAT
EST: gi|27808943|gb|CB063365.1|CB063365
EST:     CCAAAAATAGCAAGTAGCCCTCATAGAACACGTGATATCAGG                         GAGGATGCTGGGGAAATTTTGATATTGGGAAAGCATAATAAAGGGTGCCAT
genomic: CCAAAAATAGCAAGTAGCCCTCATAGAACACGTGATATCAGGgtatgtggtt ... ataaatgtagGAGGATGCTGGGGAAATTTTGATATTGGGAAAGCATAATAAAGGGTGCCAT
EST: gi|18730183|gb|BM525733.1|BM525733
EST:     CATTTAGGCCAAAAATAGCAAGTAGCCCTCATAGAACACGTGATATCAGG                         GAGGATGCTGGGGAAATTTTGATATTGGGAAAGCATAATAAAGGGTGCCAT
genomic: CATTTAGGCCAAAAATAGCAAGTAGCCCTCATAGAACACGTGATATCAGGgtatgtggtt ... ataaatgtagGAGGATGCTGGGGAAATTTTGATATTGGGAAAGCATAATAAAGGGTGCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttcttactttttaattgttgactatctgtgaacttcaaaataaatgtagGAGGATGCTGGGGAAATTTTGATATTGGGAAAGCATAATAAAGGGTGCCATTGTAAAAAATCTGGGTGCCTCAAGAAGTATTGTGAGTGCTTCCAAGCCA
     tttcttactttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttctgaactcagtaatttttctagtactggtaaagatgttgcattttttttcttactttttaattgttgactatctgtgaacttcaaaataaatgtagGAGGATGCTGGGGAAATTTTGATATTGGGAAAGCATAATAAAGGGTGCCATTGTAAAAAATCTGGGTGCCTCAAGAAGTATTGTGAGTGCTTCCAAGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT