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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaccattcgattcagaagctttccaatacatgatttgtatcccgattgaactaccatggcaaataactttggcaaccttgttttctttatttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCATCTCAAGATGTTGCAACATATGGAGGACTTTGTGCACTTGCAACATTTG

Basic information

species Glycine max
transcript GLYMA07G08370.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G08370.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S311_49V6.1 (Physcomitrella patens), 3'ss of exon 2
ttaccattcgattcagaagctttccaatacatg-atttgtatcccgattgaactaccatggcaaataactttggcaaccttgttttctttatttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCATCTCAAGATGTTGCAACATATGGAGGACTTTGTGCACTTGCAACATTTG
      |  | | |   ||   | | |   | | | ||| ||   | |  |   ||    | || |  | | |     | | |  |   | ||| | ||||||| | || ||      |||  |||||||  |||||   || ||||  ||  ||||||||||||||||||||||||| ||||| || |||||| |||| |
ccgtgttcaggtccttgagagatgcgagtgacgtagttggattaagttccagacacttctg-aagtggcgtagcagctcatatcatgggttttttacgcagTTTGTTGACACGAACTTTGAGTTGGGAAGCAACTATTCAGATGTAACAGCTCCTCAAGATGTTGCAACATATGGAGGTCTTTGCGCTCTTGCATCATTCG

upper sequence: GLYMA07G08370.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S31_338V6.1 (Physcomitrella patens), 3'ss of exon 2
-ttaccattcgattcagaagctttccaatacatgatttgtatcccga--ttgaactaccatggcaaataactttggcaaccttgttttctttatttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCATCTCAAGATGTTGCAACATATGGAGGACTTTGTGCACTTGCAACATTTG
 ||    |  |||  |  || | |||  |      ||    |    |  | | | || |||   ||     |   ||   | || | |   | |   | ||||||| | || ||       ||  |||| ||  ||||    || || || ||  | ||||||||||||||||||||||| ||||| || |||||| | ||||
attggt-tgtgatagacgagatgtcccttgaggagttaaagtgggaagttcggattagcatataaaggcgttacagc--tcatgctattggtttggtacgcagTTTGTTGACACGAACTTCGAGTTGGGTAGCAACTACTCAGATGTTATAGCTCCCCAAGATGTTGCAACATATGGAGGTCTTTGCGCGCTTGCATCGTTTG
















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|26057500|gb|CA800414.1|CA800414
EST:     CAGGATTGGCTAATCTAGAGGCCAAAAAGTACAAGCTTGCTGCCCGAAAG                         TTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCA
genomic: CAGGATTGGCTAATCTAGAGGCCAAAAAGTACAAGCTTGCTGCCCGAAAGgtctgttcct ... tttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCA
EST: gi|254321707|gb|GR825024.1|GR825024
EST:     GGCTAATCTAGAGGCCAAAAAGTACAAGCTTGCTGCCCGAAAG                         TTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCA
genomic: GGCTAATCTAGAGGCCAAAAAGTACAAGCTTGCTGCCCGAAAGgtctgttcct ... tttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCA
EST: gi|19346061|gb|BM890941.1|BM890941
EST:     CAGGATTGGCTAATCTAGAGGCCAAAAAGTACAAGCTTGCTGCCCGAAAG                         TTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATG
genomic: CAGGATTGGCTAATCTAGAGGCCAAAAAGTACAAGCTTGCTGCCCGAAAGgtctgttcct ... tttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATG
EST: gi|7685795|gb|AW756443.1|AW756443
EST:     CAGGATTGGCTAATCTAGAGGCCAAAAAGTACAAGCTTGCTGCCCGAAAG                         TTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCA
genomic: CAGGATTGGCTAATCTAGAGGCCAAAAAGTACAAGCTTGCTGCCCGAAAGgtctgttcct ... tttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCA
EST: gi|19346011|gb|BM890891.1|BM890891
EST:     CAGGATTGGCTAATCTAGAGGCCAAAAAGTACAAGCTTGCTGCCCGAAAG                         TTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCA
genomic: CAGGATTGGCTAATCTAGAGGCCAAAAAGTACAAGCTTGCTGCCCGAAAGgtctgttcct ... tttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgaactaccatggcaaataactttggcaaccttgttttctttatttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCATCTCAAGATGTTGCAACATATGGAGGACTTTGTGCACTTGCAACATTTG
                               ccttgttttctttatt  CT-rich tract
                                 ttgttttctttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaccattcgattcagaagctttccaatacatgatttgtatcccgattgaactaccatggcaaataactttggcaaccttgttttctttatttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCATCTCAAGATGTTGCAACATATGGAGGACTTTGTGCACTTGCAACATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- accattc
- - - - - - - - - gctttcc
- - - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - actacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttggc