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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgtccggatatacaactctgatattccattcatttgttaagtttattgatgactttactttttttatagGTAATGACAACATTCATGCCACCGCCTCCTGCTTCTACCTTCCTAGCTTTCCATCCCCAGGATAACAACATTATTGCCATTGGGATGGACGATTCAACCA

Basic information

species Glycine max
transcript GLYMA10G29090.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G29090.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 20
gtgtgtgtccggatat-acaactctgatattccatt--------catttgttaagtttattgatgactttactttt-tttatagGTAATGACAACATTCATGCCACCGCCTCCTGCTTCTACCTTCCTAGCTTTCCATCCCCAGGATAACAACATTATTGCCATTGGGATGGACGATTCAACCA
  || ||||   | || |||  | ||    | |||         ||||||  | | ||    ||||  || ||||  ||| ||||||||||||||||||||| |||| || |||||||| ||||||||||| |||||||| || || || ||||| || ||||| || ||||| ||||| ||||
--gtatgtctaaacatcacagttttgcatcttcatcaaatttggcatttgaaatggtttagcatgatgttgctttcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA

upper sequence: GLYMA10G29090.1 (Glycine max), 3'ss of exon 21
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 20
------------------------gtgtgtgtccggatatacaactctgatattccattcatttgttaagtttattgatgactttactttttttat--agGTAATGACAACATTCATGCCACCGCCTCCTGCTTCTACCTTCCTAGCTTTCCATCCCCAGGATAACAACATTATTGCCATTGGGATGGACGATTCAACCA
                         | |   |    |  |||    ||| |  | | |  |  ||  |  | |     |  | ||    || | ||  |||| ||||| ||||||||||| || ||||| ||  |||| || || || ||||||||||| || |||||||| |||||||| || ||||| |||||||| |
tattaaaaaaattgaagccattttttattattaaaaaattactctgctggtgatgcttgaacatggcagttctgacagttgccttcggattgtgattcagGTCATGACGACATTCATGCCGCCACCTCCAGCAGCTACTTTTCTTGCGTTCCATCCCCAAGACAACAACATCATTGCCATAGGAATGGAGGATTCAACAA
















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|207785252|gb|GD755209.1|GD755209
EST:     TGTCTGCCTGTGGTGGAAAGGTTTCTCTATTTAACATGATGACATTCAAG                         GTAATGACAACATTCATGCCACCGCCTCCTGCTTCTACCTTCCTAGCTTTC
genomic: TGTCTGCCTGTGGTGGAAAGGTTTCTCTATTTAACATGATGACATTCAAGgtgtgtgtcc ... ttttttatagGTAATGACAACATTCATGCCACCGCCTCCTGCTTCTACCTTCCTAGCTTTC
EST: gi|17519222|gb|BM188264.1|BM188264
EST:     TGTCTGCCTGTGGTGGAAAGGTTTCTCTATTTAACATGATGACATTCAAG                         GTAATGACAACATTCATGCCACCGCCTCCTGCTTCTACCTTCCTAGCTTTC
genomic: TGTCTGCCTGTGGTGGAAAGGTTTCTCTATTTAACATGATGACATTCAAGgtgtgtgtcc ... ttttttatagGTAATGACAACATTCATGCCACCGCCTCCTGCTTCTACCTTCCTAGCTTTC
EST: gi|208328481|gb|GE127553.1|GE127553
EST:     ATGATGACATTCAAG                         GTAATGACAACATTCATGCCACCGCCTCCTGCTTCTACCTTCCTAGCTTTC
genomic: ATGATGACATTCAAGgtgtgtgtcc ... ttttttatagGTAATGACAACATTCATGCCACCGCCTCCTGCTTCTACCTTCCTAGCTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actctgatattccattcatttgttaagtttattgatgactttactttttttatagGTAATGACAACATTCATGCCACCGCCTCCTGCTTCTACCTTCCTAGCTTTCCATCCCCAGGATAACAACATTATTGCCATTGGGATGGACGATTCAACCA
                             tattgat  putative branch site (score: 3)
                                      ctttactttttttat  putative PPT
                           tttattgatgacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtgtccggatatacaactctgatattccattcatttgttaagtttattgatgactttactttttttatagGTAATGACAACATTCATGCCACCGCCTCCTGCTTCTACCTTCCTAGCTTTCCATCCCCAGGATAACAACATTATTGCCATTGGGATGGACGATTCAACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA