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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcctagtaattcagattgtatttatgacctactcattagttgattctctctagtgaatttcgagaaattatctaacagttaaagtaaaacctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAGCGTGTGGGAGCAAG

Basic information

species Glycine max
transcript GLYMA12G06980.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 4
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 4
atgcctagtaattcagattgtatttatgacctactcattagttgattctctctagtgaatttcgagaaattatctaacagttaaagtaaaacctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAGCGTGTGGGAGCAAG
               | | || |  || |   |   |||  |    || |  |  |  | |  ||    |||  ||    |  ||   |    | | |||||||| ||||| ||||||||||| ||||| |||||||| |||||||| |||||||| ||||||||
---------------gttcgtgtgaat-atagatatattc-tcatatcaccttcatataatcagaatcgttagttactgatctaa--tatgtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAGCGTGTTGGAGCAAG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 4
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 4
atgcctagtaattcagattgtatttatgacctactca---ttagttgattctctctagtgaatttcgagaaattatctaacagttaaagtaaaacctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAGCGTGTGGGAGCAAG-----------------------------------
  |  |  |||      |  || | |  ||   |  |    ||| ||||    | |  ||| ||  ||    | || || |  ||  |         |  ||||| ||||| |||||||||||||| ||||| |||||| | || || |||||||| || ||||||||                                   
--gtttgttaaacttcgt--taatcaaaactcgcaaaatgctagctgatatatttttatgacttatga----tcatatatccttttcatctttctaatggcagACGATAAAAACAAATGTGATTGGCACACTTAACATGTTAGGACTAGCTAAGCGAGTTGGAGCAAGAATTTTACTTACTTCCACATCTGAAGTGTATGGTG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 5
atgcctagtaattcagattgtatttatgacctactcattagttgattctctctagtgaatttcgagaaattatctaacagttaaagtaaa-----acctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAGCGTGTGGGAGCAAG
     | |   |  ||||| | | | |    |     |    | |||    || |||||||      |||| ||| ||  ||  | | ||     || || |||||||||||| ||||| || ||||| |||||||| ||||| || ||||| || || || ||||||||
-----ttgacgtctagattttttgtgttcaatgtcagtgcagtcatttgaacttgtgaattattgagaattgtctgacttttttacttaactgtcactttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 4
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
atgcctagtaattcagattgtatttatgacctactcattagttgattctctctagtgaatttcgagaaattatctaacagttaaagtaaaacct----ttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAGCGTGTGGGAGCAAG
 |   || ||  | ||| |   |    |         | |   |||     |   | | ||||    | |  | | | | ||    | |||| |    || ||||| || ||||||||||||||||| || || ||||||||||| || ||||| || || || |||||
-tatata-tatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttca--gattggtttgaaatttggtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG

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|208312127|gb|GE107347.1|GE107347
EST:     ATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAG                         ACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTG
genomic: ATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAGgtgggggttc ... acctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTG
EST: gi|193540711|gb|FK494361.1|FK494361
EST:     AAATACAACCCTGTAAAG                         ACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAG
genomic: AAATACAACCCTGTAAAGgtgggggttc ... acctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAG
EST: gi|213606684|gb|DB959073.1|DB959073
EST:     ATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAG                         ACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAG
genomic: ATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAGgtgggggttc ... acctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctctctagtgaatttcgagaaattatctaacagttaaagtaaaacctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAGCGTGTGGGAGCAAG
                          atctaac  putative branch site (score: 2)
                                              cctttac  putative PPT
                     aaattatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcctagtaattcagattgtatttatgacctactcattagttgattctctctagtgaatttcgagaaattatctaacagttaaagtaaaacctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAGCGTGTGGGAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG