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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttttgtttgaacacgtgggtttctgaagacctctacatataatgctcagcaactgttacctctgattttgttgtgatttatgatctaatttctgcagGTACGCAGTATACTCAACAATCTTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC

Basic information

species Glycine max
transcript GLYMA20G38770.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G017835_T01 (Zea mays), 3'ss of exon 12
--tgcttttgtttgaacacgtgggtttctgaagacctctacatataatgctcagcaactgttacctctgattttgttgtgatttatgatctaatttctgcagGTACGCAGTATACTCAACAATCTTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC
  | |||||  ||   |   ||     |     ||   |     |  |   |||  | |  |   | || |  |  | |||| ||  || |    |   |||| || |  ||||| || |||||||| ||||| ||||| || || || || || |||||||||||||| |||| ||||||||||||||| ||| |||||||
ggtcctttttcttttccgaatgtagaccctgtcacgattgtgcgtctttgacag--attagtttttttgttggtcctctgatatagtatgtttgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTAAGTGGATAAACAAGAAATGGAAAGAAGGTTTTCATGTGACTGCAATGGC

upper sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 13
lower sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 13
-tgcttttgtttgaacacgtgggtttctgaagacctctaca--tataatgctcagcaactgtt---acctctgattt-tgttgtgatttatgatctaat---ttctgcagGTACGCAGTATACTCAACAATCTTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC
 |   |    ||   || |     || |||| || |       |||  |  |   | | | |    |  | ||  || |  | || ||  |  || |||   || || ||||||||||||||| || || ||||||||||| || || || ||||| ||||| |||||||||||||| ||||||||||| || ||||| || ||||||||
gtatctacactttt-catgaatacttttgaacactttcgtcattatggtattttactagtctctgaatttgtggcttattctatgtttggttttcaaatgaattatgaagGTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCAAGTGGATAAACAAGAAATGGAGAGAAGGCTTCCATGTAACCTCAATGGC

upper sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 13
-tgcttttgtttgaacacgtgggtttctgaagacctctacatataatgctcagcaactgttacctctgattttgttgtg-atttatgatctaatttctgcagGTACGCAGTATACTCAACAATCTTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC
     |||   |||| ||   | ||     || || |      ||||     | |  | ||  |    | ||| |  |      || | | ||| |||||||| || || ||||||||||| ||||||||||| || || || || ||||| ||||||||||||||||||||||||||||| || ||||| ||||| |||||
acctatttacatgaagacactgattat--gagtccccagttgctaatttatggtagttattttcagccactttatcatttgaccataaccaaatatctgcagGCACACAATATACTCAACAGTCTTACAAAGTAAGCGACTCCTTTCCCTTTAAATGGATAAACAAGAAGTGGAGAGAAGGATTCCATGTAACTTCCATGGC

upper sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 11
tgcttttgtttgaacacgtgggtttctgaagacctctacatataatgctcagcaactgttacctctgattttgttg-tgatttatgatctaatttctgcagGTACGCAGTATACTCAACAATCTTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC
                                        |||  |       |    |  || |||   |||| | |||    || |       | ||||| || |  || || |||||||| ||||||||||| || || || || ||||| ||||| ||||| |||||||| ||||| ||| | || ||||| |||||
---------------------------------------gtattgtcgctgttattgatggccactggcattgtcgctgacgcgtgtttc---ccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC

upper sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 11
tgcttttgtttgaacacgtgggtttctgaagacctctacatataatgctcagcaactgttacctctgattttgttg-tgatttatgatctaatttctgcagGTACGCAGTATACTCAACAATCTTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC
                                        |||  |       |    |  || |||   |||||| |||    ||||       | ||||| || |  || || |||||||| ||||||||||| || || || || ||||| ||||| ||||| |||||||| ||||| ||| | || ||||| |||||
---------------------------------------gtattgtcgctgttattgatggccactggcattgttgctgacgcgtgattc---ccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC

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|163927003|gb|EH039353.1|EH039353
EST:     TGGTGATGTCAAAAG                         GTACGCAGTATACTCAACAATCTTACAAAGTGAGTGCATCTTTCCCCTTCA
genomic: TGGTGATGTCAAAAGgtttgattgc ... atttctgcagGTACGCAGTATACTCAACAATCTTACAAAGTGAGTGAATCTTTCCCCTTCA
EST: gi|207754195|gb|GD725193.1|GD725193
EST:     GATGTCTAAAAG                         GTACGCAGTATACTCAACAATCTTACAAAGTGAGTGAATCTTTCCCCTTC
genomic: GATGTC-AAAAGgtttgattgc ... atttctgcagGTACGCAGTATACTCAACAATCTTACAAAGTGAGTGAATCTTTCCCCTTC
EST: gi|254339336|gb|GR848053.1|GR848053
EST:     TTCTATTGCAGGGAGCAACAATGGCAGCTCTCTTGTGGTGATGTCAAAAG                         GTACGCAGTATACTCAACAATCTTACAAAGTGAGTGAATCTTTCCCCTTCA
genomic: TTCTATTGCAGGGAGCAACAATGGCAGCTCTCTTGTGGTGATGTCAAAAGgtttgattgc ... atttctgcagGTACGCAGTATACTCAACAATCTTACAAAGTGAGTGAATCTTTCCCCTTCA
EST: gi|193362883|gb|FK324447.1|FK324447
EST:     TTCTATTGCAGGGAGCAACAATGGCAGCTCTCTTGTGGTGATGTCAAAAG                         GTACGCAGTATACTCAACAATCCTACAAAGTGAGTGAATCTTTCCCCTTCA
genomic: TTCTATTGCAGGGAGCAACAATGGCAGCTCTCTTGTGGTGATGTCAAAAGgtttgattgc ... atttctgcagGTACGCAGTATACTCAACAATCTTACAAAGTGAGTGAATCTTTCCCCTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctcagcaactgttacctctgattttgttgtgatttatgatctaatttctgcagGTACGCAGTATACTCAACAATCTTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC
                                        atctaat  putative branch site (score: 3)
                                              tttctgc  CT-rich tract
                                 atttatgatctaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcttttgtttgaacacgtgggtttctgaagacctctacatataatgctcagcaactgttacctctgattttgttgtgatttatgatctaatttctgcagGTACGCAGTATACTCAACAATCTTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
-gcttttg
- - - - - - - cacgtgg
- - - - - - - - - - -gtttctg
- - - - - - - - - - - - - - - - -ctctaca
- - - - - - - - - - - - - - - - - - - - - -aatgctc
- - - - - - - - - - - - - - - - - - - - - - - - - -gcaactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgtg