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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatttgcttatgtatccacaaaattattactaaatatttgagcaaatgtgtatggagaacctttccttgttacctgaatactttagtgttgaattgcagGCTTTGGATTACTGCCATTCTCAAGGCATTATGCATAGGGATGTCAAGCCTCATAATGTCATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT

Basic information

species Glycine max
transcript GLYMA11G05340.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g10940.1 (Oryza sativa), 3'ss of exon 3
tcatttgcttatgtatccacaaaattatt--actaaatatttgagcaaatgtgtatggagaacctttccttgttacctgaatactttagtgttgaa-ttgcagGCTTTGGATTACTGCCATTCTCAAGGCATTATGCATAGGGATGTCAAGCCTCATAATGTCATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT
  |||   ||  |  |   |    ||  |  | | | ||     | |  | | | |      |  ||   | ||  || ||| |  |  || | |  || ||||| ||||||||||| ||||||||||| ||||||||  | |||||||||||||| ||||| ||||| || |||||  | || || |||||||| || ||||
--attcagttgggcttgttcggtgttcgtcgatttagtagccagg-acttatttctaatctcctgttatcttttttctaaattccgtcctgcttaccttccagGCATTGGATTACTGTCATTCTCAAGGAATTATGCACCGCGATGTCAAGCCTCACAATGTTATGATTGACCATGAACTCCGCAAGCTTCGCTTAATTGATT

upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0129g00410.t01 (Vitis vinifera), 3'ss of exon 3
tcatttgctta--tgtatccacaaaattattactaaatatttgagcaaatgtgtatggagaacctttccttgttacctgaatactttagtgttgaat-tgcagGCTTTGGATTACTGCCATTCTCAAGGCATTATGCATAGGGATGTCAAGCCTCATAATGTCATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT
  ||      |  || |  | ||  || |  |   || || | |     | || | |     | |||| |  || | | | |   | ||| |||  | ||||||| || |||||||| ||||| ||||| || ||||| || |||||||||||||| ||||| |||||||| |||||||| ||||||||| |  |||| ||||
-tatgaaacaaactggaggctcagcatcac-agagaacatctcaaattgt-tgcaagtgcttcttttcatgcttgcttaattcagtaagtcttgcgtatgcagGCATTAGATTACTGTCATTCACAAGGAATAATGCACAGAGATGTCAAGCCTCACAATGTTATGATAGACCATGAGTTGCGAAAACTTAGACTGATTGATT

upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g09320.t01 (Vitis vinifera), 3'ss of exon 3
tcatttgcttatgtatccacaaaattattactaaatat-ttgagc--aaatgtgtatggagaacctttccttgttacctgaatactttagtgttgaattgcagGCTTTGGATTACTGCCATTCTCAAGGCATTATGCATAGGGATGTCAAGCCTCATAATGTCATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT
  | ||  |||  |   ||  ||| ||||  |   |   |||| |  |   ||     || |  ||    ||   || |   |  |||| |  |||||  ||||| || |||||||||||||| ||||| || |||||||| |||||||| ||||| ||||| ||||| ||||||||| | || |||||||||||||||||||
-taattctttaaattggcaacaaactattggttcctgccttgaactcagcagtcctctgatagactactttttaaacttatctgatttatt--tgaatatcagGCATTAGATTACTGCCATTCACAAGGTATAATGCATAGAGATGTCAAACCTCACAATGTTATGATTGATCATGAGCTTCGCAAACTTCGCTTGATAGATT

upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 3'ss of exon 4
tcatttgcttatgtatccacaaaattattactaaatatttgagcaaatgtgtatggagaacctttccttgttacctgaatactttagtgttgaat---tgcagGCTTTGGATTACTGCCATTCTCAAGGCATTATGCATAGGGATGTCAAGCCTCATAATGTCATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT
 |            ||  | ||||  | ||  ||  |  |||   | |  |  |    |   |  ||||      || ||  || |  | |  ||   ||||||||||||| ||||||||||||||||| || ||||| |||||||| ||||| || ||||| ||||| || || |||  |||||| ||  |  |||| ||||
ccccaccaccgccaataaaaaaaacgaatagaaaggaaatga---agttcggttttctactttacccttcaattttggattattgatggctttatcactgcagGCTTTGGACTACTGCCATTCTCAAGGGATCATGCACAGGGATGTGAAGCCACACAATGTAATGATTGACCACGAGCAACGAAAGCTGAGACTGATTGATT

upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 4
---tcatttgcttatgtatccacaaaattattactaaatatttgagcaaatgtgtatggagaacctttccttgttacctgaatactttagtgttgaattgcagGCTTTGGATTACTGCCATTCTCAAGGCATTATGCATAGGGATGTCAAGCCTCATAATGTCATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT
   | |  | |||                ||| ||||  | ||      ||    ||| |||   | |   |||    |    ||       |||  |||||||||||||| || |||||||||||||| |||||||| |||||||| ||||| || || || ||||| || ||||||   || || ||| |  | || || |
ttttaaaattcttcctatcttggtttgccattcctaacaacttattatcatactcatgcagaga-tataaatgtgggttactgacggagtcattg--ttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCACACAACGTGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACT

upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------------------------------------------------tcatttgcttatgtatccacaaaattattactaa---atatttgagcaaatgtgtatggagaacctttccttgttacctga-atactt-tagtgttgaattg---cagGCTTTGGATTACTGCCATTCTCAAGGCATTATGCATAGGGATGTCAAGCCTCATAATGTCATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT
                                                                            | | |||  ||| |    | | ||   |   | |         | || ||     || | |  | ||  ||   | | |||  || |  | |  |||   ||   ||||| ||||||||||| ||||| ||||| || |||||| | || ||||| || |||||||| ||||| |||||||||   |||||| |  |  | || ||||
gtaggttctacctaaactttgctcggcttgcattcaatcattacacttaattttcagtgttctatttatctgaattttagttgtgtatctgcttaaagaaacgtgcttgatgcgccgcagggctaagaaaaattgtgg-cattggctcaatgcttgatgtagtcgtggctttgccctgtttcagGCCTTGGATTACTGTCATTCGCAAGGGATAATGCATCGAGACGTCAAACCACATAATGTGATGATTGATCATGAGCAGCGAAAATTAAGGCTCATCGATT

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|213592666|gb|DB955810.1|DB955810
EST:     CAACCTTGACTGATTATGACATACGCTATTACATATATGAGCTCCTTAAG                         GCTTTGGATTACTGCCATTCTCAAGGCATTATGCATAGGGATGTCAAGCCT
genomic: CAACCTTGACTGATTATGACATACGCTATTACATATATGAGCTCCTTAAGgtaatatgat ... tgaattgcagGCTTTGGATTACTGCCATTCTCAAGGCATTATGCATAGGGATGTCAAGCCT
EST: gi|192297038|gb|FG990324.1|FG990324
EST:     CAACCTTGACTGATTATGACATACGCTATTACATATATGAGCTCCTTAAG                         GCTTTGGATTACTGCCATTCTCAAGGCATTATGCATAGGGATGTCAAGCCT
genomic: CAACCTTGACTGATTATGACATACGCTATTACATATATGAGCTCCTTAAGgtaatatgat ... tgaattgcagGCTTTGGATTACTGCCATTCTCAAGGCATTATGCATAGGGATGTCAAGCCT
EST: gi|192334448|gb|FK025569.1|FK025569
EST:     CAACCTTGACTGATTATGACATACGCTATTACATATATGAGCTCCTTAAG                         GCTTTGGATTACTGCCATTC
genomic: CAACCTTGACTGATTATGACATACGCTATTACATATATGAGCTCCTTAAGgtaatatgat ... tgaattgcagGCTTTGGATTACTGCCATTC
EST: gi|20813341|gb|BQ297819.1|BQ297819
EST:     CAACCTTGACTGATTATGACATACGCTATTACATATATGAGCTCCTTAAG                         GCCTTGGATTACTGCCATTCTCAAGGCATCATGCATAGGGATGTCAAGCCT
genomic: CAACCTTGACTGATTATGACATACGCTATTACATATATGAGCTCCTTAAGgtaatatgat ... tgaattgcagGCTTTGGATTACTGCCATTCTCAAGGCATTATGCATAGGGATGTCAAGCCT
EST: gi|208077290|gb|GD876949.1|GD876949
EST:     CAACCTTGACTGATTATGACATACGCTATTACATATATGAGCTCCTTAAG                         GCTTTGGATTA
genomic: CAACCTTGACTGATTATGACATACGCTATTACATATATGAGCTCCTTAAGgtaatatgat ... tgaattgcagGCTTTGGATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtgtatggagaacctttccttgttacctgaatactttagtgttgaattgcagGCTTTGGATTACTGCCATTCTCAAGGCATTATGCATAGGGATGTCAAGCCTCATAATGTCATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT
                                aatacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatttgcttatgtatccacaaaattattactaaatatttgagcaaatgtgtatggagaacctttccttgttacctgaatactttagtgttgaattgcagGCTTTGGATTACTGCCATTCTCAAGGCATTATGCATAGGGATGTCAAGCCTCATAATGTCATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA