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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgtgactgctcttgattgttttaaataagaacattccttttattttgtcatttgtaaaaatggttggtatttatatgctttagATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCTGACATAAAGCCTGGTTATATTGTGCAACTCAAAGTG

Basic information

species Glycine max
transcript GLYMA08G34520.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G34520.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G11750.1 (Arabidopsis thaliana), 3'ss of exon 2
gcatgtgactgctcttgattgttttaaataagaacattccttttattttgtcatttgtaaaaatggttggtatttatatgctttagATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCTGACATAAAGCCTGGTTATATTGTGCAACTCAAAGTG
   |   |||     |       |   ||    ||| || | | || || | |  | |           ||  | || | ||  ||||| ||||||||||||| || ||||| ||||||   |  |||||||| || || |||||||||||||| ||||| || || ||||||
--gtacaactcaaactagacaactatcatggatacaatcatgtcatctt-ttacctat-----------gtcataatcttctgcagATTGTAGACAAGGAGGCAGTTGAGGAAGTGAGAAATCTTAGAGAGATTCCAGAGATAAAGCCTGGTTACATTGTTCAGCTTAAAGTG

upper sequence: GLYMA08G34520.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G24240.1 (Arabidopsis thaliana), 3'ss of exon 2
gcatgtgactgctcttgattgttttaaataagaacattccttttattttgtcatttgtaaaaatggttggtatttatatgctttagATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCTGACATAAAGCCTGGTTATATTGTGCAACTCAAAGTG
   |   ||  |||    |||       ||   | ||   | | || | | ||   | ||  |  | ||  |   ||   ||  ||||| |||||||||| || || ||||| ||||||   |  |||||||| || || |||||||||||||| |||||||| || ||||||
--gtactacaactcgaacttgacacttgtatttagata--tatcatgtagaca--aggaagcaccgatgtcaca-atcctctgcagATTGTAGACAAGGAAGCAGTTGAGGAAGTGAGAACTCTTAGAGAGATTCCAGAGATAAAGCCTGGTTACATTGTGCAGCTAAAAGTG

upper sequence: GLYMA08G34520.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g09390.t01 (Vitis vinifera), 3'ss of exon 3
gcatgtgac----tgctcttgattgttttaaataagaacattc-------cttttattttgtcatttgtaaaaatggttggtatttat-atgcttta------gATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCTGACATAAAGCCTGGTTATATTGTGCAACTCAAAGTG
|||||   |    ||  |    |||   | ||||  |||| |        |||| |||   || ||| |    ||  ||  | || || ||||| ||      |||| |||| ||||| || || ||||| ||||| |   | |||||||||||||| |||||||||||||||||||| || |||||||||
gcatgcttcattttgagcactgttggaatcaatagtaacactttccaggtctttcattaattcttttatttttatttttatttttaatcatgctgtacttgcagATTCTAGATAAGGAAGCAGTGGAGGAGGTGAGGGCAAAGAGAGAGATACCTGAGATAAAGCCTGGTTATATTGTTCAGCTCAAAGTG

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|26048812|gb|CA785265.1|CA785265
EST:     CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAG                         ATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
genomic: CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAGgcatgtgact ... tatgctttagATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
EST: gi|19348978|gb|BM893510.1|BM893510
EST:     CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAG                         ATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
genomic: CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAGgcatgtgact ... tatgctttagATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
EST: gi|298184016|gb|HO029229.1|HO029229
EST:     CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAG                         ATTGTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
genomic: CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAGgcatgtgact ... tatgctttagATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
EST: gi|120532190|gb|EH260323.1|EH260323
EST:     CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAG                         ATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
genomic: CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAGgcatgtgact ... tatgctttagATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
EST: gi|298169953|gb|HO018577.1|HO018577
EST:     CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAG                         ATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
genomic: CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAGgcatgtgact ... tatgctttagATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
EST: gi|151409621|gb|EV279429.1|EV279429
EST:     CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAG                         ATTTTGGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
genomic: CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAGgcatgtgact ... tatgctttagATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
EST: gi|192330084|gb|FK020900.1|FK020900
EST:     CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAG                         ATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
genomic: CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAGgcatgtgact ... tatgctttagATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
EST: gi|22929866|gb|BU547005.1|BU547005
EST:     CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAG                         ATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
genomic: CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAGgcatgtgact ... tatgctttagATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
EST: gi|120531812|gb|EH259945.1|EH259945
EST:     CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAG                         ATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
genomic: CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAGgcatgtgact ... tatgctttagATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
EST: gi|192300410|gb|FG988827.1|FG988827
EST:     CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAG                         ATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
genomic: CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAGgcatgtgact ... tatgctttagATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
EST: gi|192330085|gb|FK020901.1|FK020901
EST:     CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAG                         ATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
genomic: CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAGgcatgtgact ... tatgctttagATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
EST: gi|20813108|gb|BQ297586.1|BQ297586
EST:     CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAG                         ATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
genomic: CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAGgcatgtgact ... tatgctttagATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
EST: gi|21994816|gb|BQ786344.1|BQ786344
EST:     CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAG                         ATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
genomic: CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAGgcatgtgact ... tatgctttagATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
EST: gi|120531982|gb|EH260115.1|EH260115
EST:     CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAG                         ATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT
genomic: CTCGCATTAAATTTAAGAGATTAGACAAAACTGCCAGGCACATTATGCAGgcatgtgact ... tatgctttagATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaacattccttttattttgtcatttgtaaaaatggttggtatttatatgctttagATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCTGACATAAAGCCTGGTTATATTGTGCAACTCAAAGTG
         ttttattttgtcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgtgactgctcttgattgttttaaataagaacattccttttattttgtcatttgtaaaaatggttggtatttatatgctttagATTTTAGACAAGGAGGCTGTAGAGGATGTGAGAGGGCAAAGAGAGATACCTGACATAAAGCCTGGTTATATTGTGCAACTCAAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA