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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCCAAGAAGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattttttgttcatattttaaaacattctttagtatttagttattctttatattaaactcataataatgccaaaattttcttagcttgatgaaaa...

Basic information

species Glycine max
transcript GLYMA13G36230.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G36230.1 (Glycine max), 5'ss of exon 16
lower sequence: AT4G27180.1 (Arabidopsis thaliana), 5'ss of exon 16
AAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCCAAGAAGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattttttgttcatattttaaaacattctttagtatttagttattctttatattaaactcataataatgccaaaattttcttagcttgatgaaaa
 || |||||  | || ||  || | ||||| ||||||||||| || ||||| || |||||  | || ||||| |||||||||||||| || || |||||||| |  ||||    |     ||| || | |  ||  |  |||  ||     ||   || |||||      ||| | |  ||                   
CAACAAAAGCTTATCGTCTCTAGGCGATGTCATATTTGCCTTAGCGAAGAAAGAAGATCACGTTCCTTTCAGAAACTCAAAGCTCACTTATCTTCTTCAGgtaagcatttaaaatcatcgtttaaacagaacctaaaagattctgt----gttgtgataaaactttgtggaattctatgatcag----------------

upper sequence: GLYMA13G36230.1 (Glycine max), 5'ss of exon 16
lower sequence: AT5G54670.1 (Arabidopsis thaliana), 5'ss of exon 16
AAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCCAAGAAGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattttttgttcatattttaaaacattctttagtatttagttattctttatattaaac-tcataataatgccaaaattttcttagcttgatgaaaa
 || |||||| |||| ||  || | ||||| ||||| ||||| || ||||| || |||||| | |||||| | ||||||||||||||||| || || |||||    |          |    | |||||||  || |  | ||  |  ||||| || |    | |||||||||   | |  |||  ||   || ||  |  
CAACAAAAGTTTGTCGTCGCTAGGCGATGTCATATTCGCCTTAGCAAAGAAAGAAGATCATGTACCATTCCGAAACTCAAAGCTCACATATCTTCTCCAGgtaccaa------accaaaccgtaaaaacatctttcaaaacttt-tgtttcttgatttgtggcatcataataaaaactatgtttgatt--tttaattcag-

upper sequence: GLYMA13G36230.1 (Glycine max), 5'ss of exon 16
lower sequence: Vv19s0014g05070.t01 (Vitis vinifera), 5'ss of exon 15
AAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCCAAGAAGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt---tttgttcatattttaaaacattctttagtatttagttattctttatattaaactcataataatgccaaaattt-tcttagcttgatgaaaa-
 ||||| ||||||||||||||||||||||| ||||||||| |||| ||||||||||| ||| | ||||| |||||||||||||| || || || |||||||| | |  |    |||   || || | |||| |         | | |  | || |    |  |   |   | | ||      ||   ||||  | |  ||   | 
CAATAAGAGTCTGTCATCATTAAGTGATGTTATATTTGCCCTGGCAAAGAAGGAGGACCATGTACCATTTAGGAACTCAAAGCTTACGTATCTTCTTCAGgtaaatgctccgatttaggcagatatgaaaaaac-----gacaatcaaattttttaagaaaaatgatttgattgatttaggtatacatcttgaccttgtgttcat

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|6667670|gb|AW279121.1|AW279121
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|193419543|gb|FK383193.1|FK383193
EST:     AGGAGGATCATGTCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTG
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTG
EST: gi|208072762|gb|GD872363.1|GD872363
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACAATTAATGTTTGTGAACATCTCTCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACA-TTAATGTTTGTGAACATCTCTCC
EST: gi|193646216|gb|FK589973.1|FK589973
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|10255088|gb|BE822854.1|BE822854
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|16996302|gb|BM085674.1|BM085674
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|193395820|gb|FK364417.1|FK364417
EST:     ATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: ATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|5820092|gb|AI988298.1|AI988298
EST:     AGGAGGATCATATCCCATTCAGGAACTCANAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|207785336|gb|GD759087.1|GD759087
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|208305868|gb|GE109547.1|GE109547
EST:     GGAGGACTCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: GGAGGA-TCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|208065379|gb|GD866305.1|GD866305
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCCCATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|208319200|gb|GE117561.1|GE117561
EST:     TTCAGGAACTCAAAGCTTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: TTCAGGAACTCAAAGC-TCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|51344240|gb|CO984973.1|CO984973
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|193372121|gb|FK334680.1|FK334680
EST:     AACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|208186092|gb|GD985433.1|GD985433
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|14205310|gb|BG838988.1|BG838988
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTTTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|6719321|gb|AW306968.1|AW306968
EST:     CATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: CATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|193511082|gb|FK468967.1|FK468967
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|193483660|gb|FK452791.1|FK452791
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|193481792|gb|FK446911.1|FK446911
EST:     ACCTACTTCAG                         CCTTGTCTAGGTGGGGACCCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: ACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|11687964|gb|BF595640.1|BF595640
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|208240996|gb|GE037782.1|GE037782
EST:     CTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: CTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|208323722|gb|GE122293.1|GE122293
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|208160078|gb|GD955714.1|GD955714
EST:     CAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: CAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|208326181|gb|GE121095.1|GE121095
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|208310247|gb|GE105523.1|GE105523
EST:     TATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: TATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|193696453|gb|FK636629.1|FK636629
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|193571531|gb|FK532762.1|FK532762
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGG-ACTCAAAGACATTAATGTT-GTGAACATCTCT
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCT
EST: gi|208292426|gb|GE091560.1|GE091560
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|208128344|gb|GD929184.1|GD929184
EST:     GGAGGTATCATATCCCATTCAGGAACTCAAAGCTCCCATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: GGAGG-ATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|208291127|gb|GE081567.1|GE081567
EST:     AACTCAAATCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|193433101|gb|FK398735.1|FK398735
EST:     ATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: ATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|207714522|gb|GD696967.1|GD696967
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCCCATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|51334869|gb|CO978735.1|CO978735
EST:     AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
EST: gi|208148830|gb|GD949340.1|GD949340
EST:     AACTCAAAGCTCACATACCTACTTCCG                         CCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC
genomic: AACTCAAAGCTCACATACCTACTTCAGgtgattattt ... ttgaacacagCCTTGTCTAGGTGGGGACTCAAAGACATTAATGTTTGTGAACATCTCTCCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCCAAGAAGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattttttgttcatattttaaaacattctttagtatttagttattctttatattaaactcataataatgccaaaattttcttagcttgatgaaaa

- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA