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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtaaaacttctgtgatatggtcaataatcaattgaccatgccataattcatgatgtgtttggtcaaattctgtctgtgattgtgatagattgctgatcactgatttgtatatgaccccattttgtaaacatgttgagtgttgacttcatttttattgcctccttgggttttttcattttacagcagAAATAGCAATGTTTGAGAATAACATTGTTCTTTACAAGTTTGTCCAAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTTAGC

Basic information

species Glycine max
transcript GLYMA15G13190.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G13190.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 3
gtgtgtaaaacttctgtgatatggtcaataatcaattgaccatgccataattcatgatgtgtttggtcaaattctgtctgtgattgtgatagattgctgatca--ctgatttgtatatgaccccattttgtaaacatgttgagtgtt--gacttcatttttattgcctccttgggttttttcattttacagcagAAATAGCAATGTTTGAGAATAACATTGTTCTTTACAAGTTTGTCCAAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTTAGC
                                                                                          || ||| ||   |   ||| || | ||| ||    |          ||| || | |   ||  | | || |      | | |   ||||     ||| |||| || ||| || |||||||   | | |||||  ||||||||||||| || || |||||||| ||||| |||| ||| ||| |||| |||||||| |||||   
------------------------------------------------------------------------------------------aggttgatggcaaggttgaatt-tgtattacttagtcactagggggtgtcgactctccagaaataaattctccctgatgcatattttttgcttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATGACCTTCACTTTTTTGTCACCGCTGGAGATGATGAGAATGAGCTCATCTT---

upper sequence: GLYMA15G13190.3 (Glycine max), 3'ss of exon 2
lower sequence: AT1G60970.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgtgtaaaacttctgtgatatggtcaataatcaattgaccatgccataattcatgatgtgtttggtcaaattctgtctgtgattgtgatagattgctgatcactgatttgtatatgaccccattttgtaaacatgttgagtgttgact-tcatttttattgcctccttgggttttttcatttt------acagcagAAATAGCAATGTTTGAGAATAACATTGTTCTTTACAAGTTTGTCCAAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTTAGC
                                                                                         ||||||   ||   |     ||| |  ||  |    | ||  || |||||||| |    | |||  | | || | || ||    ||  |  || |        ||  ||| |  ||    | ||||| ||||||||| | ||||| ||||| |||||||| || ||||||||||| || |||||  | ||||| |||||||||||   
----------------------------------------------------------------------------------------gtagatt-tcgacatcaaccatgttttagatacttcatagtgtacttgttgagtatcttttatcaaatcttttccgtcattacaattgctagttcttgatatgtagTGGAAGTGACAGCACTGGAGAACAACATTGTTGTGTACAAATTTGTGCAAGATCTCCATTTCTTTGTTACGGGCGGTGAAGAGGAAAACGAGCTTATCTT---

upper sequence: GLYMA15G13190.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0003g02760.t01 (Vitis vinifera), 3'ss of exon 3
gtgtgtaaaacttctgtgatatggtcaataatcaattgaccatgccataattcatgatgtgtttggtcaaattctgtctgtgattgtgatagattgctgatcactgatttgtatatgaccccattttgtaaacatgttgagtgttgacttcatttttattgcctccttgggttttttcattttacagcagAAATAGCAATGTTTGAGAATAACATTGTTCTTTACAAGTTTGTCCAAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTTAGC
                                                                              |   | |    | |  || | |  |    ||   || || |  || |       |   |||| ||    |||   |||| ||   |  ||  |||||||||| | ||||| || ||||||||||||||||| ||||||||| ||||||| ||||||||||| ||||||||||||||||| ||||||||  |||||||||| || |||||   
----------------------------------------------------------------------------cttaaaactagtgtggtgtgtttacaat--gttcaaatttggcttcactgc---tgctctttgaatgc---cttgccttttttttttttttt--gttttttcatct-acagCGGAGATAGCAATGTTTGAGAACAACATTGTTGTTTACAAATTTGTCCAAGACCTTCACTTCTTTGTTACTGGTGGTGAAGATGAAAATGAACTAATCTT---

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|298178201|gb|HO023936.1|HO023936
EST:     TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGGAAG                         C
genomic: TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGGAAGgtgtgtaaaa ... tttacagcag-
EST: gi|298178201|gb|HO023936.1|HO023936
EST:     TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGGAAG                         C
genomic: TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGGAAGgtgtgtaaaa ... tttacagcag-
EST: gi|298190231|gb|HO032352.1|HO032352
EST:     TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGGAAGCAG                       
genomic: TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGG-A--AGgtgtgtaaaa ... tttacagc
EST: gi|151408791|gb|EV278599.1|EV278599
EST:     TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGGAAGCAG                       
genomic: TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGG-A--AGgtgtgtaaaa ... tttacagc
EST: gi|192325778|gb|FK018000.1|FK018000
EST:     TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGGAAGCAG                       
genomic: TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGG-A--AGgtgtgtaaaa ... tttacagc
EST: gi|41145498|gb|CK605709.1|CK605709
EST:     TGAGAAAGTTGTATTCAACAAGACTCACAAAACCAATGCCCGCACGGAAGCAG                       
genomic: TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGG-A--AGgtgtgtaaaa ... tttacagc
EST: gi|58014334|gb|CX701076.1|CX701076
EST:     TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGGAAGCAG                       
genomic: TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGG-A--AGgtgtgtaaaa ... tttacagc
EST: gi|151408109|gb|EV277917.1|EV277917
EST:     TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGGAAGCAG                       
genomic: TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGG-A--AGgtgtgtaaaa ... tttacagc
EST: gi|192294109|gb|FG986198.1|FG986198
EST:     TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGGAAG                         AAATAGCAATGTTTGAGAATAACATTGTTCTTTACAAGTTTGTCCAAGATC
genomic: TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGGAAGgtgtgtaaaa ... tttacagcagAAATAGCAATGTTTGAGAATAACATTGTTCTTTACAAGTTTGTCCAAGATC
EST: gi|298194358|gb|HO041006.1|HO041006
EST:     TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGGAAGCAG                       
genomic: TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGG-A--AGgtgtgtaaaa ... tttacagc
EST: gi|209704906|gb|BW661709.1|BW661709
EST:     ACTCAGAAAACCAATGCCCGCACGGAAGCAG                       
genomic: ACTCAGAAAACCAATGCCCGCACGG-A--AGgtgtgtaaaa ... tttacagc
EST: gi|8402161|gb|BE057795.1|BE057795
EST:     TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGGAAGCAG                       
genomic: TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGG-A--AGgtgtgtaaaa ... tttacagc
EST: gi|58017732|gb|CX704474.1|CX704474
EST:     TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGGAAGCAG                       
genomic: TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGG-A--AGgtgtgtaaaa ... tttacagc
EST: gi|14258489|gb|BG881397.1|BG881397
EST:     TGAGAAAGTTGTATTCAACAAGACTCANAAAACCAATGCCCGCACGGAAG                         AAATAGCAATGTTTGAGAATAACATTGTTCTTTACAAGTTTGTCCAAGATC
genomic: TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGGAAGgtgtgtaaaa ... tttacagcagAAATAGCAATGTTTGAGAATAACATTGTTCTTTACAAGTTTGTCCAAGATC
EST: gi|5057863|gb|AI736339.1|AI736339
EST:     TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGGAAGCAG                       
genomic: TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGG-A--AGgtgtgtaaaa ... tttacagc
EST: gi|298175562|gb|HO018273.1|HO018273
EST:     TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGGAAGCAG                       
genomic: TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGG-A--AGgtgtgtaaaa ... tttacagc
EST: gi|298175469|gb|HO015102.1|HO015102
EST:     TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGGAAGCAG                       
genomic: TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGG-A--AGgtgtgtaaaa ... tttacagc
EST: gi|209704905|gb|BW661708.1|BW661708
EST:     TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGGAAGCAG                       
genomic: TGAGAAAGTTGTATTCAACAAGACTCAGAAAACCAATGCCCGCACGG-A--AGgtgtgtaaaa ... tttacagc


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgagtgttgacttcatttttattgcctccttgggttttttcattttacagcagAAATAGCAATGTTTGAGAATAACATTGTTCTTTACAAGTTTGTCCAAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTTAGC
      tgttgac  putative branch site (score: 3)
                                    ttttttcattttac  putative PPT
                                    ttttttcattttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtaaaacttctgtgatatggtcaataatcaattgaccatgccataattcatgatgtgtttggtcaaattctgtctgtgattgtgatagattgctgatcactgatttgtatatgaccccattttgtaaacatgttgagtgttgacttcatttttattgcctccttgggttttttcattttacagcagAAATAGCAATGTTTGAGAATAACATTGTTCTTTACAAGTTTGTCCAAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTTAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT