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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtccattctcactcctttgtcaagtaaaatccaatttggcttgaccagttgaccttaggataagcacatgccaatgaaaagaaaaaagtggaaaataaaaatgcaatctatacatactatgaagctttaaacaatgatcctttttttcccccctgatttagCCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAG

Basic information

species Glycine max
transcript GLYMA18G01710.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G26440.4 (Arabidopsis thaliana), 3'ss of exon 11
gtgagtccattctcactcctttgtcaagtaaaatccaatttggcttgaccagttgaccttaggataagcacatgccaatgaaaagaaaaaagtggaaaataaaaatgca-atctatacatactat----gaagctttaaacaatgatcctttttttcccccctgatttagCCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAG
                                                                         |  ||   | | | | || |     | |||   | | |  | |||| |   |    ||| ||   || ||  |   |||  |    |  | |   ||||||| |||||||||||||| ||||| |||||||| |||||  |||| |||    |||| ||  |||| |  |||
-------------------------------------------------------------------------gttaacatacaaatacaacttattcacaaacgcgtataattttacaaaacgttttcgaaactaagaagaaacactttttaatgattcaataaac-agCCTGCACATGAGAAGATTGGTGTTGTGGATTCTCAATGGATCATTCATCAAAAGATTCCTTCTTTAGGCAGCCAG

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G13000.2 (Arabidopsis thaliana), 3'ss of exon 11
gtgagtccattctcactcctttgtcaagtaaaatccaatttggcttgaccagttgaccttaggataagcacatgccaatgaaaagaaaaaagtggaaaataaaaatgcaatctatacatactatgaagctttaaacaatgatcctttttttcccccctgatttagCCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAG
                                                                           || |      | | |  | ||   | ||| | || |  | |  |  | ||     |||   | | |    |||  |        |   ||||||| ||||||||||| |||||||| |||||||| |||||  | || |||  |||||| ||  |||| |  |||
---------------------------------------------------------------------gttaatcattttgcctacataccttgactcttaaa-tacactggacatgtgtt-tggtaagttatctactaaaaagtttcctaataaaacaaacagCCTGCACATGAGAAGATAGGAGTTGTGGATTCTCAATGGATCATACATCAATCTCTTCCTTCTTTAGGCAGCCAG

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 12
gtgagtccattctcactcctttgtcaagtaaaatccaatttggcttgaccagttg-accttaggataagcacatgccaatgaaaagaaaaaagtggaaaataaaaatgcaatctatacatactatgaagctttaaacaatgatcctttttttcccccctgatttagCCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAG
                                          |   ||  ||    || | | | |       || ||   |||||| | |  |      |||  ||    ||| |  |||  | |||  | | || |        | |||| | ||   ||  ||||||| ||||||||||| ||||| ||||||||||| ||| | ||||| |||  | |||| || || || || || 
------------------------------------------gtaagaaaagagacacttgaagttcgttgtttgtcacgcaaaagacagagtt----tctaattatatcgtctgt-tatatgacgaa--tctgaata--------tattttacaccgaaatgcagCCTGCACATGAGAAGATAGGAGTAGTTGATTCTCAATGGGTCGTTCATCAATCTTTTCCTTCCCTTGGCAACCAA

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 12
gtgagtccattctcactcctttgtcaagtaaaatccaatttggcttgaccagttgaccttaggataagcacatgccaatgaaaagaaaaaagtggaaaataaaaatgcaatctatacatactatgaagctttaa-acaatgatcctttttttcccccctgatttagCCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAG
                                                                   | ||   || |||       |    |    ||||       | | | |   |  ||  | || | |  | | ||   |||    ||  |  |||   |||||||||||||||| |||||||| || |||||||| ||||| ||||| |||  | ||||||| || ||||| |||
-------------------------------------------------------------------gtactgacctatgtctgcctacttct----aatactctcatattatttgtttgttagcatgcatgatcatattggaacttcc--tcgtctttgaaacagCCTGCCCATGAGAAAATTGGAGTCGTAGATTCTCAATGGATCGTTCATCAAACTGTTCCCTCGCTTGGGAACCAG

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 7
gtgagtccattctcactcctttgtcaagtaaaatccaatttggcttgaccagttgaccttaggataagcacatgccaatgaaaagaaaaaagtggaaaataaaaatgcaatctatacatactatgaagctttaa-acaatgatcctttttttcccccctgatttagCCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAG
                                                                   | ||   || |||       |    |    |||     |  |   | |   |  ||  | || | |  | | ||   |||    ||  |  |||   |||||||||||||||| ||||||||||| |||||||| |||||  |||| |||  | ||||||| || ||||| |||
-------------------------------------------------------------------gtactgacctatgtctgcctacttct----aattctcttatatcatttgtttgttagcatgcatgatcatattggaacttcc--tcgtctttgaaacagCCTGCCCATGAGAAAATTGGAGTTGTAGATTCTCAATGGATCATTCATCAAACTTTTCCCTCGCTTGGGAACCAG

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv13s0106g00570.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtccattctcactcctttgtcaagtaaaatccaatttggcttgaccagttgaccttaggataagcacatgccaatgaaaagaaaaaagtggaaaataaaaatgcaatctatacatactatgaagctttaa-acaatgatcctttttttcccccctgatttagCCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAG
                                                                   | ||   || |||       |    |    |||     |  | | | |   |  ||  | || | |  | | ||   |||    ||  |  |||   |||||||||||||||| ||||||||||| ||||||||  |||| ||||| |||  | ||||||| || ||||| |||
-------------------------------------------------------------------gtactgacctatgtctgcctacttct----aattctcttatattatttgtttgttagcatgcatgatcatattggaacttgc--tcgtctttgaaacagCCTGCCCATGAGAAAATTGGAGTTGTAGATTCTCAAGGGATCGTTCATCAAACTGTTCCCTCGCTTGGGAACCAG

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|192319061|gb|FK010625.1|FK010625
EST:     ACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTTGAG                         CCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCAC
genomic: ACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTTGAGgtgagtccat ... cctgatttagCCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCAC
EST: gi|208113070|gb|GD912445.1|GD912445
EST:     CGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTTGAG                         CCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
genomic: CGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTTGAGgtgagtccat ... cctgatttagCCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
EST: gi|19348792|gb|BM893324.1|BM893324
EST:     ACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTTGAG                         CCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
genomic: ACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTTGAGgtgagtccat ... cctgatttagCCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
EST: gi|192319062|gb|FK010626.1|FK010626
EST:     ACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTTGAG                         CCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACTAA
genomic: ACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTTGAGgtgagtccat ... cctgatttagCCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
EST: gi|254315636|gb|GR825445.1|GR825445
EST:     ACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTTGAG                         CCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
genomic: ACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTTGAGgtgagtccat ... cctgatttagCCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
EST: gi|254347136|gb|GR856806.1|GR856806
EST:     ACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTTGAG                         CCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
genomic: ACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTTGAGgtgagtccat ... cctgatttagCCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
EST: gi|193385504|gb|FK349858.1|FK349858
EST:     CGGGCGGGGTCTTGATTTTGCTCTTAGAAGATGTGTTGAG                         CCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
genomic: CGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTTGAGgtgagtccat ... cctgatttagCCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
EST: gi|208265459|gb|GE062651.1|GE062651
EST:     ACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTTGAG                         CCTGCCCATGAGAAGATTGGAG
genomic: ACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTTGAGgtgagtccat ... cctgatttagCCTGCCCATGAGAAGATTGGAG
EST: gi|192302164|gb|FG995816.1|FG995816
EST:     ACTTGGTCCACGGGTGGGGTTTTGATTTTGCTTTTAGAAGATGTGTTGAG                         CCTGCCCATGAGAAGATTGGAGTTGTTGATTTTCAGTGGATTGTTCACCAA
genomic: ACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTTGAGgtgagtccat ... cctgatttagCCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatacatactatgaagctttaaacaatgatcctttttttcccccctgatttagCCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAG
                                            ccctgat  putative branch site (score: 4)
                               tcctttttttcccccc  CT-rich tract
                   tttaaacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtccattctcactcctttgtcaagtaaaatccaatttggcttgaccagttgaccttaggataagcacatgccaatgaaaagaaaaaagtggaaaataaaaatgcaatctatacatactatgaagctttaaacaatgatcctttttttcccccctgatttagCCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA