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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtcttcaaagtcaccataattcataaacaattcgttaatgatttttaagaacagcgataataattgggacactcggtgggtgttgagttgcaatggatatatatttctgttatgaattatatttttttacttctctaaattctttactagGTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCACACATAATATTGCTTGATGAACCATCCAATCATCTG

Basic information

species Glycine max
transcript GLYMA20G16170.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 15
------gtattgtcttcaaagtcaccataattcataaacaattcgttaatgatttttaagaacagcgataataattgggacactcggtgggtgttgagttgcaatggatatatatttctgttatgaattatattttttta-cttctctaaattctttac-----tagGTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCACACATAATATTGCTTGATGAACCATCCAATCATCTG
        |  || || | ||    | |||       | |    |   |||   |||   |    |   |  ||||| || |||       ||   | |       |||  || |    ||      ||| |||| |    | |   || |  |||| |      ||||||||||||||| |||||||||||||||||||| || ||||||||||||||||| ||  | || ||||| || || || ||||| 
gtaatgagagcgttttgatagatgtcttaagcatattaaaggctgcatatggcctttcccagtttcatgagaaattgaga-actatcctcttgcccaat-------gattcatctgctcgtagaatcttaaatttgtcagtcctgattagagcctttccaatcccagGTGGTCAGAAAAGTAGGGTTGCCTTTGCAAAGATCACCTTCAAGAAGCCACACATTATTCTTCTCGATGAGCCTTCTAACCATCTT

upper sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 15
gtattgtcttcaaagtcaccataattcataaacaattcgttaatgatttttaagaacagcgataataattgggacactcggtgggtgttgagttgcaatggatatatatttctgttatgaattatatttttttacttctctaaatt-ctttactagGTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCACACATAATATTGCTTGATGAACCATCCAATCATCTG
                                                          |    |||  | | ||   |     || | | | ||         | | |    || |  || || |   |  | ||       |||| |  | | |||||||||||| || |||||||| || || || ||||| ||||||||||| ||||| ||  | ||||| || || || || ||||| 
----------------------------------------------------------gtagaaatcgtagcgatcgtgcaaaggggctcatttctgtgtagaacacagaattgct--gatttctggatcctaacccaaagcaattgcgattccagGTGGTCAGAAGAGTAGGGTTGCATTCGCGAAAATAACCTTCAAGAAGCCGCACATCATTCTCCTTGACGAGCCTTCTAACCATCTT

upper sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 14
lower sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 15
gtattgtcttcaaagtcaccataatt-cataaacaattcgttaatgatttttaagaacagcgataataattgggacactcggtgggtgttgagttgcaatggatatatatttctgtta-tgaattatatttttttacttctctaaattctttactagGTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCACACATAATATTGCTTGATGAACCATCCAATCATCTG
    | |  |    ||      | ||  |||| ||     ||   |||    | |  |    || | |||||| ||     ||   | || |  ||   ||| |   ||  |    || ||  || ||| ||||    |   | |||     | ||||||||||||||||||| ||||| ||||| |||||||| |||||||| |||||| |  ||||||||||||| || ||||||||||| 
---gtatacttcgggtatttggagttgtataaccacaatattctagatg--caggccctagaatga-aattggaac---tagtcaatttttatgtgttgtggcttgttacgttcactaatgtgttttatgttttggggtg--tgaatgggaaattagGTGGTCAGAAAAGCAGAGTTGCATTTGCGAAGATAACATTCAAGAAACCACACTTGCTATTGCTTGATGAGCCGTCCAATCATCTT

upper sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv02s0025g02160.t01 (Vitis vinifera), 3'ss of exon 15
gtattgtcttcaaagtcaccataattcataaacaattcgttaatgatttttaagaacagcgataataattgggacactcggtgggtgttgagttgcaatggatatatatttctgttatgaattatatttttttacttctctaaattctttactagGTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCACACATAATATTGCTTGATGAACCATCCAATCATCTG
                                                 |||||      |    |  |     || ||  |   | || |  ||   | |  ||| | |  | || | |  | ||||| |  | |  |||| ||  | ||  |||||||||||||||||| ||||| |||||||| ||||||||||| || || ||||| ||| | |||||||||||||| |||||||| 
-------------------------------------------------ttaagcttgaaggctttg-tcacatcaatctct--atattaacctg---ttggcataaaatcattttctcaggtgtatttatgaattgttctatatgatgtatcagGTGGTCAGAAAAGCAGAGTTGCATTTGCAAAAATAACTTTCAAAAAACCTCACATCATACTTCTTGATGAACCATCAAATCATCTT

upper sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 14
lower sequence: PP1S47_97V6.1 (Physcomitrella patens), 3'ss of exon 15
gtattgtcttcaaagtcaccataattcataaacaattcgttaatgatttttaagaacagcgataataattgggacactcggtgggtgttgagttgcaatggatatatatttctgttatgaattatatttttttacttctctaa--------attctttactagGTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCACACATAATATTGCTTGATGAACCATCCAATCATCTG
                                                            | || | |   |||   | |||   |  | |  |  ||   || | |||  |  |||||  | | ||| |  ||||  |  ||        || || | | ||||||||| || || ||||| || |||||||| || |||||||| ||||| || ||| || |||| ||||| |||||||||||  ||
------------------------------------------------------------gttattga--aggattgttggtattttcttaaatttaagcaatctttatcacaattatgtgtcagattgtcatactcttggaatatggatgatgctgtgc-agGTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTG

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|10232016|gb|BE800904.1|BE800904
EST:     TTTTGGTGTAACCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAG                         GTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCAC
genomic: TTTTGGTGTAACCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAGgtattgtctt ... tctttactagGTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCAC
EST: gi|10254011|gb|BE821777.1|BE821777
EST:     TTNNNGTGTNNNCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAG                         GTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCAC
genomic: TTTTGGTGTAACCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAGgtattgtctt ... tctttactagGTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCAC
EST: gi|13789096|gb|BG651687.1|BG651687
EST:     TTTTGGTGTAACCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAG                         GTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCAC
genomic: TTTTGGTGTAACCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAGgtattgtctt ... tctttactagGTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCAC
EST: gi|22523787|gb|BU082598.1|BU082598
EST:     TTTTGGTGTAACCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAG                         GTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCAC
genomic: TTTTGGTGTAACCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAGgtattgtctt ... tctttactagGTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCAC
EST: gi|192322574|gb|FK014695.1|FK014695
EST:     TTTTGGTGTAACCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAG                         GTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCAC
genomic: TTTTGGTGTAACCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAGgtattgtctt ... tctttactagGTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCAC
EST: gi|15286165|gb|BI470056.1|BI470056
EST:     TTTTGGTGTAACCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAG                         GTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCAC
genomic: TTTTGGTGTAACCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAGgtattgtctt ... tctttactagGTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatatatatttctgttatgaattatatttttttacttctctaaattctttactagGTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCACACATAATATTGCTTGATGAACCATCCAATCATCTG
                                     ctctaaa  putative branch site (score: 3)
                                            ttctttact  CT-rich tract
              ttatgaattatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtcttcaaagtcaccataattcataaacaattcgttaatgatttttaagaacagcgataataattgggacactcggtgggtgttgagttgcaatggatatatatttctgttatgaattatatttttttacttctctaaattctttactagGTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCACACATAATATTGCTTGATGAACCATCCAATCATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC