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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttttgtggggttcacattgtcagttggagaaatcttcacttttggtgaatgatgatgaatatgctgaagatatctaacatgagatttgtgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTTCT

Basic information

species Glycine max
transcript GLYMA11G27870.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 23
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 21
atttttgtggggttcacattgtcagttggagaaatcttcacttttggtgaatgatgatgaatatgctgaagat------atc-taacatgagatttgtgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTTCT-
      ||| |    || || |   ||  | |   || |     | | | |  |||  |  |||  || |  |      ||| | ||   | |||| ||   ||||| | || |||||||| || ||||||||||| ||||| ||  | ||||| |||||||||||||| ||||| |||||| | | |||| |  | |  ||    | 
------gtgagaca-acgttttgcattttatatcactgctaccctagagcaccatg-cgcgtattttgcatttttgctcatcatgactgaaaatttttg--ctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAAGAGAAAAGATACAAACTCATGGAC-GCAGTGAACTCCACAGCAGGGATTT

upper sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G021846_T02 (Zea mays), 3'ss of exon 21
atttttgtggggttcacattgtcagttggagaaatcttcacttttggtgaatgatgatgaatatgctgaagatatctaacatgagatttgtgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTTCT--
                   ||    |       |  ||| || ||  |||   |    || ||||    || ||   |  ||| ||||  |    |  || | || || || || || || |||||||| ||||| |||||||||||  ||||||| || || ||||| |||||||||| |||||   | |||||   ||  
------------------gtgatgatacatttgactttc-ctcttcttgatcaaatgcga-tatgtctgagcta---atgatgtgattgttctcatgtagATGCCACTACACACCATAATCGAGATACAAATGGGCGTCACGGGTGTGGAAGAGAAGAGGTACAAACTCATGGACTGAA-TGAAT-ACATAAAAGCAGCTGG

upper sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 23
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 22
---------atttttgtggggttcacattgtc----agttggagaaatcttcacttttggtgaatgatgatgaatatgctgaagatatc-taacatgagatttgtgatttc-cagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTTCT
            || |        | | | ||    |      ||  | |   ||||  | || |  ||      | ||   | | ||  ||||||    |   || ||   ||| | || ||||| || || || |||||||||||||||||  | ||||| ||||||||| | || ||||| |||||||||| | ||   |  |  |      
gtaaaatctgaattagaaaatacgagactatcttagaacgattgagctataagctttcagagagtcttggctg-caagccacacacataataacatattttggatgtttcaacagATGCCACTTCACACTATAATAGAGATACAGATGGGAGTTTCTGGTGTGCAAGAGAAACGCTACAAACTCATGGACTGAATTCAAACAACTATTACCACAA

upper sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 23
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 22
atttttgtggggttcacattgtcagttggagaaatcttcacttttggtgaatga--tgat--gaatatgctgaagatat-ctaacatgagatttgtgatt-----tccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTTCT
              |||||  |    || | ||||      | | || |||  |    ||   ||  ||   ||| ||  |    |  |  ||  |||||     | ||||| || |||||||| || || |||||||| |||||||| || |||||||||||||||||||| || || |||||||||  |   || |   ||  |||  
----------ttaccacatcattttatgaataaattccttttctaggagaagaaaacaatccaaagttggccaagttacaccctgacaaacttaatgattcacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAAGAGAAAAGATACAAGCTCATGGACTGACTTCGCTTCACAGAATCTTTTG

upper sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 23
lower sequence: EFJ11749 (Selaginella moellendorffii), 3'ss of exon 17
atttttgtggggttcacattgtcagttggagaaatcttcacttttggtgaatgatgatgaatatgctgaagatatctaacatgagatttgtgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTTCT
                    || |||  | | ||| |      |   |      ||   ||  | ||      | ||         ||||||  | |||| | |||||||| || || |||||||| |||||||||||| | ||||| ||||||||  |||| || ||  |  |                          
--------------------gtgagtgagtggaatttatctagtcaatatgatctggccaagttccttctttaagcttctgcttcctttgtg--tgccagATGCCTCTTCACACTATCATTGAGATCCAGATGGGAGTCGCAGGTGTACAAGAGAAGCGATACAAGCTCTTATAA-------------------------

upper sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 23
lower sequence: EFJ22544 (Selaginella moellendorffii), 3'ss of exon 17
atttttgtggggttcacattgtcagttggagaaatcttcacttttggtgaatgatgatgaatatgctgaagatatctaacatgagatttgtgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTTCT
                    || |||  | | ||| |      |   |      ||   ||  | ||      | ||         ||||||  | |||| | |||||||| || || |||||||| |||||||||||| | ||||| ||||||||  |||| || ||  |  |                          
--------------------gtgagtgagtggaatttatctagtcaatatgatctggccaagttccttctttaagcttctgcttcctttgtg--tgccagATGCCTCTTCACACTATCATTGAGATCCAGATGGGAGTCCCAGGTGTACAAGAGAAGCGATACAAGCTCTTATAA-------------------------

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|51336524|gb|CO980390.1|CO980390
EST:     TATATGCTTATTTTGCTGACAGACCTTTGAACGAAATTCCGCATATAGCG                         GTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAA
genomic: TATATGCTTATTTTGCTGACAGACCTTTGAACGAAATTCCGCATATAGCGgtaatttgtg ... tgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAA
EST: gi|51336471|gb|CO980337.1|CO980337
EST:     TATATGCTTATTTTGCTGACAGACCTTTGAACGAAATTCCGCATATAGCG                         GTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAA
genomic: TATATGCTTATTTTGCTGACAGACCTTTGAACGAAATTCCGCATATAGCGgtaatttgtg ... tgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAA
EST: gi|9564592|gb|BE474101.1|BE474101
EST:     TATATGCTTATTTTGCTGACAGACCTTTGAACGAAATTCCGCATATAGCG                         GTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAA
genomic: TATATGCTTATTTTGCTGACAGACCTTTGAACGAAATTCCGCATATAGCGgtaatttgtg ... tgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAA
EST: gi|22930234|gb|BU547373.1|BU547373
EST:     TATATGCTTATTTTGCTGACAGACCTTTGAACGAAATTCCGCATATAGCG                         GTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAA
genomic: TATATGCTTATTTTGCTGACAGACCTTTGAACGAAATTCCGCATATAGCGgtaatttgtg ... tgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgaatgatgatgaatatgctgaagatatctaacatgagatttgtgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTTCT
                            atctaac  putative branch site (score: 2)
                                                tttcc  putative PPT
           atgaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttttgtggggttcacattgtcagttggagaaatcttcacttttggtgaatgatgatgaatatgctgaagatatctaacatgagatttgtgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - ttgtggg
- - - - - - - - - - - - gttggag
- - - - - - - - - - - - - - - - - - - - - - - - - - gatgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgag