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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtgcttcttcatcttcttctaaagatctggtttgtcatatactgaaaccttaagttaccttttccctgccattcattaatttaaagcacttctgagcgcagCTTAAATATCATGAAAGTGGGAAAGAAAAGAACTGTTTACCCCAAGTTGGTCAGTGGAATATGATGAACAAG

Basic information

species Glycine max
transcript GLYMA20G28970.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 9
gtaatgtgcttcttcatcttcttctaaagatctggtttgtcatatactgaaaccttaagttaccttttccctgccattcattaatttaaagcacttctgagcg--cagCTTAAATATCATGAAAGTGGGAAAGAAAAGAACTGTTTACCCCAAGTTGGTCAGTGGAATATGATGAACAAG
                          | ||| ||  ||     ||      |  |   | || ||  || | || | | |||    ||    | ||    ||   ||||| ||||||||||| | |||||| |||||| | || || || ||||||||||||||||| ||| ||||||||
------------------------gtatgatttgcctttgttaatctcagtagtt--ggctaactgctctcagctaataatttgggtatgaaattttgtggctttcagCTGAAATATCATGATACTGGGAAGGAAAAGGAGTGCTTGCCACAAGTTGGTCAGTGGAACATGGTGAACAAG

upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaatgtgcttcttcatcttcttctaaagatctggtttgtcatatactgaaaccttaagttaccttttccctgccattcattaatttaaagcactt--ctgagcgcagCTTAAATATCATGAAAGTGGGAAAGAAAAGAACTGTTTACCCCAAGTTGGTCAGTGGAATATGATGAACAAG----------------------------
                         ||| | ||     |   |   |||||  || |   ||        |||  ||   ||||||     | |||  ||     |||||||| ||||| || |  |||||||||||  | ||| | || ||||||||||||||||||||||||||||||                            
----------------------gtaaaaaacctaaacagatct---ctgaatgctcatactatgagaatactgttat--gttaattcgtctctctttgcttgctacagCTTAAGTATCACGAGAACGGGAAAGAAAAAGATTGTCTCCCGCAAGTTGGTCAGTGGAATATGATGAACAAGAAAATGATCAACGGGATGACTGTGAGCA

upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 9
gtaatgtgcttcttcatcttcttctaaagatctggtttgtcatatactgaaaccttaagttaccttttccctgccattcattaatttaaagcacttctgagcgcagCTTAAATATCATGAAAGTGGGAAAGAAAAGAACTGTTTACCCCAAGTTGGTCAGTGGAATATGATGAACAAG
                |  | ||| |     ||   ||   ||||    ||     | | ||  | || |      | | | |  | |   |  || |    |||||| ||||||||||||| |||||| |||||| | ||||| || ||||| ||||||||||||||||||||||| 
---------------gtaatattc-accatcctaaatttatatatgtgaaag----atgataggtattacacattgtgcctgatctgacttctattttatctgcagCTGAAATATCATGAAACTGGGAAGGAAAAGGATTGTTTGCCTCAAGTCGGTCAGTGGAATATGATGAACAAA

upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ15357 (Selaginella moellendorffii), 3'ss of exon 10
gtaatgtgcttcttcatcttcttctaaagatctggtttgtcatatactgaaaccttaagttaccttttccctgccattcattaatttaaagc---acttctgagcgcagCTTAAATATCATGAAAGTGGGAAAGAAAAGAACTGTTTACCCCAAGTTGGTCAGTGGAATATGATGAACAAG
                                                                | |   | |    || |||||| ||      || | |     ||| | || |||||||| | |||    || ||  ||||  | || |||||||| |||||||||||||||||||||
-------------------------------------------------------------gtatgtcttccgaagatcgttaattcaagctctaacgttttctgacagTTGAAGTATCATGATACTGGACGGGAGAAAGACTGCCTTCCTCAAGTTGGGCAGTGGAATATGATGAACAAG

upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ24991 (Selaginella moellendorffii), 3'ss of exon 10
gtaatgtgcttcttcatcttcttctaaagatctggtttgtcatatactgaaaccttaagttaccttttccctgccattcatt--aatttaaagcacttctgagcgcagCTTAAATATCATGAAAGTGGGAAAGAAAAGAACTGTTTACCCCAAGTTGGTCAGTGGAATATGATGAACAAG
                                                            |  |||       || || |||  |  | |||    ||||||   ||| | || |||||||| | |||    || ||  ||||  | || |||||||| |||||||||||||||||||||
---------------------------------------------------------gtatgtcttccgaagaccgttaattcaagctcaaacgttttctga---cagTTGAAGTATCATGATACTGGACGGGAGAAAGACTGCCTTCCTCAAGTTGGGCAGTGGAATATGATGAACAAG

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|193476564|gb|FK442169.1|FK442169
EST:     TCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCTGCTCCTTGG                         CTTAAATATCATGAAAGTGGGAAAGAAAA
genomic: TCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCTGCTCCTTGGgtaatgtgct ... ctgagcgcagCTTAAATATCATGAAAGTGGGAAAGAAAA
EST: gi|24136288|gb|BU926798.1|BU926798
EST:     TCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCTGCTCCTTGG                         CTTAAATATCATGAAAGTGGGAAAGAAAAGAACTGTTTACCCCCCAGTTGG
genomic: TCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCTGCTCCTTGGgtaatgtgct ... ctgagcgcagCTTAAATATCATGAAAGTGGGAAAGAAAAGAACTGTTTACCCCA-AGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttaagttaccttttccctgccattcattaatttaaagcacttctgagcgcagCTTAAATATCATGAAAGTGGGAAAGAAAAGAACTGTTTACCCCAAGTTGGTCAGTGGAATATGATGAACAAG
                           cattaat  putative branch site (score: 3)
                                        cacttct  putative PPT
                        attcattaatttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtgcttcttcatcttcttctaaagatctggtttgtcatatactgaaaccttaagttaccttttccctgccattcattaatttaaagcacttctgagcgcagCTTAAATATCATGAAAGTGGGAAAGAAAAGAACTGTTTACCCCAAGTTGGTCAGTGGAATATGATGAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA