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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgttttttttttttttttccactttctgtattccaactaatttagtatcagtattttcataccctataattctcctgaatttgattaatcaatgaatgttctatagaaaagctagcacggaaatttgagaagaatctatttgtgttatgcagCTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCTCGCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGG

Basic information

species Glycine max
transcript GLYMA15G09090.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G09090.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 3'ss of exon 10
gttagtgttttttttttttttttccactttctgtattccaactaatttagtatcagtattttcataccctataattctcctgaatttgattaatcaatgaatgttctatagaaaagctagcacggaaatttgagaagaatcta--------tttgtgttatgcagCTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCTCGCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGG
                                                                 |   | |||  ||  ||  || | |  |  |  | ||  ||| || |  |||  ||  ||| ||||   ||||   ||        ||  |  |||||||||||| |||||||||||| | ||||||||||| || ||||| ||| |||| ||||||||||||||||||||||| |||||||| || |||||||| || |
----------------------------------------------------------------aattgtttaaagcttatgctttagctggaaaacagtataatctctaaagcagcatgc-tggacattttcaaagagcttagcatttggttgattatatgcagCTTGACGCATGTGCACATTCCTTCTTTGATGAGCTACGAGAGCCCAATGCACGCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATG

upper sequence: GLYMA15G09090.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os05g11730.1 (Oryza sativa), 3'ss of exon 10
gttagtgttttttttttttttttccactttctgtattccaactaatttagtatcagtattttcataccctataattctcctg---aatttgattaatca-atgaatgttctatagaaaagctagcacggaaatttgagaagaatctatttgtgttatgcagCTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCTCGCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGG
                                                             ||||      |  || | | |   ||||  | ||  || ||||    |  |||   |   |    | ||  |        | |  | |    ||||||||||||| |||||||||||||||||||||||||| || ||||| ||  |||| ||| ||||||| || ||||||||||| || ||||| ||||||||||| |
-------------------------------------------------------------tcatgtttagtcgttattcagtgtaattgcaatagccagatgacaacttaatattgattttttttccgatgtgcttattcatttgaatatctttatgcagCTTGATGCATGTGCACATCCTTTCTTTGATGAGCTGCGAGAGCCGAATGCACGCTTGCCAAACGGACGTCCATTTCCACCACTATTCAACTTCAAACACG

upper sequence: GLYMA15G09090.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G472625_T01 (Zea mays), 3'ss of exon 10
gttagtgttttttttttttttttccactttctgtattccaactaatttagtatcagtattttcataccctataattctcctgaatttgattaatcaatgaatgttctatagaaaagctagcacggaaatttgagaagaatctatttgtgttatgcagCTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCTCGCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGG
                                         || |  |  | |  |   |  || || | |||||         ||| ||  |||| |   ||||   |||||| | |   | |    |        | ||||||| | ||   |||||||| ||||| || ||||| ||||||||||| || || |  ||  |||| || || ||||| || |||||||| ||||| || |||||||||||||| |
---------------------------------------ttctcacatgctgtaggg--tggcacacaccataatc--------tttaatgcatcagtt--tgttggttagaaatgttctaatgtgcttc---atgtattctatttctatt---cagCTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCACGTCTACCAAACGGCCGTCCATTCCCTCCGCTCTTTAACTTCAAACATG

upper sequence: GLYMA15G09090.1 (Glycine max), 3'ss of exon 10
lower sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 9
gttagtgttttttttttttttttccactttctgtattccaactaatttagtatcagtattttcataccctataattctcctgaatttgattaatcaatgaatgttctatagaaaagctagcacggaaatttgagaagaatctatttgtgttatgcagCTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCTCGCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGG
                                                                ||  |  |  |  |      |||  | | ||  | |   | | |  |||    ||  |   |  ||         | |  | || ||   ||||| ||||| ||||||||||| ||||||||||||||  |||||||  | |||||  | |||||||| || || || || ||||| || ||||||||||| |
---------------------------------------------------------------gtaagcattggtctt--gaggtttcttcagtctctaagaatccaactgaatccttactatatatttt--------gtttcctcgtattt--cagCTCGAAGCTTGTGCACATCCGTTCTTTGATGAACTCAGAGAACCAAACGCTCGTTTACCAAATGGACGGCCTTTCCCGCCTCTCTTCAACTTCAAACAAG

upper sequence: GLYMA15G09090.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 3'ss of exon 10
gttagtgttttttttttttttttccactttctgtattccaactaatttagtatcagtattttcatacccta--taattctcctgaatttgattaatcaatgaatgttctatagaaaagctagcacggaaatttgagaagaatctatttgtgttat-gcagCTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCTCGCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGG
                                                      ||| | || | | ||||  ||||| |    | |   |||    |||  |  || |  |          |       |||||  |   | ||||| ||| || |||||| ||||||||||||||||||||||||||||| || ||||||||| |||| ||||||||||||||||||||||| || ||||| || || || || ||||
-----------------------------------------------------tagtttctttaaatcctaagtaattattagtagtactattttgaaatatacattgtccatttccatcctc-------tttgactaagctatatttttgtcattgcagCTAGAAGCATGTGCACATCCTTTCTTTGATGAGCTCCGAGAACCCAATGCCCGCCTGCCAAATGGTCGTCCATTACCACCTCTCTTCAATTTTAAGCAGG

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|208236435|gb|GE031587.1|GE031587
EST:     CTTGCATCCCGGCTTTTGTCAATACTCCCCAACGTCTCCGATGCTCTGCG                         CTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCA
genomic: CTTGCATCCCGGCTTTTG-CAATACTCCCCAA-GTCTCCGATGCACTGCGgttagtgttt ... tgttatgcagCTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCA
EST: gi|254330723|gb|GR841988.1|GR841988
EST:     ATCTTGCATCCCGGCTTTTGCAATACTCCCCAAGTCTCCGATGCACTGCG                         CTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCT
genomic: ATCTTGCATCCCGGCTTTTGCAATACTCCCCAAGTCTCCGATGCACTGCGgttagtgttt ... tgttatgcagCTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCT
EST: gi|254329846|gb|GR839399.1|GR839399
EST:     ATCTTGCATCCCGGCTTTTGCAATACTCCCCAAGTCTCCGATGCACTGCG                         CTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCT
genomic: ATCTTGCATCCCGGCTTTTGCAATACTCCCCAAGTCTCCGATGCACTGCGgttagtgttt ... tgttatgcagCTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCT
EST: gi|23731206|gb|BU763715.1|BU763715
EST:     ATCTTGCATCCCGGCTTTTGCAATACTCCCCAAGTCTCCGATGCACTGCG                         CTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCT
genomic: ATCTTGCATCCCGGCTTTTGCAATACTCCCCAAGTCTCCGATGCACTGCGgttagtgttt ... tgttatgcagCTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCT
EST: gi|12774190|gb|BG239117.1|BG239117
EST:     ATCTTGCATCCCGGCTTTTGCAATACTCCCCAAGTCTCCGATGCACTGCG                         CTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCT
genomic: ATCTTGCATCCCGGCTTTTGCAATACTCCCCAAGTCTCCGATGCACTGCGgttagtgttt ... tgttatgcagCTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCT
EST: gi|193615193|gb|FK560613.1|FK560613
EST:     ATCTTGCATCCCGGCTTTTGCAATACTCCCCAAGTCTCCGATGCACTGCG                         CTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCT
genomic: ATCTTGCATCCCGGCTTTTGCAATACTCCCCAAGTCTCCGATGCACTGCGgttagtgttt ... tgttatgcagCTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctatagaaaagctagcacggaaatttgagaagaatctatttgtgttatgcagCTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCTCGCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGG
                                   aatctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgttttttttttttttttccactttctgtattccaactaatttagtatcagtattttcataccctataattctcctgaatttgattaatcaatgaatgttctatagaaaagctagcacggaaatttgagaagaatctatttgtgttatgcagCTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCTCGCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC