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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattatattcatttaattactttcaactcttcctaaaacatgttgaccttacctaccacaacataaaatgtgacacatatgctacgtggtactacatagtcatatcataggttagtttcataatgatcatttgtttactaagaaatgttgctgttttgggaccttaatgcagGAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGAAAGACAGAACAACAGTGGAAGATATGGACCTTGCTGTTCGTGCTAGTCT

Basic information

species Glycine max
transcript GLYMA11G19490.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G19490.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaattatattcatttaattactttcaactcttcctaaaacatgttgaccttacctaccacaacataaaatgtgacacatatgctacgtggtact---acatagtcatatcataggttagtttcataatgatcatttgtttactaagaaatgttgctgttttgggaccttaatgcagGAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGAAAGACAGAACAACAGTGGAAGATATGGACCTTGCTGTTCGTGCTAGTCT
| || || || ||| | | || || | | | | ||||| | | ||| | ||| || | | |||||| ||| | || | |||||| || || || ||||||||||| || || || |||||||||||||||||||| | || || |||||||||||||| || || || || || |||||
-------------------------------------------------------------------tagtg-gaagcaaatggaaggcggatcttaaatgtgtttttgtcataaatca-tttaaaaattattgtagatgtactaaa----gttatca----aaaataatattatagGAACCGCCGGAATATGGAGAATAGCGGCGATAAATGAAGCTGGTGGGTGGAAAGATCGGACCACCGTGGAAGATATGGATCTCGCCGTCCGAGCAAGTCT

upper sequence: GLYMA11G19490.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0061g01230.t01 (Vitis vinifera), 3'ss of exon 4
gtaattatattcatttaattactttcaactcttcctaaaacatgttgaccttacctaccacaacataaaatgtgacacatatgctacgtggtactacatagtcatatcataggttagtttcataatgatcatttgtttactaagaaatgttgctgttttgggaccttaatgcagGAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGAAAGACAGAACAACAGTGGAAGATATGGACCTTGCTGTTCGTGCTAGTCT
| ||| | | |||| | | || || | | | | ||| || | |||||||||| || | | ||||||| || |||||| | |||||||| || ||||||||||| |||||||||||||| ||||||||||| ||||| || ||||| ||||| || |||||||||||
--------------------------------------------------------------------------gtaaatacgtt----ggtatttattgaacaaatgacaaatacatcccatgattctttgagagaagctaagaaatgaaaaatattaatggc----atgcagGTACAGCTGGTGTGTGGAGAATTGCAGCTATCAACGAGGCTGGTGGGTGGAAGGACAGAACAACCGTGGAGGACATGGATCTTGCCGTCCGTGCTAGTCT
















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|7478387|gb|AW666245.1|AW666245
EST:     AGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTTCGGTTTCAACG                         GAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGA
genomic: AGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTTCGGTTTCAACGgtaattatat ... cttaatgcagGAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGA
EST: gi|8283320|gb|BE020881.1|BE020881
EST:     AGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTTCGGTTTCAACG                         GAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGA
genomic: AGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTTCGGTTTCAACGgtaattatat ... cttaatgcagGAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGA
EST: gi|16346811|gb|BI972406.1|BI972406
EST:     AGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTTCGGTTTCAACG                         GAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGA
genomic: AGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTTCGGTTTCAACGgtaattatat ... cttaatgcagGAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGA
EST: gi|8284807|gb|BE022366.1|BE022366
EST:     AGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTTCGGTTTCAACG                         GAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGA
genomic: AGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTTCGGTTTCAACGgtaattatat ... cttaatgcagGAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGA
EST: gi|193422352|gb|FK389741.1|FK389741
EST:     AGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTTCGGTTTCAACG                         GAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGA
genomic: AGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTTCGGTTTCAACGgtaattatat ... cttaatgcagGAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGA
EST: gi|10847333|gb|BF070038.1|BF070038
EST:     AGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTTCCGTTTCAACG                         GGAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGG
genomic: AGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTTCGGTTTCAACGgtaattatat ... cttaatgcagG-AACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGG
EST: gi|10846450|gb|BF071342.1|BF071342
EST:     AGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTTCGGTTTCAACG                         GAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGA
genomic: AGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTTCGGTTTCAACGgtaattatat ... cttaatgcagGAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGA
EST: gi|15337505|gb|BI498161.1|BI498161
EST:     AGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTTCGGTTTCAACG                         GAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGA
genomic: AGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTTCGGTTTCAACGgtaattatat ... cttaatgcagGAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGA
EST: gi|6567149|gb|AW234774.1|AW234774
EST:     AGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTTCGGTTTCAACG                         GAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGA
genomic: AGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTTCGGTTTCAACGgtaattatat ... cttaatgcagGAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcataatgatcatttgtttactaagaaatgttgctgttttgggaccttaatgcagGAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGAAAGACAGAACAACAGTGGAAGATATGGACCTTGCTGTTCGTGCTAGTCT
                                            ccttaat  putative branch site (score: 4)
 atttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattatattcatttaattactttcaactcttcctaaaacatgttgaccttacctaccacaacataaaatgtgacacatatgctacgtggtactacatagtcatatcataggttagtttcataatgatcatttgtttactaagaaatgttgctgttttgggaccttaatgcagGAACTGCTGGTATTTGGAGAATAGCTGCTATCAACGAAGCTGGTGGGTGGAAAGACAGAACAACAGTGGAAGATATGGACCTTGCTGTTCGTGCTAGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT