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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattcctatttcatccttctaattttgatctagttttactaatcaaacatgttatagacaagacatacgttgattaatccacaattctatttcactttagGTTGCTAGCTGGGGTGGTGACTTGCTAGATCGTGGGATTCTAACTCTTTCTCTTGCACCAAGAGATAACCATGAAGCTCAGGTTCAATTTGCTCTGGAGC

Basic information

species Glycine max
transcript GLYMA16G17500.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G17500.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G31850.2 (Arabidopsis thaliana), 3'ss of exon 3
aattcctatttcatccttctaattttgatctagttttactaatcaaacatgttatagacaagacatacgttgattaatccacaattctatttcactttagGTTGCTAGCTGGGGTGGTGACTTGCTAGATCGTGGGATTCTAACTCTTTCTCTTGCACCAAGAGATAACCATGAAGCTCAGGTTCAATTTGCTCTGGAGC
         ||  ||  |||     |  || |||| | |||||||    || |      | |  |||  ||      |||    ||   ||      |||||||| |||||||| || ||  |  | || |||||||| ||| | || |||||||| |||||||||||||||||||||||||||||||||||||| || |
--------gttagtctctcttcaactactcaagttct-ctaatcagttctgatcggtcgaggttataattt------tccgtggtttctttgg----tagGTTGCGAGCTGGGGAGGCGATCTTTTGGACCGTGGGATACTATCACTCTCTCTTGCTCCAAGAGATAACCATGAAGCTCAGGTTCAATTTGCTCTTGAAC

upper sequence: GLYMA16G17500.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0033g01120.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------------------------------------aattcctatttcatccttctaattttgatctagttttactaatcaaacatgttatagacaagacatacgttgattaatccacaattctatttcactt-tagGTTGCTAGCTGGGGTGGTGACTTGCTAGATCGTGGGATTCTAACTCTTTCTCTTGCACCAAGAGATAACCATGAAGCTCAGGTTCAATTTGCTCTGGAGC
                                                                        |||     || || ||   |  |||||| ||     |  |       || |  |   ||| |  |  ||   ||| ||        |  || | || |||||||| |||||||| ||||| ||  |||||||||| || |||||  | ||| | || ||||||||||| ||||| ||||| || ||||||||  |||| |
gtgagccctgattcatactattgtttcttcacggagttgatcatatgaaccaattcgataacctattaatctatttgatgtttattctggaagctttgatttatgaccatcacctttgtatat-gttcccaaaaattgtgtcacttagtctgtgtaattgctttatttctagGTTGCGAGCTGGGGAGGTGATTTATTAGATCGTGGCATACTAACAATGTCTTTGGCTCCAAGAGATAATCATGAGGCTCAAGTCCAATTTGCATTGGAAC

upper sequence: GLYMA16G17500.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ23765 (Selaginella moellendorffii), 3'ss of exon 3
aattcctatttcatccttctaattttgatctagttttactaatcaaacatgttatagacaagacatacgttgattaatccacaattctatttcacttt-agGTTGCTAGCTGGGGTGGTGACTTGCTAGATCGTGGGATTCTAACTCTTTCTCTTGCACCAAGAGATAACCATGAAGCTCAGGTTCAATTTGCTCTGGAGC
                                       |||  | | |    |   |        |   | | || ||     |||  ||  ||||| |||| || ||||||||||| |   |||| ||||||   ||  ||||  | || || ||||||||||||||||| ||||| || ||||| |||||| ||||||
--------------------------------------gtaagaagagaaaaaacgcattctcgtaagccttaatagtcttt--ttcctttaaactttcagGTGGCAAGCTGGGGTGGAGCTCTGCTGGATCGTAACATCATAACCATGTCACTGGCACCAAGAGATAACCACGAAGCGCAAGTTCAGTTTGCTTTGGAGC

upper sequence: GLYMA16G17500.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ21402 (Selaginella moellendorffii), 3'ss of exon 3
aattcctatttcatccttctaattttgatctagttttactaatcaaacatgttatagacaagacatacgttgattaatcc--acaattctatttc-----acttt-agGTTGCTAGCTGGGGTGGTGACTTGCTAGATCGTGGGATTCTAACTCTTTCTCTTGCACCAAGAGATAACCATGAAGCTCAGGTTCAATTTGCTCTGGAGC
                                                | |    ||| || ||  |   |  | |  |   ||| |  | || |     ||||| |||| || ||||||||||| |   |||| ||||||   ||  ||||  | || || ||||||||||||||||| ||||| || ||||| |||||| ||||||
----------------------------------------------gtaaga-ggagaaaaaacgcattctcgtaagccttaacagtctttttcctttaaactttcagGTGGCAAGCTGGGGTGGAGCTCTGCTGGATCGTAACATCATAACCATGTCACTGGCACCAAGAGATAACCACGAAGCGCAAGTTCAGTTTGCTTTGGAGC

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|254342914|gb|GR859076.1|GR859076
EST:     CAGAAATGAAAGATGGGTCCATTCGAACTGCCATTGATACTGGTTGTGGA                         GTTGCTAGCTGGGGTGGTGACTTGCTAGATCGTGGGATTCTAACTCTTTCT
genomic: CAGAAATGAAAGATGGGTCCATTCGAACTGCCATTGATACTGGTTGTGGAgtgagttttt ... ttcactttagGTTGCTAGCTGGGGTGGTGACTTGCTAGATCGTGGGATTCTAACTCTTTCT
EST: gi|16105942|gb|BI893682.1|BI893682
EST:     CAGAAATGAAAGATGGGTCCATTCGAACTGCCATTGATACTGGTTGTGGA                         GTTGCTAGCTGGGGTGGTGACTTGCTAGATCGTGGGATTCTAACTCTTTCT
genomic: CAGAAATGAAAGATGGGTCCATTCGAACTGCCATTGATACTGGTTGTGGAgtgagttttt ... ttcactttagGTTGCTAGCTGGGGTGGTGACTTGCTAGATCGTGGGATTCTAACTCTTTCT
EST: gi|22524234|gb|BU083045.1|BU083045
EST:     CAGAAATGAAAGATGGGTCCATTCGAACTGCCATTGATACTGGTTGTTTA                         GTTGCTAGCTGGGGTGGTGACTTGCTAGATCGTGGGATTCTAACTCTTTCT
genomic: CAGAAATGAAAGATGGGTCCATTCGAACTGCCATTGATACTGGTTGTGGAgtgagttttt ... ttcactttagGTTGCTAGCTGGGGTGGTGACTTGCTAGATCGTGGGATTCTAACTCTTTCT
EST: gi|6567183|gb|AW234800.1|AW234800
EST:     CAGAAATGAAAGATGGGTCCATTCGAACTGCCATTGATACTGGTTGTGGA                         GTTGCTAGCTGGGGTGGTGACTTGCTAGATCGTGGGATTCTAACTCTTTCT
genomic: CAGAAATGAAAGATGGGTCCATTCGAACTGCCATTGATACTGGTTGTGGAgtgagttttt ... ttcactttagGTTGCTAGCTGGGGTGGTGACTTGCTAGATCGTGGGATTCTAACTCTTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatgttatagacaagacatacgttgattaatccacaattctatttcactttagGTTGCTAGCTGGGGTGGTGACTTGCTAGATCGTGGGATTCTAACTCTTTCTCTTGCACCAAGAGATAACCATGAAGCTCAGGTTCAATTTGCTCTGGAGC
                          gattaat  putative branch site (score: 3)
                                       ttctatttcacttt  putative PPT
                                     aattctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattcctatttcatccttctaattttgatctagttttactaatcaaacatgttatagacaagacatacgttgattaatccacaattctatttcactttagGTTGCTAGCTGGGGTGGTGACTTGCTAGATCGTGGGATTCTAACTCTTTCTCTTGCACCAAGAGATAACCATGAAGCTCAGGTTCAATTTGCTCTGGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - ccttcta
- - - - - - - - - - - - - - - - - - - - - -caaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - caagaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atccaca