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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttatatgaaactgttactggttctgtttagtcgaaacttaaactgtgctatattatgcattggtatatgatagttatgaatctttaatgattgtgaagGTTATTCCATGGGGAGACCTAGACTCACTGGCAATGCTACAGAGGCAGCTCGATGTAGACATCCTTGTCACAG

Basic information

species Glycine max
transcript GLYMA02G43610.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G43610.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g05880.t01 (Vitis vinifera), 3'ss of exon 2
ttttatatgaaactgttactggttctgtttagtcgaaactta--aactgtgctatattatgcattggtatatgat--agttatgaatctttaatgattgtgaagGTTATTCCATGGGGAGACCTAGACTCACTGGCAATGCTACAGAGGCAGCTCGATGTAGACATCCTTGTCACAG---------------------------
    |        ||||        || | ||  |     |    | | |   ||||| ||  |      |  ||  |||| ||  |   | ||  || ||||||||||||||||||| ||| |||||||||| || ||||| ||||||||| | ||||||||||||||||| ||||                           
---cagccagtcttgttctcataagtgatcaggtgttctcttctgaatttctcatatt-tgattcaaatcacaattaagttctgcgtggcttattgttctgaagGTTATTCCATGGGGGGACTTAGACTCACTAGCCATGCTCCAGAGGCAGTTGGATGTAGACATCCTTGTGACAGGTCATACCCATCGATTCACAGCTTACA

upper sequence: GLYMA02G43610.3 (Glycine max), 3'ss of exon 4
lower sequence: EFJ29006 (Selaginella moellendorffii), 3'ss of exon 2
ttttatatgaaactgttactggttctgtttagtcgaaacttaaactgtgctatattatgcattggtatatgatagttatgaatctttaatgattgtgaagGTTATTCCATGGGGAGACCTAGACTCACTGGCAATGCTACAGAGGCAGCTCGATGTAGACATCCTTGTCACAG---------------------------
                                        |||    | |          ||    ||        | ||   || |  || |  | | ||| || || ||||| ||| | || || ||||||||||| |||||||||||||| || ||||||||  |||| |                           
-------------------------------------gtataattcattcatcgcccctgatctccatccatctcctgtg---ctcttgtgctcttca-gGTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTCGACGTTGACATCCTCATCACCGGGCACACGCACCAGTTCAAGGCGTACA
















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|4286973|gb|AI441123.1|AI441123
EST:     AAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGTCATCAG                         GTTATTCCATGGGGAGACCTAGACTCACTGGCAATGCTACA
genomic: AAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGTCATCAGgtctgatttt ... gattgtgaagGTTATTCCATGGGGAGACCTAGACTCACTGGCAATGCTACA
EST: gi|15285030|gb|BI468921.1|BI468921
EST:     AAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGTCATCAG                         GTTATTCCATGGNGAGACCTAGACTCACTGGCAATGCTA
genomic: AAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGTCATCAGgtctgatttt ... gattgtgaagGTTATTCCATGGGGAGACCTAGACTCACTGGCAATGCTA
EST: gi|298195454|gb|HO043845.1|HO043845
EST:     AAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGTCATCAG                         GTTATTCCATGGGGAGAC
genomic: AAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGTCATCAGgtctgatttt ... gattgtgaagGTTATTCCATGGGGAGAC
EST: gi|192331560|gb|FK019949.1|FK019949
EST:     AAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGTCATCAG                         GTTATTCCATGGGGAGACCTATACTCACTGGCAATGCTACAGAGGCAGCTC
genomic: AAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGTCATCAGgtctgatttt ... gattgtgaagGTTATTCCATGGGGAGACCTAGACTCACTGGCAATGCTACAGAGGCAGCTC
EST: gi|23057396|gb|BU578070.1|BU578070
EST:     AAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGTCATCAG                         GTTATTCCATGGGGAGACCTAGACTCACTGGCAATGCTACAGAGGCAGCTC
genomic: AAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGTCATCAGgtctgatttt ... gattgtgaagGTTATTCCATGGGGAGACCTAGACTCACTGGCAATGCTACAGAGGCAGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgctatattatgcattggtatatgatagttatgaatctttaatgattgtgaagGTTATTCCATGGGGAGACCTAGACTCACTGGCAATGCTACAGAGGCAGCTCGATGTAGACATCCTTGTCACAG
                                      ctttaat  putative branch site (score: 4)
                              ttatgaatctttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttatatgaaactgttactggttctgtttagtcgaaacttaaactgtgctatattatgcattggtatatgatagttatgaatctttaatgattgtgaagGTTATTCCATGGGGAGACCTAGACTCACTGGCAATGCTACAGAGGCAGCTCGATGTAGACATCCTTGTCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC