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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgcagttggaatttgggacatttatttggcttctgctttggcaggtttgagtacaaggaacacgacatgcttttcattgattgattggcttacctactgtttcatgttttcatcagGATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGCCATCATGGCGTCGACAAGGAGGGAAGGCCTGTTTATATTGAAAGACTTG

Basic information

species Glycine max
transcript GLYMA04G01220.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G01220.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 3'ss of exon 4
gtaaatgcagttggaatttgggacatttatttggct-tctgctttggcaggtttgagtacaaggaacacgacatgcttttcattga-ttgattggcttacctac-tgtttcatgttttcatcagGATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGCCATCATGGCGTCGACAAGGAGGGAAGGCCTGTTTATATTGAAAGACTTG
                         | ||| |  || | |        |   ||   |  |    | | |   || |||  |   | ||  ||| | |   ||| ||||| || || | ||||||||||||||||||| |||||  |||| ||  |||| || ||||| ||||| |||||||| || || ||||||||||| |||||||| ||||||||||| |
------------------------gtctatctatctatatatgcatatatcctttcttcaattttataagtgctgttttgtaccaaattctttgacatgtttacctgtttgatattgttatcagGATTTTGAGTTCAAAGAGTTGAATGAGGTGTTGAAATACTATCCCCATGGTCATCATGGTGTGGATAAGGAGGGAAGACCTGTTTACATTGAAAGACTAG

upper sequence: GLYMA04G01220.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ17479 (Selaginella moellendorffii), 3'ss of exon 2
gtaaatgcagttggaatttgggacatttatttggcttctgctttggcaggtttgagtacaaggaacacgacatgcttttcattgattgattggcttacctactgtttcatgttttcatcagGATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGCCATCATGGCGTCGACAAGGAGGGAAGGCCTGTTTATATTGAAAGACTTG
                                          ||||     |  | |  || |   ||| | || || || || ||      | ||   |  | ||   ||   |    |||||||  | || || ||| | || |||||   ||| || |||||||| ||||| ||||| || ||||| || ||||||||||| |||||||| ||  | |
-----------------------------------------gttggtgccatccatttaaacgcttacggc-tggttctctttaat------gtttttttcttcttctttggactgtctagGATTTCCATTTTAAAGAGCTGGAGGAAGTGAGGAAATACTATCCACAGGGCCACCATGGAGTGGACAAAGAAGGAAGGCCTGTATATATTGAGAGGATCG

upper sequence: GLYMA04G01220.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ28804 (Selaginella moellendorffii), 3'ss of exon 2
gtaaatgcagttggaatttgggacatttatttggcttctgctttggcaggtttgagtacaaggaacacgacatgcttttcattgattgattggcttacctactgtttcatgttttcatcagGATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGCCATCATGGCGTCGACAAGGAGGGAAGGCCTGTTTATATTGAAAGACTTG
                                          | ||     |  | |  || |   ||| | || || || || || | || | |   || || |    ||| |     |||||||  | ||||| ||| | || |||||   ||| || |||||||| ||||| ||||| || ||||| || ||||||||||| |||||||| ||  | |
-----------------------------------------gtcggtgccatccatttaaaagcttacggc-tggttctctttaat-gttttgttcttcttctttggactgtct-----agGATTTCCATTTCAAAGAGCTGGAGGAAGTGAGGAAATACTATCCACAAGGCCACCATGGAGTGGACAAAGAAGGAAGGCCTGTATATATTGAGAGGATCG

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|208237495|gb|GE028825.1|GE028825
EST:     CTGATATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTGTGCAG                         GATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGC
genomic: CTGACATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTGTGCAGgtaaatgcag ... ttttcatcagGATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGC
EST: gi|16347849|gb|BI973444.1|BI973444
EST:     CTGACATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTGTGCAG                         GATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGC
genomic: CTGACATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTGTGCAGgtaaatgcag ... ttttcatcagGATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGC
EST: gi|209709869|gb|BW657267.1|BW657267
EST:     CTGACATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTGTGCAG                         GATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGC
genomic: CTGACATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTGTGCAGgtaaatgcag ... ttttcatcagGATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGC
EST: gi|151406570|gb|EV276385.1|EV276385
EST:     CTGACATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTGTGCAG                         GATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGC
genomic: CTGACATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTGTGCAGgtaaatgcag ... ttttcatcagGATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGC
EST: gi|209712291|gb|BW668485.1|BW668485
EST:     CTGACATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTGTGCAG                         GATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGC
genomic: CTGACATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTGTGCAGgtaaatgcag ... ttttcatcagGATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGC
EST: gi|209728326|gb|BW658538.1|BW658538
EST:     CTGACATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTGTGCAG                         GATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGC
genomic: CTGACATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTGTGCAGgtaaatgcag ... ttttcatcagGATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGC
EST: gi|151395356|gb|EV265227.1|EV265227
EST:     CTGACATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTGTGCAG                         GATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGC
genomic: CTGACATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTGTGCAGgtaaatgcag ... ttttcatcagGATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGC
EST: gi|254346081|gb|GR859694.1|GR859694
EST:     CTGACATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTGTGCAG                         GATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGC
genomic: CTGACATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTGTGCAGgtaaatgcag ... ttttcatcagGATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgacatgcttttcattgattgattggcttacctactgtttcatgttttcatcagGATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGCCATCATGGCGTCGACAAGGAGGGAAGGCCTGTTTATATTGAAAGACTTG
                         ggcttac  putative branch site (score: 3)
                                             ttttcatc  putative PPT
         ttttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgcagttggaatttgggacatttatttggcttctgctttggcaggtttgagtacaaggaacacgacatgcttttcattgattgattggcttacctactgtttcatgttttcatcagGATTTTGAGTTCAAGGAGTTAGATGAAGTCGTGAAGTATTATCCACATGGCCATCATGGCGTCGACAAGGAGGGAAGGCCTGTTTATATTGAAAGACTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG