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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttatctatcctccatgtaggtttatgagttctttttctgaaaagagatttatgagttaattataatttaggtcggcttaccaatattattttaataatttttattaaagGACTACATCTATGAAGACGAGTTGAATCACTTCGTTAATACTGGTGCACTTTCTGAGCTCATTCTTGCCTTCTCTCGAGAGGGACCCACCAAGGAGTATG

Basic information

species Glycine max
transcript GLYMA13G00990.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G00990.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv11s0052g00880.t01 (Vitis vinifera), 3'ss of exon 15
gtgagttatctatcctccatgtaggtttatgagttctttttctgaaaagagatttatgagttaattataatttaggtcggcttaccaatattattttaata-atttttat---taaagGACTACATCTATGAAGACGAGTTGAATCACTTCGTTAATACTGGTGCACTTTCTGAGCTCATTCTTGCCTTCTCTCGAGAGGGACCCACCAAGGAGTATG
                  | ||  |    | | |   |||| |||| | |  |            |||| |||  |||   |    ||  ||| |||  |    || |||   |  |||||||||| |||||||| ||| |||||  ||| ||| |  ||||||| || || ||||| ||| |||| ||||| || || |||||||||||||| ||||
----------------gtaagtcagaccctaa-tctattttatgaacaaatgt---------ggctatattttgtgtcaaatgtgaaactttaattttgtgtgcttctatctttgcagGACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTCTCAGAGCTGATTGTTGCTTTCTCACGTGAAGGACCCACCAAGGAATATG
















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|209728345|gb|BW659982.1|BW659982
EST:     CTGAACTTGGCCCTTCAGTTTTATTCTTTGGATGCAGGAACCGTCAAATG                         GACTACATCTATGAAGACGAGTTGAATCACTTCGTTAATACTGGTGCACTT
genomic: CTGAACTTGGCCCTTCAGTTTTATTCTTTGGATGCAGGAACCGTCAAATGgtgagttatc ... tttattaaagGACTACATCTATGAAGACGAGTTGAATCACTTCGTTAATACTGGTGCACTT
EST: gi|254318721|gb|GR828665.1|GR828665
EST:     CTGAACTTGGCCCTTCAGTTTTATTCTTTGGATGCAGGAACCGTCAAATG                         GACTACATCTATGAAGACGAGTTGAATCACTTCGTTAATACTGGTGCACTT
genomic: CTGAACTTGGCCCTTCAGTTTTATTCTTTGGATGCAGGAACCGTCAAATGgtgagttatc ... tttattaaagGACTACATCTATGAAGACGAGTTGAATCACTTCGTTAATACTGGTGCACTT
EST: gi|209729002|gb|BW655032.1|BW655032
EST:     CTGAACTTGGCCCTTCAGTTTTATTCTTTGGATGCAGGAACCGTCAAATG                         GACTACATCTATGAAGACGAGTTGAATCACTTCGTTAATACTGGTGCACTT
genomic: CTGAACTTGGCCCTTCAGTTTTATTCTTTGGATGCAGGAACCGTCAAATGgtgagttatc ... tttattaaagGACTACATCTATGAAGACGAGTTGAATCACTTCGTTAATACTGGTGCACTT
EST: gi|6914702|gb|AW396232.1|AW396232
EST:     CTGAACTTGGCCCTTCAGTTTTATTCTTTGGATGCAGGAACCGTCAAATG                         GACTACATCTATGAAGACGAGTTGAATCACTTCGTTAATACTGGTGCACTT
genomic: CTGAACTTGGCCCTTCAGTTTTATTCTTTGGATGCAGGAACCGTCAAATGgtgagttatc ... tttattaaagGACTACATCTATGAAGACGAGTTGAATCACTTCGTTAATACTGGTGCACTT
EST: gi|4313809|gb|AI460928.1|AI460928
EST:     CTGAACTTGGCCCTTCAGTTTTATTCTTTGGATGCAGGAACCGTCAAATG                         GACTACATCTATGAAGACGAGTTGAATCACTTCGTTAATACTG-TGCACTT
genomic: CTGAACTTGGCCCTTCAGTTTTATTCTTTGGATGCAGGAACCGTCAAATGgtgagttatc ... tttattaaagGACTACATCTATGAAGACGAGTTGAATCACTTCGTTAATACTGGTGCACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaattataatttaggtcggcttaccaatattattttaataatttttattaaagGACTACATCTATGAAGACGAGTTGAATCACTTCGTTAATACTGGTGCACTTTCTGAGCTCATTCTTGCCTTCTCTCGAGAGGGACCCACCAAGGAGTATG
                                  ttttaat  putative branch site (score: 3)
                                           tttttatt  putative PPT
                      ttaccaatattatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttatctatcctccatgtaggtttatgagttctttttctgaaaagagatttatgagttaattataatttaggtcggcttaccaatattattttaataatttttattaaagGACTACATCTATGAAGACGAGTTGAATCACTTCGTTAATACTGGTGCACTTTCTGAGCTCATTCTTGCCTTCTCTCGAGAGGGACCCACCAAGGAGTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG