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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttcatttgtgtttgcctttggttttgcaccatttgcattgcttgcttggtttttgtttactctagtttcagaactattctcatccttagttctttttattggttgccagGTTCTTCATGATGCATTCTTTAAATACCAAACAAAGCCTAAACTGACCTCTCTTGGAGACCTGTATCATGAAGGAAAAGAGTTTGAG

Basic information

species Glycine max
transcript GLYMA13G31550.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g58090.1 (Oryza sativa), 3'ss of exon 7
gtttcatttgtgtttgcctttggttttgcaccatttgcattgcttgcttggtttttgtttactctagtttcagaactattctcatccttagttctttttattggttgccagGTTCTTCATGATGCATTCTTTAAATACCAAACAAAGCCTAAACTGACCTCTCTTGGAGACCTGTATCATGAAGGAAAAGAGTTTGAG
         ||  ||    |    | | || |    || |   ||      |  |    |  |  |    ||| |  | |    ||     ||  |||  |||||   |||||  | ||||| || ||||| ||||||||||||||||| ||| ||||   || ||| ||||||||| ||||||| ||||||||||||
--------agtaatttatctcatatatccagctggggcctgagttatcaactcctgacatgattcacaggcaggaaaaataa-gtctcaccttgatttcgttggta--cagGTCTTGCATGACGCCTTCTTCAAATACCAAACAAAGCCAAAATTGACTAGTCATGGTGACCTGTATTATGAAGGGAAAGAGTTTGAG

upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 7
lower sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 6
gtttcatttgtgtttgcctttggttttgcaccatttgcattgcttgcttggtttttgtttactctagtttcagaactattctcatccttagttctttttattggttgccagGTTCTTCATGATGCATTCTTTAAATACCAAACAAAGCCTAAACTGACCTCTCTTGGAGACCTGTATCATGAAGGAAAAGAGTTTGAG
                  ||   ||||     || |   ||   || |  || |||| | |     |||  | ||||     ||     || | || || |   ||  ||||| |||||||||||||| || |||||||||||||||||||| ||| |  |||| || ||  |||||  |||||| ||||| ||||||
----------------gtttctattttttttaatctttgttttgtgatgagtatttgctgatatctgttctataactga---caagtgaagctattctt-tcctttctcagGTACTTCATGATGCATTTTTCAAATACCAAACAAAGCCTAAGCTGTCAGCTCTAGGCGATTTGTATTTTGAAGGGAAAGAATTTGAG
















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|24136279|gb|BU926789.1|BU926789
EST:     AAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG                         GTTCTTCATGATGCATTCTTTAAATACCAAACAAAGCCTAAACTGACCTCT
genomic: AAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAGgtttcatttg ... tggttgccagGTTCTTCATGATGCATTCTTTAAATACCAAACAAAGCCTAAACTGACCTCT
EST: gi|7234841|gb|AW570174.1|AW570174
EST:     GAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG                         GTTCTTCATGATGCATTCTTTAAATACCAAACAAAGCCTAAACTGACCTCT
genomic: AAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAGgtttcatttg ... tggttgccagGTTCTTCATGATGCATTCTTTAAATACCAAACAAAGCCTAAACTGACCTCT
EST: gi|23725417|gb|BU760662.1|BU760662
EST:     AAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG                         GTTCTTCATGATGCATTCTTTAAATACCAAACAAAGCCTAAACTGACCTCT
genomic: AAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAGgtttcatttg ... tggttgccagGTTCTTCATGATGCATTCTTTAAATACCAAACAAAGCCTAAACTGACCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttactctagtttcagaactattctcatccttagttctttttattggttgccagGTTCTTCATGATGCATTCTTTAAATACCAAACAAAGCCTAAACTGACCTCTCTTGGAGACCTGTATCATGAAGGAAAAGAGTTTGAG
                                   ttctttttatt  CT-rich tract
                               ttagttctttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttcatttgtgtttgcctttggttttgcaccatttgcattgcttgcttggtttttgtttactctagtttcagaactattctcatccttagttctttttattggttgccagGTTCTTCATGATGCATTCTTTAAATACCAAACAAAGCCTAAACTGACCTCTCTTGGAGACCTGTATCATGAAGGAAAAGAGTTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA