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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactaacaaataaggtctttctctagagtctgcataatgccgtgcatttcttgtctgaatgttaatttttgggtgaatgatactgcaaatatccatacagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATCAATAAGAGGTTGTCCAGAAAGCTTGATAAAAAATGGAAGAAAAGCATTG

Basic information

species Glycine max
transcript GLYMA05G31160.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G31160.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0121g00010.t01 (Vitis vinifera), 3'ss of exon 1
tactaacaaataag-gtctttctctagagtctgcataatgccgtgcatttcttgtctgaatgttaatttttgggtgaatgatactgcaaa--tatccat-----acagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATCAATAAGAGGTTGTCCAGAAAGCTTGATAAAAAATGGAAGAAAAGCATTG
        | || | || |||   | | |  |||  ||        ||  || |    ||  ||   ||||||  | ||  |  |  |||  | | | |     | || ||||||||||||| ||||| || |||||||| || || |||||||| ||||| ||||||||||| |||||||| ||     | ||||||||||||||||
------tgagtatgagtgttttggtgggggttgctgaaaatgacttatgcctcgat--aacctttgattttggtagcatattgatttaaagcttttcttcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATCAACAAGAGGTTGTCAAGAAAGCTCGACCGGCAGTGGAAGAAAAGCATTG

upper sequence: GLYMA05G31160.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0141g00200.t01 (Vitis vinifera), 3'ss of exon 1
tactaacaaataaggtctttctctagagtctgcataatgccgtgcatttcttgtctgaatgttaatttttgggtgaatgatactgcaaa--tatccat-----acagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATCAATAAGAGGTTGTCCAGAAAGCTTGATAAAAAATGGAAGAAAAGCATTG
         ||||| | |||   | | |  |||  |||       ||  || |  |||   || ||||| |  | |    |  | ||||  | | | |     | || ||||||||||||| ||||| || |||||||| || || |||||||| ||||| ||||||||||| |||||||| ||     | ||||||||||||||||
-----gaggataag-tgttttggtgggggttgctgaatatgacttatgcctcga-tgacctttgattttggtatcatatttgattcaaagcttttcttcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATCAACAAGAGGTTGTCAAGAAAGCTCGACCGGCAGTGGAAGAAAAGCATTG
















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|298189378|gb|HO037781.1|HO037781
EST:     CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGG                         ATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
genomic: CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGGgtacttcatt ... atccatacagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
EST: gi|31459666|gb|CD401694.1|CD401694
EST:     CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGG                         ATTTCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
genomic: CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGGgtacttcatt ... atccatacagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
EST: gi|120531952|gb|EH260085.1|EH260085
EST:     CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGG                         ATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
genomic: CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGGgtacttcatt ... atccatacagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
EST: gi|120532014|gb|EH260147.1|EH260147
EST:     CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGG                         ATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
genomic: CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGGgtacttcatt ... atccatacagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
EST: gi|31468283|gb|CD410311.1|CD410311
EST:     CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGG                         ATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
genomic: CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGGgtacttcatt ... atccatacagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
EST: gi|15204876|gb|BI427644.1|BI427644
EST:     CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGG                         ATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
genomic: CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGGgtacttcatt ... atccatacagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
EST: gi|193447205|gb|FK412392.1|FK412392
EST:     CGGCTCGCAACGAGTTCAAGTCCAGCGATTTCGGTCGCATGCGCAAGAGG                         ATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
genomic: CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGGgtacttcatt ... atccatacagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
EST: gi|15284877|gb|BI468768.1|BI468768
EST:     CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGG                         ATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
genomic: CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGGgtacttcatt ... atccatacagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
EST: gi|19053242|gb|BM731909.1|BM731909
EST:     CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGG                         ATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
genomic: CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGGgtacttcatt ... atccatacagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
EST: gi|20814477|gb|BQ298955.1|BQ298955
EST:     CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGG                         ATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
genomic: CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGGgtacttcatt ... atccatacagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
EST: gi|10231518|gb|BE800406.1|BE800406
EST:     CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGG                         ATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
genomic: CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGGgtacttcatt ... atccatacagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
EST: gi|8669411|gb|BE190518.1|BE190518
EST:     CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGG                         ATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGACGAGGGTATC
genomic: CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGGgtacttcatt ... atccatacagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
EST: gi|7283855|gb|AW596457.1|AW596457
EST:     CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGG                         ATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC
genomic: CGGCTCGCAACGAGTTCAAGTCCAGCGAATTCGGTCGCATGCGCAAGAGGgtacttcatt ... atccatacagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcttgtctgaatgttaatttttgggtgaatgatactgcaaatatccatacagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATCAATAAGAGGTTGTCCAGAAAGCTTGATAAAAAATGGAAGAAAAGCATTG
              tgttaat  putative branch site (score: 3)
          tgaatgttaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactaacaaataaggtctttctctagagtctgcataatgccgtgcatttcttgtctgaatgttaatttttgggtgaatgatactgcaaatatccatacagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATCAATAAGAGGTTGTCCAGAAAGCTTGATAAAAAATGGAAGAAAAGCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
-actaaca
- - - - - - - - - - - - - - - tgcataa
- - - - - - - - - - - - - - - - - - - gccgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgca