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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accagttatgacttttgtgatgaataggtttaagtgcaatagtgcagtagttccaagatgtatcgcttattgtcttatgatagtgtgctcaatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATATATTGAAGAATTTCG

Basic information

species Glycine max
transcript GLYMA03G39530.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G39530.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0060g02220.t01 (Vitis vinifera), 3'ss of exon 3
----accagttatgacttttgtgatgaataggtttaagtgcaatagtgcagtagttccaagatgtatcgcttattgtcttatgatagtgtgctcaat-gtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATATATTGAAGAATTTCG
     | ||| |||   |    | |    |   ||       ||| |    |  ||  || | | ||| ||| |||| ||||  |     ||| ||| |  |||||||||||||||||||||||| ||  | || ||||||||  ||||| ||||| |||| ||||||||
tttttcaagtcatgttctccaagttttccatcctttttgtttataat----tttttttaataggcatccctttttgt-ttattgtgacacgctaaattggttcagGTTTGTACAGAGGTGAGACCCGCTGCTGATGAAGAACTGCCATCTGCATATGTTGAGGAATTTCG
















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|192308192|gb|FK001290.1|FK001290
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|213613616|gb|DB963304.1|DB963304
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|151403727|gb|EV273537.1|EV273537
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACCGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|7692294|gb|AW760404.1|AW760404
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|192295129|gb|FG986848.1|FG986848
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|192303311|gb|FG995619.1|FG995619
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|192322679|gb|FK015016.1|FK015016
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAG-CAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTTCATCTCCATA
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTT-CATCTCCATA
EST: gi|298184947|gb|HO030160.1|HO030160
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|9903152|gb|BE612120.1|BE612120
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|21677242|gb|BQ629593.1|BQ629593
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|18040959|gb|BM309253.1|BM309253
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|24135512|gb|BU926022.1|BU926022
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|9987385|gb|BE661493.1|BE661493
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|151397822|gb|EV267695.1|EV267695
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|22541742|gb|BU091585.1|BU091585
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|192313101|gb|FK004691.1|FK004691
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|192299932|gb|FG992145.1|FG992145
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|298194345|gb|HO040993.1|HO040993
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|298180513|gb|HO022066.1|HO022066
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|151399910|gb|EV269781.1|EV269781
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|192313102|gb|FK004692.1|FK004692
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
EST: gi|9203900|gb|BE330124.1|BE330124
EST:     TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTTGCAATTGTTGACCATGCTAAACAAgtaactctta ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtagttccaagatgtatcgcttattgtcttatgatagtgtgctcaatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATATATTGAAGAATTTCG
                             ttatgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accagttatgacttttgtgatgaataggtttaagtgcaatagtgcagtagttccaagatgtatcgcttattgtcttatgatagtgtgctcaatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTTCATCTCCATATATTGAAGAATTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - ttttgtg
- - - - - - - - - - - - - - - - agtgcaa
- - - - - - - - - - - - - - - - - - - - - tgcagta
- - - - - - - - - - - - - - - - - - - - - - - - - ttccaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtgct