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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgctactttaacctaggaaatgttaattgtaattcaattgatgaatttgctaccagttcctgttctttatgtcaacaaatttgtgtggttaataattttttagtgctgacttcatttatttaacagGCTGAGGCACTTGATCTGGAAAAAACAGTGCTCGAGACAGTAGAGGAAGCTGCAGAGGACTGGAGGATTGATGATATTAAAGGGCTTCTTGGGCGTTGTA

Basic information

species Glycine max
transcript GLYMA04G39670.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39670.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g39020.1 (Oryza sativa), 3'ss of exon 4
gtgtgctactttaacctaggaaatgttaattgtaattcaattgatgaatttgctaccagttcctgttctttatgtcaacaaatttgtgtggttaataattttttagtgctgacttcatttatttaacagGCTGAGGCACTTGATCTGGAAAAAACAGTGCTCGAGACAGTAGAGGAAGCTGCAGAGGACTGGAGGATTGATGATATTAAAGGGCTTCTTGGGCGTTGTA
            | ||||   |   ||||||| |   ||  | || ||  |   |  | |||       |  |   || | |||| | |  | | ||  ||  |     |||  |       ||| |||||||| ||||||||| |||| ||||| ||||| || || ||||  ||||| |||||||| ||||  ||||||||||| ||||| || ||||| ||||| |
------------agcctattga---ttaattgcagcgca--tcatcaacctttcattatttcag-----tagtaaaaaaatatttttttcctgactagattcatgtacatgatct-------ttaccagGCTGAAGCACTTGATTTGGAGAAAACTGTGCTGGATACTGTAGCAGAAGCAGCAGAGGATTGGAAAATTGATGATATCAAAGGTCTCCTTGGTCGTTGCA

upper sequence: GLYMA04G39670.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G64840.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgtgctactttaacctaggaaatgttaattgtaattcaattgatgaatttgctaccagttcctgttctttatgtcaacaaatttgtgtggttaataattttttagtgctgacttcatttatttaacagGCTGAGGCACTTGATCTGGAAAAAACAGTGCTCGAGACAGTAGAGGAAGCTGCAGAGGACTGGAGGATTGATGATATTAAAGGGCTTCTTGGGCGTTGTA
  || |   ||| || ||   |||   ||||  |    |  | |  |||| |  ||  |||  || ||  | | |  ||| | ||   |||||   ||   ||| |        | |||  ||    |||||||||  |||||| |||| ||||||||||| || || ||    ||||||||||| |||||||| | ||||||||| ||||| |||||||| || || |
--gt-cagttttcacttactcaat--caattcaag---agctaaacaattggagacaggtt--tgctcactttattgacataatt---tggttt-caaccctttgg--------ttattctttcgctagGCTGAGGTCCTTGATTTGGATAAAACAGTGCTTGAAACTGTTTGTGAAGCTGCAGAAGACTGGAGAAGTGATGATATAAAAGGTCTTCTTGGACGCTGCA

upper sequence: GLYMA04G39670.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0031g01640.t01 (Vitis vinifera), 3'ss of exon 4
gtgtgctactttaacctaggaaatgtt-----aattgtaattcaattgatgaatttgctaccagttcctgttctttatgtcaacaa-------atttgtgtggttaataattttttagtg---ctgacttcatttatttaacagGCTGAGGCACTTGATCTGGAAAAAACAGTGCTCGAGACAGTAGAGGAAGCTGCAGAGGACTGGAGGATTGATGATATTAAAGGGCTTCTTGGGCGTTGTA
|||||  |   | |     |   || |      |||| |  | |  | |||    | |||  | ||| || | ||  ||  |  |         ||  | ||  |    |||| | | ||    |||| | | ||| ||  |||||||||||||||||| |||| ||||||||| |  | || ||||| || | ||||||| | ||||  ||||| ||||| || || || |||||||||||||
gtgtgtcatagttattactggtgtgcttgttggattggatcttatatcatggcaattctagtaattcatgct-ttggtgcaagtaccacttttgttcatatgtattgccatttctgaatgaaattgacct-acttaattttcagGCTGAGGCACTTGATTTGGATAAAACAGTGTTGCAAACTGTAGAAGACGTTGCAGAGAATTGGAAAATTGACGATATAAAGGGACTACTTGGGCGTTGTA

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|192312580|gb|FK003274.1|FK003274
EST:     TTTTGCTTGGGGAGCATAATGTATTACCTAACTATTTTGAGCAGAATCAG                         GCTGAGGCACTTGATCTGGAAAAAACAGTGCTCGAGACAGTAGAGGAAGCT
genomic: TTTTGCTTGGGGAGCATAATGTATTACCTAACTATTTTGAGCAGAATCAGgtgtgctact ... tatttaacagGCTGAGGCACTTGATCTGGAAAAAACAGTGCTCGAGACAGTAGAGGAAGCT
EST: gi|254327296|gb|GR836905.1|GR836905
EST:     TTTTGCTTGGGGAGCATAATGTATTACCTAACTATTTTGAGCAGAATCAG                         -CTGAGGCACTTGATCTGGAAAAAACAGTGCTCGAGACAGTAGAGGA-GCT
genomic: TTTTGCTTGGGGAGCATAATGTATTACCTAACTATTTTGAGCAGAATCAGgtgtgctact ... tatttaacagGCTGAGGCACTTGATCTGGAAAAAACAGTGCTCGAGACAGTAGAGGAAGCT
EST: gi|151403285|gb|EV273095.1|EV273095
EST:     TTTTGCTTGGGGAGCATAATGTATTACCTAACTATTTTGAGCAGAATCAG                         GCTGAGGCACTTGATCTGGAAAAAACAGTGCTCGAGACAGTAGAGGAAGCT
genomic: TTTTGCTTGGGGAGCATAATGTATTACCTAACTATTTTGAGCAGAATCAGgtgtgctact ... tatttaacagGCTGAGGCACTTGATCTGGAAAAAACAGTGCTCGAGACAGTAGAGGAAGCT
EST: gi|16342504|gb|BI968099.1|BI968099
EST:     GCTTGGGGAGCATAATGTATTACCTAACTA-TTTGAGCAGAATCAG                         GCTGAGGCACTTGATCTGGAAAAAACAGTGCTCGAGACAGTAGAGGAAGCT
genomic: GCTTGGGGAGCATAATGTATTACCTAACTATTTTGAGCAGAATCAGgtgtgctact ... tatttaacagGCTGAGGCACTTGATCTGGAAAAAACAGTGCTCGAGACAGTAGAGGAAGCT
EST: gi|254327297|gb|GR836906.1|GR836906
EST:     ACTA-TTTGAGCAGAATCAG                         GCTGAGGCACTTGATCTGG-AAAAACAGTGCTCGAGACAGTAGAGGAAGCT
genomic: ACTATTTTGAGCAGAATCAGgtgtgctact ... tatttaacagGCTGAGGCACTTGATCTGGAAAAAACAGTGCTCGAGACAGTAGAGGAAGCT
EST: gi|151402499|gb|EV272312.1|EV272312
EST:     TTTTGCTTGGGGAGCATAATGTATTACCTAACTATTTTGAGCAGAATCAG                         GCTGAGGCACTTGATCTGGAAAAAACAGTGCTCGAGACAGTAGAGGAAGCT
genomic: TTTTGCTTGGGGAGCATAATGTATTACCTAACTATTTTGAGCAGAATCAGgtgtgctact ... tatttaacagGCTGAGGCACTTGATCTGGAAAAAACAGTGCTCGAGACAGTAGAGGAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaacaaatttgtgtggttaataattttttagtgctgacttcatttatttaacagGCTGAGGCACTTGATCTGGAAAAAACAGTGCTCGAGACAGTAGAGGAAGCTGCAGAGGACTGGAGGATTGATGATATTAAAGGGCTTCTTGGGCGTTGTA
                                tgctgac  putative branch site (score: 2)
                                      cttcattt  CT-rich tract
                 ttaataattttttagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgctactttaacctaggaaatgttaattgtaattcaattgatgaatttgctaccagttcctgttctttatgtcaacaaatttgtgtggttaataattttttagtgctgacttcatttatttaacagGCTGAGGCACTTGATCTGGAAAAAACAGTGCTCGAGACAGTAGAGGAAGCTGCAGAGGACTGGAGGATTGATGATATTAAAGGGCTTCTTGGGCGTTGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT