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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaattggaattacatgcattacttagcattatccatcagttctgttgtcagacaaattgatttgcatgaaataacaatggatattggaattgttttgcagAATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG

Basic information

species Glycine max
transcript GLYMA19G24250.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G130230_T02 (Zea mays), 3'ss of exon 14
--------------------------------------------------------------------------gaattgga---attacatgcattac---ttagcattatc-catcagttctgttgtcagacaaattgatttgcat----gaaataacaatgga-tattggaattgttttgcagAATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
                                                                           || |  |   ||  ||||  ||     ||   |  ||  ||    |||   | |   | |  |||  || | |    | |   ||| ||   |||    ||  || |||||||| | ||||||||||||||| |||||||||||||||||| |  ||
gtaagtgtcacccttttcgaccattctaacatatcgttcattacaaagaaactctctcaccctgaaatcgtggataactctacatatatcatgtcttgtgtgttgatagcattgcaaggcttcctctatgcaaaattttgcctttctttactgcacctacactgatctatacccatgtttctgcagAATAAGAGGTGATCAGCAGCACTTTGTTCGCAGAGATGAGCTACAG

upper sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 14
--gaattggaattacatgcattacttagcattatccatcagttctgttgtcagacaaattgatttgcatgaaataacaatggatattggaatt--gttttgcagAATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
     ||| | ||| |      |   |  |  |      ||        |   |  |   |    |    ||  ||  || || || ||  ||  ||||  ||| ||   ||||||||||||||||||||||||||||||||||||||||
ctatcttgcacttaaaaaggaaaaaaaataaaag----tagaataaacctagaaggatggggcacgtggaaatcaaatattgagatcgggttttggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
















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|193324115|gb|FK288783.1|FK288783
EST:     GGCTTATGAACGCCTAATTCTTGACAC                         AATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: GGCTTATGAACGCCTAATTCTTGACACgtatgttccc ... tgttttgcagAATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|7232264|gb|AW567621.1|AW567621
EST:     TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACAC                         AATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACACgtatgttccc ... tgttttgcagAATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|213602022|gb|DB976241.1|DB976241
EST:     ATGAACGCCTAATTCTTGACAC                         AATTAAAGGTGATCAGCAGCATTTTTATT-GCAGAGATGAGTTGAAG
genomic: ATGAACGCCTAATTCTTGACACgtatgttccc ... tgttttgcagAATTAAAGGTGATCAGCAGCA-TTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|192300568|gb|FG991520.1|FG991520
EST:     TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACAC                         AATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACACgtatgttccc ... tgttttgcagAATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|37997266|gb|CF808855.1|CF808855
EST:     TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACAC                         AATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACACgtatgttccc ... tgttttgcagAATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|254346861|gb|GR856583.1|GR856583
EST:     TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACAC                         AATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACACgtatgttccc ... tgttttgcagAATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|214005475|gb|DB985541.1|DB985541
EST:     TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACAC                         AATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACACgtatgttccc ... tgttttgcagAATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|254334915|gb|GR844700.1|GR844700
EST:     TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACAC                         AATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACACgtatgttccc ... tgttttgcagAATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|193323071|gb|FK287963.1|FK287963
EST:     GGCTTATGAACGCCTAATTCTTGACAC                         AATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: GGCTTATGAACGCCTAATTCTTGACACgtatgttccc ... tgttttgcagAATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|151404199|gb|EV274009.1|EV274009
EST:     TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACAC                         AATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACACgtatgttccc ... tgttttgcagAATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|16280271|gb|BI943875.1|BI943875
EST:     GAACGCCTAATTCTTGACAC                         AATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: GAACGCCTAATTCTTGACACgtatgttccc ... tgttttgcagAATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|254338292|gb|GR849817.1|GR849817
EST:     TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACAC                         AATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACACgtatgttccc ... tgttttgcagAATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|10256519|gb|BE824285.1|BE824285
EST:     TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACAC                         AATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACACgtatgttccc ... tgttttgcagAATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|37994077|gb|CF805823.1|CF805823
EST:     TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACAC                         AATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGAGTAACCATTCCTGAGGCTTATGAACGCCTAATTCTTGACACgtatgttccc ... tgttttgcagAATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcagacaaattgatttgcatgaaataacaatggatattggaattgttttgcagAATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
                       aaataac  putative branch site (score: 2)
                                            ttgtttt  putative PPT
        aaattgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaattggaattacatgcattacttagcattatccatcagttctgttgtcagacaaattgatttgcatgaaataacaatggatattggaattgttttgcagAATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG