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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACACTTCTCTTCCGTTCACCCTGGTTCCGTCACCGTCAACCTTGGCTCTTCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAGgtccatccttttttcttcagtatcttattttctcatgatttttgggtcgaaaaatataaattcccttgtttcatgtctttcctttatttgggttcttttg...

Basic information

species Glycine max
transcript GLYMA20G28930.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G28930.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv05s0020g04160.t01 (Vitis vinifera), 5'ss of exon 1
AACACTTCTCTTCCGTTCACCCTGGTTCCGTCACCGTCAACCTTGGCTCTTCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAGgtccatccttttttc--ttcagtatcttattttctcatgatttttgggtcgaaaaatataaattcccttgtttcatgtctttcctttatttgggttcttttg--
||   ||  ||||  |||| |||  | | ||||||||||||||||||||||||||   | |  | || ||| || | |  ||||| || ||||| ||||||| ||   ||| | |  ||   | | | ||||| || |||| |    | |       | |  |||   |   |    | | | ||||| | |  || || |   
AATTTTTTGCTTCTCTTCATCCTTCTGCTGTCACCGTCAACCTTGGCTCTTCCGGCGCCATCTCTTACTCCGTTGATAAGCAGAATCCTCTTCTTCCAAGgtacaatgtttatacatttttctttgtgattttttcttgatct----ggccttgcgcacagtttctggttggttccatttgttctttactggatttgttgttta
















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|209702369|gb|BW656344.1|BW656344
EST:     TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAG                         GCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
genomic: TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAGgtccatcctt ... atgttgtcagGCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
EST: gi|192299300|gb|FG988700.1|FG988700
EST:     TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTTCCAAG                         GCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
genomic: TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAGgtccatcctt ... atgttgtcagGCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
EST: gi|151404166|gb|EV273976.1|EV273976
EST:     TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAG                         GCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
genomic: TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAGgtccatcctt ... atgttgtcagGCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
EST: gi|21888440|gb|BQ741653.1|BQ741653
EST:     TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAG                         GCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
genomic: TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAGgtccatcctt ... atgttgtcagGCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
EST: gi|213608423|gb|DB963115.1|DB963115
EST:     TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAG                         GCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
genomic: TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAGgtccatcctt ... atgttgtcagGCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
EST: gi|19934623|gb|BQ079653.1|BQ079653
EST:     TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAG                         GCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
genomic: TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAGgtccatcctt ... atgttgtcagGCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
EST: gi|10845849|gb|BF068885.1|BF068885
EST:     TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAG                         GCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
genomic: TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAGgtccatcctt ... atgttgtcagGCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
EST: gi|151401746|gb|EV271559.1|EV271559
EST:     TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAG                         GCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
genomic: TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAGgtccatcctt ... atgttgtcagGCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
EST: gi|209700713|gb|BW670475.1|BW670475
EST:     TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAG                         GCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
genomic: TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAGgtccatcctt ... atgttgtcagGCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
EST: gi|15813151|gb|BI785426.1|BI785426
EST:     TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAG                         GCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
genomic: TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAGgtccatcctt ... atgttgtcagGCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
EST: gi|21595604|gb|BQ610543.1|BQ610543
EST:     TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAG                         GCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
genomic: TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAGgtccatcctt ... atgttgtcagGCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
EST: gi|192307091|gb|FK000041.1|FK000041
EST:     TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAG                         GCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA
genomic: TCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAGgtccatcctt ... atgttgtcagGCTGTTTGCAGTTGTGGACGACATTTTCTGTTTGTTTCAAGGTCACCTTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACACTTCTCTTCCGTTCACCCTGGTTCCGTCACCGTCAACCTTGGCTCTTCCGGTCTCTTGGCCTATTCCCTTCACAGACAGAACCCCCTTCTCCCAAGgtccatccttttttcttcagtatcttattttctcatgatttttgggtcgaaaaatataaattcccttgtttcatgtctttcctttatttgggttcttttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaata