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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAAGACTGGCTATCTTTAGTTGCTGTTCATAGTGATGCATGGTTACTTGCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAGgtatttcgtacactgaacatacttcttatttgaagttaacttaagttggtggaaaatcacaaagcagttgaatcctgcttgtctgatttatccatctcattggtttagttcttttcttcacgtgtctcattcactcatgatttgaatatgtaatgcag

Basic information

species Glycine max
transcript GLYMA07G04040.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G04040.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S97_167V6.2 (Physcomitrella patens), 5'ss of exon 3
------AAAAAGACTGGCTATCTTTAGTTGCTGTTCATAGTGATGCATGGTTACTTGCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAGgtatttcgtac--actgaacatacttcttatttgaagttaacttaagttggtggaaaatcacaaagcagttgaatcctgcttgtctgatttatccatctcattggtttagttcttttcttcacgtgtctcattcactcatgatttgaatatgtaatgcag
        ||||||||||| |||||||||||||| || |||||||| ||| |||||||| |||| |||||||  |||||      | ||||||||||    || |||| |    |    |||  | ||| | ||  ||     ||   ||   |||  |    ||  || | |  || |    |  ||  |   |  |   |   |||                                                          
TGCAGCGTAAAGACTGGCTTTCTTTAGTTGCTGTGCACAGTGATGCCTGGCTACTTGCTGTTGCTTTCTATTACGGAGC------TCGGTTTGATAAGAACGAGAGgtctgctatctgaacttgatataatgctgcttcttttttgtattt--ttgacgagttatgccacacccattcatgtattatttccaattgaaattactacat----------------------------------------------------------
















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|193435677|gb|FK402431.1|FK402431
EST:     GCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAG                         GAAACGGCTTTT
genomic: GCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAGgtatttcgta ... tgtaatgcagGAAACGGCTTTT
EST: gi|21994611|gb|BQ786139.1|BQ786139
EST:     GCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAG                         GAAACGGCTTTTCAACATGATCAATGAACTGCCAACAATATTTGAAGTTGT
genomic: GCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAGgtatttcgta ... tgtaatgcagGAAACGGCTTTTCAACATGATCAATGAACTGCCAACAATATTTGAAGTTGT
EST: gi|192326234|gb|FK015826.1|FK015826
EST:     GCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAG                         GAAACGGCTTTTCAACATGATCAATGAACTGCCAACAATATTTGAAGTTGT
genomic: GCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAGgtatttcgta ... tgtaatgcagGAAACGGCTTTTCAACATGATCAATGAACTGCCAACAATATTTGAAGTTGT
EST: gi|192297449|gb|FG989513.1|FG989513
EST:     GCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAG                         GAAACGGCTTTTCAACATGATCAATGAACTGCCAACAATATTTGAAGTTGT
genomic: GCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAGgtatttcgta ... tgtaatgcagGAAACGGCTTTTCAACATGATCAATGAACTGCCAACAATATTTGAAGTTGT
EST: gi|192333136|gb|FK026465.1|FK026465
EST:     GCTAGTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAG                         GAAACGGCTTTTCAACATGATCAATGAACTGCCAATAATATTTGAAGTTGT
genomic: GCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAGgtatttcgta ... tgtaatgcagGAAACGGCTTTTCAACATGATCAATGAACTGCCAACAATATTTGAAGTTGT
EST: gi|151405473|gb|EV275287.1|EV275287
EST:     GCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAG                         GAAACGGCTTTTCAACATGATCAATGAACTGCCAACAATATTTGAAGTTGT
genomic: GCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAGgtatttcgta ... tgtaatgcagGAAACGGCTTTTCAACATGATCAATGAACTGCCAACAATATTTGAAGTTGT
EST: gi|58014682|gb|CX701424.1|CX701424
EST:     GCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAG                         GAAACGGCTTTTCAACATGATCAATGAACTGCCAACAATATTTGAAGTTGT
genomic: GCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAGgtatttcgta ... tgtaatgcagGAAACGGCTTTTCAACATGATCAATGAACTGCCAACAATATTTGAAGTTGT
EST: gi|18039623|gb|BM307917.1|BM307917
EST:     GCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAG                         GAAACGGCTTTTCAACATGATCAATGAACTGCCAACAATATTTGAAGTTGT
genomic: GCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAGgtatttcgta ... tgtaatgcagGAAACGGCTTTTCAACATGATCAATGAACTGCCAACAATATTTGAAGTTGT
EST: gi|120532679|gb|EH260812.1|EH260812
EST:     GCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAG                         GAAACGGCTTTTCAACATGATCAATGAACTGCCAACAATATTTGAAGTTGT
genomic: GCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAGgtatttcgta ... tgtaatgcagGAAACGGCTTTTCAACATGATCAATGAACTGCCAACAATATTTGAAGTTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAAGACTGGCTATCTTTAGTTGCTGTTCATAGTGATGCATGGTTACTTGCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAGgtatttcgtacactgaacatacttcttatttgaagttaacttaagttggtggaaaatcacaaagcagttgaatcctgcttgtctgatttatccatctcattggtttagttcttttcttcacgtgtctcattcactcatgatttgaatatgtaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA