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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTGCTAGTGGTGAACTTGGTCACGCCATGGAAGCCGTTAAGTGGGGTACGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAGgtaccttattttcttattttaattttaatacaatgttttattcctagttgaatttagatgctattacaccaagtagtaatttatttatgaataaagaatgtcgttggtgttgtgacaattag

Basic information

species Glycine max
transcript GLYMA08G02610.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G02610.1 (Glycine max), 5'ss of exon 2
lower sequence: AT4G11050.1 (Arabidopsis thaliana), 5'ss of exon 2
GGCTGCTAGTGGTGAACTTGGTCACGCCATGGAAGCCGTTAAGTGGGGTACGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAGgtaccttattttcttattttaattttaatacaatgttttattcctagttgaatttagatgctattacaccaagtagtaatttatttatgaataaagaatgtcgttggtgttgtgacaattag
|| | | || |||||||| || ||||| || |||||||||||||| || || || ||||| ||||| |||||| || | || |||||||||||||||||| | || | | | |||| | || | | || | || || | | | |||| | || | | ||||| ||||| || || | || | |||||
GGAATCCAACGGCGAACTTGGCCATGCCATTGACGCCGTTAAGTGGGGAACTGATTATTTCATTAAAGCCCACCCTGAACCTAACGTTCTCTATGGAGAGgtaaca-ataataacactctaatcactaatcactttctt--tattaattagactaa----ctat-atacataatttcaatttggttatgg--taattattttgtaactcatgtgaag-----

upper sequence: GLYMA08G02610.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv02s0025g01380.t01 (Vitis vinifera), 5'ss of exon 4
GGCTGCTAGTGGTGAACTTGGTCACGCCATGGAAGCCGTTAAGTGGGGTACGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAGgtaccttattttcttattttaattttaatacaatgttttattccta-gttgaatttagatgctattacaccaagtagtaatttatttatgaataaagaatgtcgttggtgttgtgacaattag
|||||| | ||| || || ||||| ||||||||||| || |||||||| || |||||| |||||||||| ||||| || || |||| ||||| |||||||| || | | | | ||| | | | |||||| | | | || || | ||||| || | || | | || ||| | || |
GGCTGCAAATGGAGAGCTGGGTCATGCCATGGAAGCTGTGAAGTGGGGCACTGACTACCTCATCAAAGCTCACCCCCACCCCGATGTCCTCTACGGAGAGgt---ttgtgcgcct--caacacttttccatatttctttattattctgctcaactt-gttgctagcttgacaccgctcacttcctgtgtgtgggcagact-tcatac----------------
















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|213595559|gb|DB972113.1|DB972113
EST:     CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAG                         GTGGGAGATGGGAACACTGACCATTACTGTTGGCAAAGACCAGAGGACATG
genomic: CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAGgtaccttatt ... tgacaattagGTGGGAGATGGGAACACTGACCATTACTGTTGGCAAAGACCAGAGGACATG
EST: gi|209709618|gb|BW661945.1|BW661945
EST:     CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAG                         GTGGGAGATGGGAACACTGACCATTACTGTTGGCAAAGACCAGAGGACATG
genomic: CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAGgtaccttatt ... tgacaattagGTGGGAGATGGGAACACTGACCATTACTGTTGGCAAAGACCAGAGGACATG
EST: gi|213591044|gb|DB973785.1|DB973785
EST:     CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAG                         GTGGGAGAATGG-AACACTGACCATTACTGTTGGCAA
genomic: CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAGgtaccttatt ... tgacaattagGTGGGAGA-TGGGAACACTGACCATTACTGTTGGCAA
EST: gi|209712791|gb|BW681647.1|BW681647
EST:     CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAG                         GTGGGAGATGGGAACACTGACCATTACTGTTGGCAAAGACCCAGAG-ACAT
genomic: CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAGgtaccttatt ... tgacaattagGTGGGAGATGGGAACACTGACCATTACTGTTGGCAAAGACC-AGAGGACAT
EST: gi|14205538|gb|BG839216.1|BG839216
EST:     CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAG                         GTGGGAGATGGGAACACTGACCATTACTGTTGGCAAAGACCAGAGGACATG
genomic: CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAGgtaccttatt ... tgacaattagGTGGGAGATGGGAACACTGACCATTACTGTTGGCAAAGACCAGAGGACATG
EST: gi|213617200|gb|DB963763.1|DB963763
EST:     CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAG                         GTGGGAGATGGGAACACTGACCATTACTGTTGGCAAAGACCAGAGGACATG
genomic: CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAGgtaccttatt ... tgacaattagGTGGGAGATGGGAACACTGACCATTACTGTTGGCAAAGACCAGAGGACATG
EST: gi|209729310|gb|BW660356.1|BW660356
EST:     CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAG                         GTGGGAGATGGGAACACTGACCATTACTGTTGGCAAAGACCAGAGGACATG
genomic: CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAGgtaccttatt ... tgacaattagGTGGGAGATGGGAACACTGACCATTACTGTTGGCAAAGACCAGAGGACATG
EST: gi|209718838|gb|BW669025.1|BW669025
EST:     CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAG                         GTGGGAGATGGGAACACTGACCATTACTGTTGGC
genomic: CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAGgtaccttatt ... tgacaattagGTGGGAGATGGGAACACTGACCATTACTGTTGGC
EST: gi|213593138|gb|DB966075.1|DB966075
EST:     CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAG                         GTGGGAGATGGGAACACTGACCATTACTGTTGGCAAAGACCAGAGGACATG
genomic: CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAGgtaccttatt ... tgacaattagGTGGGAGATGGGAACACTGACCATTACTGTTGGCAAAGACCAGAGGACATG
EST: gi|20449462|gb|BQ253586.1|BQ253586
EST:     CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAG                         GTGGGAGATGGGAAC
genomic: CGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAGgtaccttatt ... tgacaattagGTGGGAGATGGGAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTGCTAGTGGTGAACTTGGTCACGCCATGGAAGCCGTTAAGTGGGGTACGGACTACTTCATCAAAGCGCACCCTCAAGCCAATGTTCTCTATGGAGAGgtaccttattttcttattttaattttaatacaatgttttattcctagttgaatttagatgctattacaccaagtagtaatttatttatgaataaagaatgtcgttggtgttgtgacaattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA