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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcacctttttttgtgtctttttttttccaccctcaaaaccttatcacaagccttttattagttatgatcattgaccccctccattgagaaatttaataatgacattatggtgttattaccttattgtgaaattgcttattttgtgttagtaactgatattaacttgggacattttcagGGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCCAGCTTAAGCTCGTGGAAGGTGACTCTGCTGGAACAGTCACTGCTTTCTA

Basic information

species Glycine max
transcript GLYMA06G45860.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G45860.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0134g00160.t01 (Vitis vinifera), 3'ss of exon 1
gtaaatcacctttttttgtgtctttttttttccaccctcaaaaccttatcacaagccttttattagttatgatcattg-accccctccattgagaaatttaataatgacattatggtgttattaccttattgtgaaat-tgcttattttgtgttagta-actgatattaacttgggacattttcagGGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCCAGCTTAAGCTCGTGGAAGGTGACTCTGCTGGAACAGTCACTGCTTTCTA
|||    |||||        ||||   ||||          || | | |        |||| | |  ||||| || ||   |  ||   ||      |||  | |||| || | | |||| |||| || ||     || ||  |   |   ||| ||  | | ||  | |     ||   ||||||| ||||| ||| | ||||| |||||||| |||||||| || || |  || ||| | ||||||||||| || ||||||||||| || ||||||||||||||
gtaccataccttcaccaaaatcttccctttt----------aatcctttttttttttttttttcatatatgaccaatgtgtcttctgggttccatttttttctcatga-atca-gctgtttttacattgtttcagtatctgtgtgactgaagtttgtgtattaatggtgatc---gatgatttcagGAGCTGGGTTTTCCTCCAAAAGCAAGTACATGTTTGGAAAGGTCAGTATTCAGATCAAGCTCGTGGAGGGCGACTCTGCTGGGACTGTCACTGCTTTCTA
















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|151409451|gb|EV279259.1|EV279259
EST:     CTTTATTCATGAAAGGGATCTTCTCAAACTCAAACTTGACAAATTTTCCG                         GGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCC
genomic: CTTTATTCATGAAAGGGATCTTCTCAAACTCAAACTTGACAAATTTTCCGgtaaatcacc ... acattttcagGGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCC
EST: gi|18039092|gb|BM307386.1|BM307386
EST:     CTCAAACTCAAACTTGACAAATTTTCCG                         GGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCC
genomic: CTCAAACTCAAACTTGACAAATTTTCCGgtaaatcacc ... acattttcagGGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCC
EST: gi|15201267|gb|BI424781.1|BI424781
EST:     CTTTATTCATGAAAGGGATCTTCTCAAACTCAAACTTGACAAATTTTCCG                         GGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCC
genomic: CTTTATTCATGAAAGGGATCTTCTCAAACTCAAACTTGACAAATTTTCCGgtaaatcacc ... acattttcagGGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCC
EST: gi|17023921|gb|BM094955.1|BM094955
EST:     TCAAACTTGACAAATTTTCCG                         GGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCC
genomic: TCAAACTTGACAAATTTTCCGgtaaatcacc ... acattttcagGGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCC
EST: gi|298168120|gb|HO013383.1|HO013383
EST:     CTTTATTCATGAAAGGGATCTTCTCAAACTCAAACTTGACAAATTTTCCG                         GGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCC
genomic: CTTTATTCATGAAAGGGATCTTCTCAAACTCAAACTTGACAAATTTTCCGgtaaatcacc ... acattttcagGGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCC
EST: gi|192295505|gb|FG988079.1|FG988079
EST:     CTTTATTCATGAAAGGGATCTTCTCAAACTCAAACTTGACAAATTTTCCG                         GGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCC
genomic: CTTTATTCATGAAAGGGATCTTCTCAAACTCAAACTTGACAAATTTTCCGgtaaatcacc ... acattttcagGGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCC
EST: gi|151395082|gb|EV264953.1|EV264953
EST:     CTTTATTCATGAAAGGGATCTTCTCAAACTCAAACTTGACAAATTTTCCG                         GGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCC
genomic: CTTTATTCATGAAAGGGATCTTCTCAAACTCAAACTTGACAAATTTTCCGgtaaatcacc ... acattttcagGGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCC
EST: gi|26046084|gb|CA783420.1|CA783420
EST:     CTTTATTCATGAAAGGGATCTTCTCAAACTCAAACTTGACAAATTTTCCG                         GGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCC
genomic: CTTTATTCATGAAAGGGATCTTCTCAAACTCAAACTTGACAAATTTTCCGgtaaatcacc ... acattttcagGGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgaaattgcttattttgtgttagtaactgatattaacttgggacattttcagGGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCCAGCTTAAGCTCGTGGAAGGTGACTCTGCTGGAACAGTCACTGCTTTCTA
                                 tattaac  putative branch site (score: 1)
                                              cattttc  putative PPT
     aaattgcttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatcacctttttttgtgtctttttttttccaccctcaaaaccttatcacaagccttttattagttatgatcattgaccccctccattgagaaatttaataatgacattatggtgttattaccttattgtgaaattgcttattttgtgttagtaactgatattaacttgggacattttcagGGGCTGGTTTTACTTCCAAGAGCAAGTATATGTTTGGGAAAGTTACCATCCAGCTTAAGCTCGTGGAAGGTGACTCTGCTGGAACAGTCACTGCTTTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA