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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACATGGACAAGAAGCTTCAGAgtaagtctgctttgcattttttttttttttttgcttctcttattctctatttttacatgttcgttcgtgtcttccttttgtttttgtttttgtttttgtt...

Basic information

species Glycine max
transcript GLYMA11G09150.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G09150.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os03g29740.1 (Oryza sativa), 5'ss of exon 2
GTACATGGACAAGAAGCTTCAGAgtaagtctgctttgcattttttttttttttttgcttctcttattctctatttttacatgttcgttcgtgtcttccttttgtttttgtttttgtttttgtt-----
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GTACATGGACAAGAAGCTCCAGAgtaagtaaaata-atattaataatccttcgtggtttagcta---ttgtaattgta-gtactcgggtagattcgcttttggaagatagtttactgatagctagaac

upper sequence: GLYMA11G09150.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G057865_T01 (Zea mays), 5'ss of exon 2
GTACATGGACAAGAAGCTTCAGAgtaagtctgctttgcattttttttttttttttgcttctcttattctctatttttacatgttcgttcgtgtcttccttttgtttttgtttt---tgtttttgtt
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GTACATGGACAAGAAGCTTCAGAgtaagtggtactctcgattccgctatccagtcccaatagtacacctgtggttttgc---ttcaagaaagtttttcttcttcccatgtgcccagtacgtttgtt

upper sequence: GLYMA11G09150.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G083642_T02 (Zea mays), 5'ss of exon 2
GTACATGGACAAGAAGCTTCAGAgtaagtctgctttgcattttttttttttttttgcttctcttattctctatt--tttacatgttcgttcgtgtcttccttttgtttttgtttttgtttttgtt
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GTACATGGACAAGAAGCTTCAGAgtaagtgatattctctcgattctacaatccaagccccaatagttcatttgcagttcagaaaatttttctttagttttaaagggtgaaacatgcatgtgtg--

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|18730335|gb|BM525820.1|BM525820
EST:     AAGTACATGGACAAGAAGCTTCAGA                         TTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
genomic: AAGTACATGGACAAGAAGCTTCAGAgtaagtctgc ... ccccttgcagTTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
EST: gi|31561892|gb|CD487730.1|CD487730
EST:     AAGTACATGGACAAGAAGCTTCAGA                         TTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
genomic: AAGTACATGGACAAGAAGCTTCAGAgtaagtctgc ... ccccttgcagTTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
EST: gi|254346216|gb|GR859829.1|GR859829
EST:     AAGTACATGGACAAGAAGCTTCAGA                         TTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
genomic: AAGTACATGGACAAGAAGCTTCAGAgtaagtctgc ... ccccttgcagTTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
EST: gi|298176503|gb|HO026738.1|HO026738
EST:     AAGTACATGGACAAGAAGCTTCAGA                         TTAAACTGAATGGAAATCGCATGATTGTTGGCACTCCCCGTGGCTTTGACC
genomic: AAGTACATGGACAAGAAGCTTCAGAgtaagtctgc ... ccccttgcagTTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
EST: gi|151398942|gb|EV268813.1|EV268813
EST:     AAGTACATGGACAAGAAGCTTCAGA                         TTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
genomic: AAGTACATGGACAAGAAGCTTCAGAgtaagtctgc ... ccccttgcagTTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
EST: gi|192327127|gb|FK015519.1|FK015519
EST:     AAGTACATGGACAAGAAGCTTCAGA                         TTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
genomic: AAGTACATGGACAAGAAGCTTCAGAgtaagtctgc ... ccccttgcagTTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
EST: gi|31467429|gb|CD409457.1|CD409457
EST:     AAGTACATGGACAAGAAGCTTCAGA                         TTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
genomic: AAGTACATGGACAAGAAGCTTCAGAgtaagtctgc ... ccccttgcagTTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
EST: gi|31306974|gb|CD392177.1|CD392177
EST:     AAGTACATGGACAAGAAGCTTCAGA                         TTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
genomic: AAGTACATGGACAAGAAGCTTCAGAgtaagtctgc ... ccccttgcagTTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
EST: gi|151412914|gb|EV282726.1|EV282726
EST:     AAGTACATGGACAAGAAGCTTCAGA                         TTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
genomic: AAGTACATGGACAAGAAGCTTCAGAgtaagtctgc ... ccccttgcagTTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
EST: gi|19452429|gb|BM953839.1|BM953839
EST:     AAGTACATGGACAAGAAGCTTCAGA                         TTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
genomic: AAGTACATGGACAAGAAGCTTCAGAgtaagtctgc ... ccccttgcagTTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
EST: gi|33388212|gb|CA851419.1|CA851419
EST:     AAGTACATGGACAAGAAGCTTCAGA                         TTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
genomic: AAGTACATGGACAAGAAGCTTCAGAgtaagtctgc ... ccccttgcagTTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
EST: gi|6667111|gb|AW278570.1|AW278570
EST:     AAGTACATGGACAAGAAGCTTCAGA                         TTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
genomic: AAGTACATGGACAAGAAGCTTCAGAgtaagtctgc ... ccccttgcagTTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
EST: gi|193327961|gb|FK295550.1|FK295550
EST:     AAGTACATGGACAAGAAGCTTCAGA                         TTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
genomic: AAGTACATGGACAAGAAGCTTCAGAgtaagtctgc ... ccccttgcagTTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
EST: gi|151410461|gb|EV280276.1|EV280276
EST:     AAGTACATGGACAAGAAGCTTCAGA                         TTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC
genomic: AAGTACATGGACAAGAAGCTTCAGAgtaagtctgc ... ccccttgcagTTAAACTGAATGGAAATCGCATGATTGTTGGCACTCTCCGTGGCTTTGACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACATGGACAAGAAGCTTCAGAgtaagtctgctttgcattttttttttttttttgcttctcttattctctatttttacatgttcgttcgtgtcttccttttgtttttgtttttgtttttgtt

- CATGGA
- - - - - AAGAAG
- - - - - AGAAGC