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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgtacttcatttgtaatatagaggctttagtccctggcagtatttatatgctgattccaaattgacatgctgtgtgctctatgaagaaatgaaggaccaat...

Basic information

species Glycine max
transcript GLYMA20G18980.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G18980.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM5G848768_T03 (Zea mays), 5'ss of exon 10
GTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgt-acttcatttgtaatatagaggctttagtccctggcagtatttatatgctgat-tccaaattgacatgctgtgtgctctatgaagaaatgaaggaccaat----------------
| ||||| ||||| |||||||||||||||| ||||||||| || ||||||||| ||| || || | || ||||| |||||||||||||| ||||||| | || || ||| | ||||||| | || ||| | | ||| | || | |||| || | | | || | | |
GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaatctgccctatcttga--ttagtccacgtt-gtgtttgt-cgtcgatgttcagac--acattttgctcaattccttgttacatttaacgctgcttggtatcgtctattag

upper sequence: GLYMA20G18980.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G152442_T02 (Zea mays), 5'ss of exon 3
GTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgt-acttcatttgtaatatagaggctttagtccctggcagtatttatatgctgattccaaattgacatgctgtgtgctctatgaagaaatgaaggaccaat----------------
| ||||| ||||| |||||||||||||||| ||||||||| || ||||||||| ||| || | | || ||||| |||||||||||||| ||||||| | || || ||| | ||||||| | || ||| | | || || | |||| || | | | || | | |
GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTTAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaatctgccctatcatga--ttagtccacgtt-gtgtttgtcgtcgattttcagac--acattttgctcaattcctttttacatttaacgctgcttggcatcgtatattag

upper sequence: GLYMA20G18980.1 (Glycine max), 5'ss of exon 10
lower sequence: AT1G04710.1 (Arabidopsis thaliana), 5'ss of exon 10
GTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgtacttcatttgtaatatagaggctttagtccctggcagtatttatatgctg-attccaaattgacatgctgtgtgctctatgaagaaatgaaggaccaat
| |||||||| || | ||||| ||||||| ||||||||| || |||| |||| ||| || |||| || || || |||||||||||||||||||||| ||| | || || || | ||| | |||| ||| | || || || | | | ||
GGAATTCTAGCCAATTAAGTGACGGTGCTGGAGCTGTTCTCCTTATGAGGAGAAATGTCGCAATGCAGAAAGGCCTTCCCATTCTTGGTGTATTCAGgtg---ggcttg------atagttgatactctatattgacctttctttgcttcatttagtaacagcactct-tggacacattacag---------------

upper sequence: GLYMA20G18980.1 (Glycine max), 5'ss of exon 10
lower sequence: AT2G33150.1 (Arabidopsis thaliana), 5'ss of exon 10
GTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgtacttcatttgtaatatagaggctttagtccctggcagtatttatat-gctgattccaaattgacatgctgtgtgc-tctatgaagaaatga-aggaccaat-----------------------------------------------------------------
| ||||| || || || ||||||||||| | ||| ||||| || ||||| ||||||||||| ||||||| || || ||| |||||||||||||||||| | | | | | || | | | | ||| ||| | | | | | | | | | || | | | | || ||| ||| || | |
GAAATTCCAGCCAAGTAAGTGATGGTGCAGGAGCGGTTCTCCTAATGAAGAGAAGTGTTGCAATGCAAAAAGGACTTCCCGTTCTTGGTGTATTCAGgtgggt-aataattacttacaaagctacgactgtggaagtctgaaaaccgaaaaaactgcagaggcttgtgatttccatttacacagatatgctagtatacgtggaaaatacattgttctttctgtatttggctttttctaagtagcacactattggacatattgcag

upper sequence: GLYMA20G18980.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv05s0051g00720.t01 (Vitis vinifera), 5'ss of exon 10
GTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgtacttcatttgt--aatatagaggctttagtccctggcagtatttatatgctgattccaaattgacatgctgtgtgctctatgaagaaatgaaggaccaat
| |||||||| || |||||||||||||||| ||||||||| || ||||| ||||||||||| ||| || ||| |||| |||||||||||||||||||| | | | | || || | | | || || || |||| | || | | | || | | | | | |
GGAATTCTAGCCAAGTGAGTGATGGTGCTGGAGCTGTTCTCCTCATGAAGAGAAGTGTTGCAATGCGTAAAGGGTTACCTATTCTTGGTGTATTCAGgtatataaatccttagatgtatatgtacatatttatgaatttaggtaaatgcctctggtgtctttagcttatatggatatggtttatactcttggtataa--

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|51336044|gb|CO979910.1|CO979910
EST:     AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAG                         GACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
genomic: AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgtacttcatt ... tgtcatgtagGACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
EST: gi|254346645|gb|GR856367.1|GR856367
EST:     AAAAGAAGTGGTGCGTTGCAAAAGGGCCTACCCATTCTTGGTGTATTCAG                         GACTTTCGCAGCAGTGGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
genomic: AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgtacttcatt ... tgtcatgtagGACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
EST: gi|192299235|gb|FG992473.1|FG992473
EST:     AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAG                         GACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
genomic: AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgtacttcatt ... tgtcatgtagGACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
EST: gi|192310414|gb|FG999157.1|FG999157
EST:     AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAG                         GACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
genomic: AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgtacttcatt ... tgtcatgtagGACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
EST: gi|254331906|gb|GR843649.1|GR843649
EST:     AAAAGAAGTGTTGCGTTGCAAAAGGGGCTA-CCATTCTTGGTGTATTCAG                         GACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
genomic: AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgtacttcatt ... tgtcatgtagGACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
EST: gi|308099050|gb|HO760891.1|HO760891
EST:     AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAG                         GACTTTCGCAGCAGTTTGGTGTTGATCCTGCCATAATGGGGTGTTGGGTCC
genomic: AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgtacttcatt ... tgtcatgtagGACTTTCGCAGCAGTT-GGTGTTGATCCTGCCATAATGGG-TGTTGG-TCC
EST: gi|7591443|gb|AW707176.1|AW707176
EST:     GGCTACCCATTCTTGGTGTATTCAG                         GACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
genomic: GGCTACCCATTCTTGGTGTATTCAGgtacttcatt ... tgtcatgtagGACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
EST: gi|254319377|gb|GR828997.1|GR828997
EST:     AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAG                         GACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGT-CTGC
genomic: AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgtacttcatt ... tgtcatgtagGACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
EST: gi|298174872|gb|HO014789.1|HO014789
EST:     AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAG                         GACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
genomic: AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgtacttcatt ... tgtcatgtagGACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
EST: gi|51335173|gb|CO979039.1|CO979039
EST:     AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAG                         GACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
genomic: AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgtacttcatt ... tgtcatgtagGACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
EST: gi|4397476|gb|AI496473.1|AI496473
EST:     AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAG                         CACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
genomic: AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgtacttcatt ... tgtcatgtagGACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
EST: gi|254346644|gb|GR856366.1|GR856366
EST:     AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAG                         GACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC
genomic: AAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgtacttcatt ... tgtcatgtagGACTTTCGCAGCAGTTGGTGTTGATCCTGCCATAATGGGTGTTGGTCCTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgtacttcatttgtaatatagaggctttagtccctggcagtatttatatgctgattccaaattgacatgctgtgtgctctatgaagaaatgaaggaccaat

- - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT