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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actcttttaatcattttcaccttttaattataaagctaatcataatatatatacattgctaataacgtatctcttttttttttttttttttttgtgacagTGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATTACCATTTCACAGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTT

Basic information

species Glycine max
transcript GLYMA11G19490.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G19490.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g42020.1 (Oryza sativa), 3'ss of exon 3
actcttttaatcattttcaccttttaattataaagctaatcataatatatatacattgctaataacgtatctctttttttt-----ttttttttttttgtga-cagTGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATTACCATTTCACAGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTT
      |  |  | | |  |    |     |       |   |  | | |   ||| | | || || | | | ||  |  |     |  |  |    ||||| |||||||| |  | || ||| |  ||||||| ||||| ||||||||| |||||||||| |||| ||||||||||||||| || ||  |||| || || |||||
-----ctatactagtgtagcacactggccttgttttggacttttttcttttggcatgg-tgatgacatgtttgttgctgctgacggtggtgatggcgtgtgagcagTGAATGCAAATGAATGCCTGATGACAAGGATGCAGGAGATGTCCTTGGATTACCACTTCAAAGTAGAGCAAGAAGTGGGTTCCTCCACACACGCCTTCTT

upper sequence: GLYMA11G19490.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 3
actcttttaatcattttcaccttttaattataaa--gctaatcataatatat-atacattgctaataacgtatctcttttttttttttttttttttgtgacagTGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATTACCATTTCACAGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTT
  ||| | |   ||  | |   |||||||       | |  || || || ||  ||  ||  |    ||  || | ||  |  ||| || | |  | |  |||| |||||||| |||||||||||||| ||||||||||| |||||  |||||||||||||||| || ||||||||||| || ||| | || |||||||| ||
--tctctaataaataattaagatttaattgagctttgtttgtcttattaaattgtatgttttttg-gactaatgttttaatcctttgttgtatacttttgcagTAAATTCTGATGAGTGCTTATTGACGAGAATGCAAGAAATGTCATTGGATTACCATTTCACTGTTGAGCAAGAAGTGGGTTCATCAACACATGCTTTTTT

upper sequence: GLYMA11G19490.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0061g01230.t01 (Vitis vinifera), 3'ss of exon 3
actcttttaatcattttcaccttttaattataaagctaatcataatatatatacattgctaataacgtatctcttttttttttttttt---tttttgtgacagTGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATTACCATTTCACAGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTT
 || |   |||       |  || |||| ||||   |||| ||||||| |||   | | | ||||   ||       |   ||| |     |  || || |||| ||| | |||||||||||| ||||||| ||||||||||||||  ||||||| ||||| ||||| |||||||||||||||||||| |||||||| |||||
cctttccaaattggacaaaaattataataataa---taataataatatttatgattggttgataaatgatactaaaatggatttatacgggtaattttggcagTAAATGCGGACGAGTGCTTAATGACAAGGATGCAAGAGATGTCATTGGATTATCATTTTACAGTGGAGCAAGAAGTTGGATCAGCTACTCATGCCTTCTT

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|7478387|gb|AW666245.1|AW666245
EST:     GTTGGAGATTTG                         TGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATT
genomic: GTTGGAGATTTGgtaaataatt ... tttgtgacagTGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATT
EST: gi|8283320|gb|BE020881.1|BE020881
EST:     CTTGGTGGGCAACCCCGACATTGCTCTTGTTCAAGCTCGTTGGAGATTTG                         TGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATT
genomic: CTTGGTGGGCAACCCCGACATTGCTCTTGTTCAAGCTCGTTGGAGATTTGgtaaataatt ... tttgtgacagTGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATT
EST: gi|16346811|gb|BI972406.1|BI972406
EST:     CTTGGTGTTTTTTCCCGACATTGCTCTTGTTCAAGCTCGTTGGAGATTTG                         TGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATT
genomic: CTTGGTGGGCAACCCCGACATTGCTCTTGTTCAAGCTCGTTGGAGATTTGgtaaataatt ... tttgtgacagTGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATT
EST: gi|8284807|gb|BE022366.1|BE022366
EST:     CTTGGTGGGCAACCCCGACATTGCTCTTGTTCAAGCTCGTTGGAGATTTG                         TGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATT
genomic: CTTGGTGGGCAACCCCGACATTGCTCTTGTTCAAGCTCGTTGGAGATTTGgtaaataatt ... tttgtgacagTGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATT
EST: gi|10847333|gb|BF070038.1|BF070038
EST:     CTTGGTGGGCAACCCCGACATTGCTCTTGTTCAAGCTCGTTGGAGATTTG                         TGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATT
genomic: CTTGGTGGGCAACCCCGACATTGCTCTTGTTCAAGCTCGTTGGAGATTTGgtaaataatt ... tttgtgacagTGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATT
EST: gi|10846450|gb|BF071342.1|BF071342
EST:     CTTGGTGGGCAACCCCGACATTGCTCTTGTTCAAGCTCGTTGGAGATTTG                         TGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATT
genomic: CTTGGTGGGCAACCCCGACATTGCTCTTGTTCAAGCTCGTTGGAGATTTGgtaaataatt ... tttgtgacagTGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATT
EST: gi|15337505|gb|BI498161.1|BI498161
EST:     CTTGGTGGGCAACCCCGACATTGCTCTTGTTCAAGCTCGTTGGAGATTTG                         TGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATT
genomic: CTTGGTGGGCAACCCCGACATTGCTCTTGTTCAAGCTCGTTGGAGATTTGgtaaataatt ... tttgtgacagTGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATT
EST: gi|6567149|gb|AW234774.1|AW234774
EST:     CTTGGTGGGCAACCCCGACATTGCTCTTGTTCAAGCTCGTTGGAGATTTG                         TGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATT
genomic: CTTGGTGGGCAACCCCGACATTGCTCTTGTTCAAGCTCGTTGGAGATTTGgtaaataatt ... tttgtgacagTGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATT
EST: gi|14999810|gb|BI320624.1|BI320624
EST:     CTTGGTGGGCAACCCCGACATTGCTCTTGTTCAAGCTCGTTGGAGATTTG                         TGAATTCTGACGAGTGCTTATTGACCAGAATGCAAGAGATGTCCCTGGATT
genomic: CTTGGTGGGCAACCCCGACATTGCTCTTGTTCAAGCTCGTTGGAGATTTGgtaaataatt ... tttgtgacagTGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatatacattgctaataacgtatctcttttttttttttttttttttgtgacagTGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATTACCATTTCACAGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTT
              taataac  putative branch site (score: 1)
                    cgtatctctttttttt  CT-rich tract
              taataacgtatctctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actcttttaatcattttcaccttttaattataaagctaatcataatatatatacattgctaataacgtatctcttttttttttttttttttttgtgacagTGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATTACCATTTCACAGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - tcacctt