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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGTATTGTTGCTGAAGATGTACCAGTTGATCAGTTCACCCCATTGGGTCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatttaattgatttctagttttacagcaagcttattttgttgtataaccaactagggttaattcacactaatttaaggaatgcaaacataaatc...

Basic information

species Glycine max
transcript GLYMA18G47770.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47770.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os07g36190.1 (Oryza sativa), 5'ss of exon 5
-TTGGTATTGTTGCTGAAGATGTACCAGTTGATCAGTTCACCCCATTGGGTCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagcc---aatttaattgatttctagttttacagcaagcttattttgttgtataaccaactagggttaatt--cacactaatttaaggaatgcaaacataaatc
 | || ||    ||||||||||| |||||||| || ||||||||  | ||||| || ||||||||||| || |||||||| |||||||| || || || ||| ||       ||||||   || ||   ||  | |||  ||||||||  |  ||        |   || | |   |  || ||||    ||  |||  |      
CTGGGCATCCCAGCTGAAGATGTGCCAGTTGACCAATTCACCCCTCTTGGTCGGATGCTTTACAAGGCCCCATCTGATGGAAAATGGGGTGAACACGAGCgtaagttttagttttaataccttacttaattacctgcacacttatttttattcattgaagctcaacctttagtgttattctcatttctataagccaatta------

upper sequence: GLYMA18G47770.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os05g34180.1 (Oryza sativa), 5'ss of exon 5
-TTGGTATTGTTGCTGAAGATGTACCAGTTGATCAGTTCACCCCATTGGGTCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagc----------------caatttaattgatttctagtttta-----------cagcaa--gcttattttgt-tgtataaccaactagggttaattcacactaatttaaggaatgcaaacataaatc----------
 | || ||    ||||||||  |||| ||||| || ||||  ||  | ||  | || ||||||||||| || |||||||| |||||||| || ||||||||| |                  | |  | ||  |||||    || |           |||| |   |||   |  | |||||   ||| |   ||   || |    |||||   ||||  || |||   ||          
CTGGGAATACAAGCTGAAGAACTACCTGTTGACCAATTCATTCCTCTTGGGAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatatttgccctctgccctctacctgatacatttcagccttcatacttatcgtccagctatcacttgcctcttgtgtattttcaattgctgtcttttga----aatttttagaatataaccatctttcgccatttcag

upper sequence: GLYMA18G47770.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G108285_T01 (Zea mays), 5'ss of exon 5
-TTGGTATTGTTGCTGAAGATGTACCAGTTGATCAGTTCACCCCATTGGGTCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatttaattgatttctagttttacagcaagcttattttgttgtataaccaactagg-gttaattcacactaatttaagga-atgcaaacataaatc
 | || ||    || |||||||  |||||||| || ||||||||  |||| || || |||||||||||||| ||||| || |||||||| |||||||| ||| ||    |   |   || ||    | |||    | |    |   |||  |  |||| | |  | |  |    | ||   |   || |  | |  |||    
CTGGGCATCCCAGCAGAAGATGCCCCAGTTGACCAATTCACCCCTCTGGGCCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttctaccacctatctcctcatctacttgcatccagatagtttgagttgccaattggtcgatggtatggaatagactgttgacacactagtatag---

upper sequence: GLYMA18G47770.1 (Glycine max), 5'ss of exon 5
lower sequence: AT5G16440.1 (Arabidopsis thaliana), 5'ss of exon 5
-TTGGTATTGTTGCTGAAGATGTACCAGTTGATCAGTTCACCCCATTGGGTCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatttaattgatttctagttttacagcaagcttattttgttgtataaccaactagggtt--aattcacactaatttaaggaatgcaaacataaatc
 | |||||||| || |||||||||||||| ||| ||||||| || ||||| ||||| ||||||||||||||||||||||| |||||||||||||| ||| || | |      |||    ||| |  |||       | | ||||   | | ||||    |    ||   |||   | |   || |||| |        |    
CTCGGTATTGTAGCAGAAGATGTACCAGTCGATGAGTTCACTCCCTTGGGACGCATGCTTTACAAGGCACCTTCTGATGGGAAATGGGGAGAGCACGAAGgtaaac------aatc--cttccatgttt-------gatcatttctctttttaactcctttaacttcagattttgaatctcttgaggatttttgttgcag---

upper sequence: GLYMA18G47770.1 (Glycine max), 5'ss of exon 5
lower sequence: AT3G02780.1 (Arabidopsis thaliana), 5'ss of exon 5
-TTGGTATTGTTGCTGAAGATGTACCAGTTGATCAGTTCACCCCATTGGGTCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgag--ccaatttaattgatttctagttttacagcaagcttattttgttgtataaccaa---ctagggttaattcacactaatttaaggaatgcaaacataaatc
 |||||||||| ||||||||||||||||| ||| ||||||| || ||||| || || || |||||||| ||||||||||||||||||||||||||||||||| |   ||| ||     || |  | |||      | |  || ||     | ||||  ||    || | ||  |      |    |      ||||          
CTTGGTATTGTAGCTGAAGATGTACCAGTCGATGAGTTCACTCCCTTGGGACGTATGCTGTACAAGGCTCCTTCTGATGGCAAATGGGGAGAGCATGAACgtaaataccatttctcaagactcttggttc-----ccattttcttgaacagaataataaaaccttaagcttcttctgtgttggccttccttttgcag---------

upper sequence: GLYMA18G47770.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv04s0023g00600.t01 (Vitis vinifera), 5'ss of exon 5
-TTGGTATTGTTGCTGAAGATGTACCAGTTGATCAGTTCACCCCATTGGGTCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatttaattgatttctagttttacagcaagcttattttgttgtataaccaactagggttaattcacactaatttaaggaa-tgcaaacataaatc
 | || |||  ||||||||||| ||| |||||||||||||| ||| |||| ||||| |||||||||||||| || |||||||| |||||||||||||||||| |   ||| | |    |   |  ||| | | |     |  ||| |    |       |     |  |||| |    | |  | |  |   | |     ||
CTCGGCATTCCTGCTGAAGATGCACCTGTTGATCAGTTCACTCCACTGGGCCGCATGCTTTACAAGGCACCATCAGATGGCAAGTGGGGAGAGCATGAACgtaa--taatctgaactttgatttatttcaaatctcaactgatttatatggtgctttgttttaactgtttcataaagttgtctgaagctttgagccagggtc

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|37997447|gb|CF809036.1|CF809036
EST:     CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACT                         GGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
genomic: CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatt ... tgattgcagtGGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
EST: gi|26057349|gb|CA800263.1|CA800263
EST:     CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACT                         GGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
genomic: CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatt ... tgattgcagtGGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
EST: gi|209715425|gb|BW682130.1|BW682130
EST:     CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACT                         GGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
genomic: CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatt ... tgattgcagtGGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
EST: gi|192320456|gb|FK012314.1|FK012314
EST:     CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACT                         GGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
genomic: CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatt ... tgattgcagtGGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
EST: gi|18733450|gb|BM527614.1|BM527614
EST:     CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACT                         GGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
genomic: CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatt ... tgattgcagtGGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
EST: gi|15000069|gb|BI320883.1|BI320883
EST:     CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACT                         GGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
genomic: CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatt ... tgattgcagtGGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
EST: gi|19271109|gb|BM887365.1|BM887365
EST:     CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACT                         GGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACC
genomic: CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatt ... tgattgcagtGGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACC
EST: gi|15204731|gb|BI427499.1|BI427499
EST:     TACAAGCCACCTTCTGATGGCAAATGGGGAGAGCATGAACT                         GGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
genomic: TACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatt ... tgattgcagtGGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
EST: gi|17400107|gb|BM176889.1|BM176889
EST:     ATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGACCT                         GGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
genomic: ATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatt ... tgattgcagtGGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
EST: gi|254336566|gb|GR842745.1|GR842745
EST:     CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACT                         GGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
genomic: CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatt ... tgattgcagtGGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
EST: gi|38191978|gb|CF921184.1|CF921184
EST:     CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACT                         GGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
genomic: CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatt ... tgattgcagtGGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
EST: gi|209727624|gb|BW663784.1|BW663784
EST:     CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACT                         GGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
genomic: CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatt ... tgattgcagtGGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
EST: gi|208064082|gb|GD867024.1|GD867024
EST:     CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACT                         GGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
genomic: CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatt ... tgattgcagtGGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
EST: gi|207777605|gb|GD747538.1|GD747538
EST:     CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACT                         GGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
genomic: CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatt ... tgattgcagtGGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
EST: gi|207820807|gb|GD792574.1|GD792574
EST:     CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACT                         GGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA
genomic: CGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatt ... tgattgcagtGGACTATCTGCTTTTCATTGTCCGGGATGTTAACGTGAACCCCAATCCTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGTATTGTTGCTGAAGATGTACCAGTTGATCAGTTCACCCCATTGGGTCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagccaatttaattgatttctagttttacagcaagcttattttgttgtataaccaactagggttaattcacactaatttaaggaatgcaaacataaatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA