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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaataaacaaagttgcttgcatcggttatagttgttgttactgttgttcttttattcacattttttagtgcttttacccccccaccaaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGTCGTCTCTTGAGAGATGCCAAACTCTACGAGATTGGTGCAGGAACTAGTG

Basic information

species Glycine max
transcript GLYMA11G15900.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G15900.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G381051_T03 (Zea mays), 3'ss of exon 13
-----gtaaataaacaaagttgcttgcatcggttatagttg-ttgttactgttgttcttttattcacattttttagtgcttttacccccccaccaaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGTCGTCTCTTGAGAGATGCCAAACTCTACGAGATTGGTGCAGGAACTAGTG
      | |  || || |     ||   |  |  |||      || || | |||   | |   |||  || | |  | |  | || |   | | |   |  |||||||| || ||| | ||||| ||||| ||  | |||||||| || |||||||||||| |||||||||| ||| | |  ||||||||||| || |||||||
aacacatcataaatcataacaagtttttttagaaataacgaactgataat-ttgcagtatgcatcattttatatgttccactaactctttctcta---tggcagGCAATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGTCGTCTCCTGAGAGATGCAAAATTGTTTGAGATTGGTGCCGGTACTAGTG

upper sequence: GLYMA11G15900.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G052630_T01 (Zea mays), 3'ss of exon 12
gtaaataa--acaaagttgcttgcatcggtta-tagttgttgttactgttgttcttttattcacattttttagtgcttttacccccccaccaaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGTCGTCTCTTGAGAGATGCCAAACTCTACGAGATTGGTGCAGGAACTAGTG
 ||||| |  |||   ||  ||  ||     | || |  ||  || | |    | ||| |  |  ||          || |   | |   ||   |  ||||| || || ||| | ||||| ||||| ||  | |||||||| || |||||||||||| |||||||||| ||| | |  ||||||||||| || ||||| |
-taaatcataacaggattttttaaattttgaactaatattttgtagtatgcaccatttttatatgttccactaactcttcataactctttcactatggcagGCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGTCGTCTCCTGAGAGATGCAAAATTGTTTGAGATTGGTGCTGGTACTAGCG

upper sequence: GLYMA11G15900.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv06s0004g03140.t01 (Vitis vinifera), 3'ss of exon 14
---gtaaataaacaaagttgcttgcatcggttatagt-tgttgttactgttgttcttttattcacattttttagtgcttttacccccccaccaaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGTCGTCTCTTGAGAGATGCCAAACTCTACGAGATTGGTGCAGGAACTAGTG
   ||||  || ||   | |   |  ||   || | | |   | | |||   || | |  ||  ||  | |  |   |   |         ||| ||| |||||||| |||||||||||||| ||||| |||||||| ||||| || |||||||||||  |  ||||||||||||| || || ||||| ||||| || ||||
aacgtaaccaaccatcataga--gtttcaagtacaatatacggattctgcaattatatagttgtcaaatgtatgatttaggagtttatattcaattttgcagGCAATTCAATGTTTAGGTGGCAATGGGTATGTGAACGAGTACCCAACTGGTCGTCTTCTTCGAGATGCCAAACTGTATGAAATTGGGGCAGGGACAAGTG

upper sequence: GLYMA11G15900.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ07135 (Selaginella moellendorffii), 3'ss of exon 15
gtaaataaacaaagttgcttgcatcggttatagttgttgttactgttgttcttttattcacattttttagtgcttttacccccccaccaaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGTCGTCTCTTGAGAGATGCCAAACTCTACGAGATTGGTGCAGGAACTAGTG
                                               |     |  ||||   || |   |  ||     | | ||    || | ||||| || || ||  ||||||||||||| ||||| || |||||||| |||||  | || ||||||||||| ||||| || |||||||| || ||||| ||||
-----------------------------------------------gcaagctctttcatgattctactttgttcctaactctcagatcatgtccagGCTATCCAGTGCCTAGGTGGGAATGGCTATGTAAACGAGTATCCCACTGGAAGGCTGTTGAGAGATGCAAAACTATATGAGATTGGAGCTGGAACAAGTG

upper sequence: GLYMA11G15900.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ09244 (Selaginella moellendorffii), 3'ss of exon 14
-------------------------------------------------------------gtaaataaacaaagttgcttgcatcggttatagttgttgttactgttgttcttttattcacattttttagtgc---ttttacccccccaccaaatt---ttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGTCGTCTCTTGAGAGATGCCAAACTCTACGAGATTGGTGCAGGAACTAGTG
                                                             ||     | | |   |  || |||| |  |  |    |   |  | | | |    |  | | ||  | | |     |||||||   |   |  ||    | ||||| || || ||  ||||||||||||| ||||| || |||||||| |||||  | || ||||||||||| ||||| || |||||||| || ||||| ||||
gtgagattcaacttacaaaatgctgtgaatttctagactaaagcgccttgtctacaggattgtgctgcagctattcttttttcatcagagaacgcaactcaaatggctttgcaggcaagctctttcataattctactttttacctaactctcggatcatgtccagGCTATCCAGTGCCTAGGTGGGAATGGCTATGTAAACGAGTATCCCACTGGAAGGCTGTTGAGAGATGCAAAACTATATGAGATTGGAGCTGGAACAAGTG

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|209699170|gb|BW656185.1|BW656185
EST:     CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAG                         GCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
genomic: CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAGgtaaataaac ... aaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
EST: gi|209712355|gb|BW671207.1|BW671207
EST:     CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAG                         GCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
genomic: CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAGgtaaataaac ... aaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
EST: gi|213613458|gb|DB974627.1|DB974627
EST:     TTTGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAG                         GCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
genomic: CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAGgtaaataaac ... aaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
EST: gi|16995570|gb|BM084942.1|BM084942
EST:     CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAG                         GCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
genomic: CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAGgtaaataaac ... aaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
EST: gi|193340854|gb|FK307131.1|FK307131
EST:     CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAG                         GCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
genomic: CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAGgtaaataaac ... aaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
EST: gi|31476129|gb|CD418157.1|CD418157
EST:     CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAG                         GCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
genomic: CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAGgtaaataaac ... aaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
EST: gi|13478283|gb|BG507821.1|BG507821
EST:     CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACNCAGGTTGCTTTGCAG                         GCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
genomic: CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAGgtaaataaac ... aaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
EST: gi|254338024|gb|GR849656.1|GR849656
EST:     CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAG                         GCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
genomic: CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAGgtaaataaac ... aaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
EST: gi|208096252|gb|GD891736.1|GD891736
EST:     TTGTGCAGCTTGAAAGAGCAACCCAGGTTGCTTTGCAG                         GCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
genomic: TTGTGCAGC-TGAAAGAGCAACCCAGGTTGCTTTGCAGgtaaataaac ... aaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
EST: gi|9901994|gb|BE610962.1|BE610962
EST:     CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAG                         GCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
genomic: CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAGgtaaataaac ... aaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
EST: gi|10255205|gb|BE822971.1|BE822971
EST:     CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAG                         GCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
genomic: CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAGgtaaataaac ... aaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
EST: gi|254338023|gb|GR849655.1|GR849655
EST:     CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAG-TTGCTTTGCAG                         GCAATACAATGTTTAG-TGGGAATGGTTA
genomic: CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAGgtaaataaac ... aaattttcagGCAATACAATGTTTAGGTGGGAATGGTTA
EST: gi|193642370|gb|FK587244.1|FK587244
EST:     CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAG                         GCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT
genomic: CTGGAGCTATACTTTGTGCAGCTGAAAGAGCAACCCAGGTTGCTTTGCAGgtaaataaac ... aaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgttcttttattcacattttttagtgcttttacccccccaccaaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGTCGTCTCTTGAGAGATGCCAAACTCTACGAGATTGGTGCAGGAACTAGTG
                                                ttttc  CT-rich tract
     ttcttttattcacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaataaacaaagttgcttgcatcggttatagttgttgttactgttgttcttttattcacattttttagtgcttttacccccccaccaaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGTCGTCTCTTGAGAGATGCCAAACTCTACGAGATTGGTGCAGGAACTAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG