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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacctgttccacttgaaatagttttcattttgcaattatttttttagggtgaatttcatctaatgatctattaacatcgtggacag

Basic information

species Glycine max
transcript GLYMA15G42300.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G42300.1 (Glycine max), 5'ss of exon 18
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 18
GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacctgttccacttg--aaatagttttcattttgcaattatttttttagggtgaatttcatcta--atgatctattaacatc-gtggacag------------
|| ||||| |||||||| ||||||||||| ||||||||||| || |||||| ||| |||  || |||| |    |||||   |||| | ||     |     | ||   ||  |  ||| || ||| |   ||  |   |  || ||| |  |  |  | ||    |||| |   | || ||             
GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgt--ttacctgtcctggttaaataatttagtaaccaaatttaatcttgaacccatgatggaatagtaaatgtacttcagaacgagtacttaataaaagcggccatctaattacgcag

upper sequence: GLYMA15G42300.1 (Glycine max), 5'ss of exon 18
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 18
GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacctgttccacttgaaatagt-tttcattttgcaattatttttttagggtgaatttcatctaatgatctattaacatcgtggacag------------------
|| ||||| |||||||| ||||||||||| ||||| ||||| ||||||||| ||| |||  || |||| |    |||||   |||  | | |    |   | |  | |     | | | ||||     | |  || | |  | | |    ||||||   |  |   |   | |    |                   
GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCGgtatgt--ttatctgtattggttaaacaatctaatgccatgtctaatttaatcttgaacttatgatagagtagcaaatctaactttagaacgagtacttaagaaaacttctctaactgcgcag

upper sequence: GLYMA15G42300.1 (Glycine max), 5'ss of exon 18
lower sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 19
GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacctg--ttccacttga--aatagttt---tcattttgcaattatttttttagggtgaatttcatctaatgatctattaacatcgtggacag
|| || || || ||||||||||||||||| |||||||||||  | |||||| ||| ||| ||| |||| | |  |||||    | ||| | |||  |   ||||| || |   ||  |||   | | || | || ||   || |          |||| |   || | | ||||   |  |    
GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttatgctt-tgtcatttagattccaatttagtgatgtttttatttacttagtaaataaagttctgaatgagcactcatgtctggaac-actaactgtgcag----

upper sequence: GLYMA15G42300.1 (Glycine max), 5'ss of exon 18
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 5'ss of exon 17
GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacctgttccacttgaaatagttttcattttgcaattatttttttagggtgaatttcatctaatgatctattaacatcgtggacag
|| || || || ||||| || |||||||| || || |||||||| |||||||||||||||||||| || | || ||| ||   ||||| | |  |  |      ||||  | |||||   |      |  || || ||| ||||  ||| | | |  || ||                
GTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAGgta-ggaactacttgtgtatcgaggct---ttgaccttgtttt-gctgaatcttggttattatagagtgacattcctttca-aatatag---------------

upper sequence: GLYMA15G42300.1 (Glycine max), 5'ss of exon 18
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 18
GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggtt-acttctctcacctgttccacttgaaatagttttcattttgcaattatttttttagggtgaatttcatctaatgatctattaacatcgtggacag
|| || || || ||||| ||||||||||| |||||||| ||  | |||||| ||||||||||||| || | || ||| |  ||  ||  |||   |  ||  || ||||          |     ||| |||  | |  | | |  ||  |                            
GTGAAGAACCCGTGGCCAAATGTTGATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAGgtaagaagtagacacctccttcaagtatca-ttgagccttaggatagcactcaaatataatatctgtgcgttttatag---------------------------

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|10847452|gb|BF070139.1|BF070139
EST:     GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCCTCTTTG-TGTATCAACGAGCCTTGGA
genomic: GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggtt ... tcgtggacagCTATTATACTGTTC-TCTTTGGTGTATCAAGGAGCTTTGGA
EST: gi|214008142|gb|DB987047.1|DB987047
EST:     AGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: AGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggtt ... tcgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
EST: gi|192324528|gb|FK016449.1|FK016449
EST:     GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggtt ... tcgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
EST: gi|254349123|gb|GR860395.1|GR860395
EST:     GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggtt ... tcgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
EST: gi|15813913|gb|BI786188.1|BI786188
EST:     GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggtt ... tcgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
EST: gi|254349122|gb|GR860394.1|GR860394
EST:     GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggtt ... tcgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
EST: gi|6666249|gb|AW277708.1|AW277708
EST:     GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggtt ... tcgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
EST: gi|17020863|gb|BM091897.1|BM091897
EST:     GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggtt ... tcgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
EST: gi|15815591|gb|BI787866.1|BI787866
EST:     GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggtt ... tcgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
EST: gi|7795790|gb|AW781187.1|AW781187
EST:     GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggtt ... tcgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
EST: gi|213598475|gb|DB975934.1|DB975934
EST:     GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggtt ... tcgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacctgttccacttgaaatagttttcattttgcaattatttttttagggtgaatttcatctaatgatctattaacatcgtggacag

- - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - GTGGAG