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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgacatttgtctgttttccctgtaacttgttattattttttaacatccttcatatttaattataactttacatggtatgttatgcagTTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATACTGGAGGATGCTATTAGAAGTGGATACCCTATATTAATTATTGCTGAGG

Basic information

species Glycine max
transcript GLYMA15G40110.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 6
-----gtgtgacatttgtctgttttccctgtaacttgttattattttttaacatccttcatatttaa-----ttataactttaca-tggt----atgttat--gcagTTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATACTGGAGGATGCTATTAGAAGTGGATACCCTATATTAATTATTGCTGAGG
      ||   |  ||     || | |    || |   || |  | | ||  |       | ||||       | ||   ||||  || |    ||  |||   ||| | ||  | || ||||| || || | |||||| || ||||||||||  || |||||||||||||||||||||||||| || ||  ||||  | || ||||
gtttgatgctccccttcatcattgtactaaaaattctgtagtgctatctagtaatagcagtttttatgacttctgtacgcttacggtgattttaattctattaccagCTTCTCCTTGTGGACAAGAAAATTAACAATGCCAGAGATCTTATCACTATCCTGGAGGATGCTATTAGAAGTGGATATCCAATTCTAATAGTGGCAGAGG

upper sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------gtgtgacatttgtctgttttccctgtaacttgttattattttttaacatc--cttcatatttaattataactttacatggtatgttatgcagTTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATACTGGAGGATGCTATTAGAAGTGGATACCCTATATTAATTATTGCTGAGG
                             |||  |||||  |    |  | || |   | |  || |||  | ||     | | |   |  | |||  ||   ||||||| | ||||||| ||  | |||||||| || || |||||||||||||||||| |     |  |||||||||| |||||| | |||||||| ||||||||||||||||| |
gtagatgtttcttgaatctgagtagaagatgaattttgttggcagactatttagccactaaagatatttatatatgagtataacaacgatctttaatgtt--ttggtatgat-tgcagTTACTTCTCGTTGACAAGAAAATTACCAATGCAAGGGATCTTGTTGGTGTTTTGGAGGATGCAATTAGAGGCGGATACCCAATATTAATTATTGCTGAAG

upper sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G56500.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgtgacatttgtctgttttccctgtaacttgttattattttttaacatccttcatatttaattataactttacatggtatg-ttatgcagTTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATACTGGAGGATGCTATTAGAAGTGGATACCCTATATTAATTATTGCTGAGG
|| | |   |||| | |    |   ||| |  | ||   |  | || | ||    |||||  | |  |  |  |      || || || ||||| |  | ||||||||||||||||| ||||| || ||| |||| | ||| ||||| ||||| |||| | ||||||||||  | || || |||||||| |
gtattattattgtttat---acagttaaatcttaatagctgataaaaaaccgcagtattttttgactatatgtctcttcttgcttttgtagTTGTTTCTTGTTGACAAAAAGATAACAAATGCTAGAGATATTATTAGCATTCTGGAAGATGCGATTAAAGGTGGATACCCGCTTTTGATCATTGCTGAAG

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|209696896|gb|BW660461.1|BW660461
EST:     ACTTTGTTACTGACAGTGAGAAAATGGCTGTTGAATATGAGAACTGTAAG                         TTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATA
genomic: ACTTTGTTACTGACAGTGAGAAAATGGCCGTTGAATATGAGAACTGTAAGgtgtgacatt ... tgttatgcagTTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATA
EST: gi|208194397|gb|GD987652.1|GD987652
EST:     ACTTTGTTACTGACAGTGAGAAAATGGCCGTTGAATATGAGAACTGTAAG                         TTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATA
genomic: ACTTTGTTACTGACAGTGAGAAAATGGCCGTTGAATATGAGAACTGTAAGgtgtgacatt ... tgttatgcagTTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATA
EST: gi|26046015|gb|CA783382.1|CA783382
EST:     AGAACTGTAAG                         TTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATA
genomic: AGAACTGTAAGgtgtgacatt ... tgttatgcagTTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATA
EST: gi|24135545|gb|BU926055.1|BU926055
EST:     ACTTTGTTACTGACAGTGAGAAAATGGCCGTTGAATATGAGAACTGTAAG                         TTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATA
genomic: ACTTTGTTACTGACAGTGAGAAAATGGCCGTTGAATATGAGAACTGTAAGgtgtgacatt ... tgttatgcagTTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATA
EST: gi|193539802|gb|FK493788.1|FK493788
EST:     ATATGAGAACTGTAAG                         TTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATA
genomic: ATATGAGAACTGTAAGgtgtgacatt ... tgttatgcagTTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATA
EST: gi|193404242|gb|FK366576.1|FK366576
EST:     ACTTTGTTACTGACAGTGAGAAAATGGCCGTTGAATATGAGAACTGTAAG                         TTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATA
genomic: ACTTTGTTACTGACAGTGAGAAAATGGCCGTTGAATATGAGAACTGTAAGgtgtgacatt ... tgttatgcagTTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATA
EST: gi|24136477|gb|BU926987.1|BU926987
EST:     ACTTTGTTACTGACAGTGAGAAAATGGCCGTTGAATATGAGAACTGTAAG                         TTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATA
genomic: ACTTTGTTACTGACAGTGAGAAAATGGCCGTTGAATATGAGAACTGTAAGgtgtgacatt ... tgttatgcagTTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATA
EST: gi|208221819|gb|GE016841.1|GE016841
EST:     ACTTTGTTACTGATAGTGAGAAAATGGCCGTTGAATATGAGAACTGTAAG                         TTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATA
genomic: ACTTTGTTACTGACAGTGAGAAAATGGCCGTTGAATATGAGAACTGTAAGgtgtgacatt ... tgttatgcagTTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattttttaacatccttcatatttaattataactttacatggtatgttatgcagTTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATACTGGAGGATGCTATTAGAAGTGGATACCCTATATTAATTATTGCTGAGG
                           ttataac  putative branch site (score: 2)
     ttttaacatccttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgacatttgtctgttttccctgtaacttgttattattttttaacatccttcatatttaattataactttacatggtatgttatgcagTTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATACTGGAGGATGCTATTAGAAGTGGATACCCTATATTAATTATTGCTGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA