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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcatgagttgggctcttataattacaatagatgttacaaatgtactggtttacaaagtgttaaagagttctaaacaacagattaacatgtgcaaattttgttcatgtattcagAGATCCTGCAGAGATCCCATGGAGTGATTTTGGGGCTGATTATGTCATTGAGTCTTCAGGAGTTTTTACAACAGTGGAGAAAGCTTCATCACATTTGAAG

Basic information

species Glycine max
transcript GLYMA03G22790.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 6
gtatcatgagttgggctcttataattacaatagatgttacaaatgtactggtttacaaagtgttaaagagttctaaacaacagattaacatgtgcaaattttgttcatgtattc-agAGATCCTGCAGAGATCCCATGGAGTGATTTTGGGGCTGATTATGTCATTGAGTCTTCAGGAGTTTTTACAACAGTGGAGAAAGCTTCATCACATTTGAAG
   ||||    ||   | || |  ||   ||   | || |        |||| | ||  || ||| |   || ||  | |   | | |||      ||||||| |     |||| ||||||||||||||||| |||||| || | ||||||||||| |||||  |||| ||||| || || ||||||||    || ||||| ||| |||| || |||
---tcatataatgatttgttgtgttttgcattactatttc-------ttggtctgca--gttttacaattttttattctaagaactcaca-----gaattttgcttcaacattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTTACAACGACTGATAAAGCATCAGCACACTTAAAG

upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 6
gtatcatgagttgggctcttataattacaatagatgttacaaatgtactggtttacaaagtgttaaagagttctaaacaacagattaacatgtgcaa-attttgttcatgtattc-agAGATCCTGCAGAGATCCCATGGAGTGATTTTGGGGCTGATTATGTCATTGAGTCTTCAGGAGTTTTTACAACAGTGGAGAAAGCTTCATCACATTTGAAG
             |  |   ||   ||          | ||  | ||| | ||||| |  | |||      || ||   |    | |  ||   ||| |||||| |  | ||||| ||||||||||||||||| |||||| || | ||||||||||| |||||  |||| ||||| || || || || ||    || ||||| ||| |||| || |||
-------------gttttgcattgctatttcttggtctgcagttttaccgttttaccatttttta-----ctccaagatatgtctaagaattcacaacattttgcttctatattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAG

upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G79530.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatcatgagttgggctcttataattacaatagatgttacaaatgtactggtttacaaagtgttaaagagttctaaacaacagattaacatgtgcaaattttgttcatgtattcagAGATCCTGCAGAGATCCCATGGAGTGATTTTGGGGCTGATTATGTCATTGAGTCTTCAGGAGTTTTTACAACAGTGGAGAAAGCTTCATCACATTTGAAG
                            |  |  |   |      |  |   ||  |  |  |   |||           ||  |||  |  |     | ||  |  | |  ||||||||||  | ||||||||||||  |||| |||| |||||||||||  |||||||||| || || || || ||  ||   || ||| |||| |||||||||
--------------------------gtatcacctaaaagtggcatgttatcttctatcgc-tctgagaacaggtgttttcactttagaacttaatcctcttaattct-tcctcagAGATCCATCTGAGATCCCATGGGCTGATCTTGGAGCTGATTATGTTGTTGAGTCTTCCGGTGTATTCACCACCCTGTCAAAGGCTGCATCCCATTTGAAG

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|192322626|gb|FK014363.1|FK014363
EST:     GACTCTACTTTGGAAATTAATGGGAAGCATGTTAAAGTTGTGAGCAAAAG                         AGATCCTGCAGAGATCCCATGGAGCGATTTTGGGGCTGATTATGTCATTGA
genomic: GACTCTACTTTGGAAATTAATGGGAAGCATGTTAAAGTTGTGAGCAAAAGgtatcatgag ... atgtattcagAGATCCTGCAGAGATCCCATGGAGTGATTTTGGGGCTGATTATGTCATTGA
EST: gi|208297585|gb|GE090588.1|GE090588
EST:     GACTCTACTTTGGAAATTAATGGGAAGCATGTTAAAGTTGTGAGCAAAAG                         AGATCCTGCAGAGATCCCATGGAGTGATTTTGGGGCTGATTACGTCATTGA
genomic: GACTCTACTTTGGAAATTAATGGGAAGCATGTTAAAGTTGTGAGCAAAAGgtatcatgag ... atgtattcagAGATCCTGCAGAGATCCCATGGAGTGATTTTGGGGCTGATTATGTCATTGA
EST: gi|207800666|gb|GD775055.1|GD775055
EST:     GACTCTACTTTGGAAATTAATGGGAAGCATGTTAAAGTTGTGAGCAAAAG                         AGATCCTGCAGAGATCCCATGGAGTGATTTTGGGGCTGATTACGTCATTGA
genomic: GACTCTACTTTGGAAATTAATGGGAAGCATGTTAAAGTTGTGAGCAAAAGgtatcatgag ... atgtattcagAGATCCTGCAGAGATCCCATGGAGTGATTTTGGGGCTGATTATGTCATTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaaagagttctaaacaacagattaacatgtgcaaattttgttcatgtattcagAGATCCTGCAGAGATCCCATGGAGTGATTTTGGGGCTGATTATGTCATTGAGTCTTCAGGAGTTTTTACAACAGTGGAGAAAGCTTCATCACATTTGAAG
                     gattaac  putative branch site (score: 2)
                                  aaattttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcatgagttgggctcttataattacaatagatgttacaaatgtactggtttacaaagtgttaaagagttctaaacaacagattaacatgtgcaaattttgttcatgtattcagAGATCCTGCAGAGATCCCATGGAGTGATTTTGGGGCTGATTATGTCATTGAGTCTTCAGGAGTTTTTACAACAGTGGAGAAAGCTTCATCACATTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG