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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgatttcctcttatatttacgaaggtccagattcagtgtcctataaatttaactggttatgtttcttaagattttctcgtcactattattttgtaaagAACGGAATTGGTTCCTGCCTATGTGCGGTTGCTTCGAGACAATGAAGCTGAAGTACGGATTGCAGCTGCTGGGAAAGTGACCAAGTTTTGCCGGATATTA

Basic information

species Glycine max
transcript GLYMA02G10790.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 5
---------------attgatttcctcttatatttacgaag---------gtccagattc---agtgtcctataaatttaactggttatgtttcttaagattttctcgtcactattattttgtaaagAACGGAATTGGTTCCTGCCTATGTGCGGTTGCTTCGAGACAATGAAGCTGAAGTACGGATTGCAGCTGCTGGGAAAGTGACCAAGTTTTGCCGGATATTA
                 ||| |||  | |||  || |   |         |||   ||||   ||| || | ||||   |     || |       |  |  |     || ||  | ||  |   ||| | || ||||| ||||||||||| ||  | ||||| || ||||| |||||||| ||||| ||||||||||| ||||| || ||||||||||| ||||||
gtattatttgtcctagctgaattcaacctattattgcagggaaaccatgtgtctgaattcttgagtatcatgtaaacccatagccttttcaaatggattaactgtaaatctctgcttttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGAAGTGCGGATAGCAGCTGCTGGAAAAGTAACTAAGTTTTGCCGCATATTA

upper sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 5
----------------------------attgatttcct--cttatatttacgaaggtcc---agattcagtgtcctataaatttaactggttatgtttcttaagattttctcgtcactattattttgtaaagAACGGAATTGGTTCCTGCCTATGTGCGGTTGCTTCGAGACAATGAAGCTGAAGTACGGATTGCAGCTGCTGGGAAAGTGACCAAGTTTTGCCGGATATTA
                            | |||||   |  | || ||| |  |  |      | ||  |  |    || ||  |||   |  |||  || |    | ||     || |    |||   | ||    ||  ||||  | || ||||| ||  | ||  | |||||||| |||||||| ||||||||||||||||| ||||| || || || |||   ||||||
gtgttcaatcttctttctttatgttaaaaatgattctttgacataaattgattattgctttatacatggaaagattaatcaacataat--gccatgactcgtttactattgagaccattgccttttataatagGGGTGATCTGGTGTCAGCGTATGTTCGCCTTCTCTGTGACAATGAGGCTGAAGTGCGGATTGCAGCTGCTGGAAAAGTTACAAAATTCTGCAAAATATTA

upper sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 5
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 5
-attgatttcctcttatatttacgaaggtccagattcagtgtcctataaatttaactggttatgtttcttaagattttctcgtcactattattttgtaaagAACGGAATTGGTTCCTGCCTATGTGCGGTTGCTTCGAGACAATGAAGCTGAAGTACGGATTGCAGCTGCTGGGAAAGTGACCAAGTTTTGCCGGATATTA
  || |||   | |  |   ||  |  | |     |    || ||||   | ||  ||  | | ||| ||  ||     |      ||| || |  |  || ||||| |||||||| || |||||| | |||||  | |||||||| |||||||| || || ||||| || || |||||||||||||| || ||| | || 
tctttattctttttcgttcatataagagccttccatggtagttctatgtttgtacatgtatctttttattttgacacaatttatgttataatatc-tctagGACGGATTTGGTTCCAGCATATGTGAGATTGCTAAGGGACAATGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTG

upper sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 5
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------------------------------------attgatttcc----tcttatatttacgaaggtccagattcagtg--tcctataaatttaactggttatgt--ttcttaagattttctcgtcactattattttgtaaagAACGGAATTGGTTCCTGCCTATGTGCGGTTGCTTCGAGACAATGAAGCTGAAGTACGGATTGCAGCTGCTGGGAAAGTGACCAAGTTTTGCCGGATATTA
                                                                                 | ||| |||     | ||   |    | | |||||  ||   ||  || | | |||  |  |  ||  ||  || || | | |||||| |     |||| |  | ||| |||||  |||| ||||| ||||  ||  | ||| | || ||||| || ||||| ||||| ||||||||||| ||||| ||||||||||| || || |||
gtaagcagtgatggttgaagttagttatggtttaatgtagtattgacctttagtatgcaattctatatcaaacaatagattactgacttcagaggtatttggtacttggaagtccatgtttgttgagtcatcttaataaatttctttgagtcgttttttatactttctcatgtgccttatgt-attaagGACGGATCTGGTGCCTGCATATGCTCGTCTACTTTGTGATAATGAGGCAGAAGTTCGGATAGCAGCTGCTGGAAAAGTTACCAAGTTTTGTCGCATTTTA

upper sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 5
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------------attgatttcctcttatatttacgaaggtccagattcag--tgtcctataaatttaactggtt--atgtttc--ttaagattttctcgtcactatt------attttgta----aagAACGGAATTGGTTCCTGCCTATGTGCGGTTGCTTCGAGACAATGAAGCTGAAGTACGGATTGCAGCTGCTGGGAAAGTGACCAAGTTTTGCCGGATATTA
                                             |||||   ||  | || |    ||  |  | || ||     ||| |||   ||||     |  ||| | |  || |  |  ||| |  ||||||       | || ||    ||| |||||  |||| ||||| ||||||||  | ||||| || ||||||||||||||||| || |||||||| || ||||| || |||||||| |||||  ||
gtaagaacgttttgcataaacctaatgcagcatgttttaatacctttgatgggctaatttaatgttcaatatagaaatgcatatcatccaataggcttaaggaacttgatgatcccatttacttcctcttgatactatttactgtgtcttctattttaagGACGGAGCTGGTGCCTGCATATGTGCGCCTACTTCGTGATAATGAAGCTGAAGTACGCATAGCAGCTGCCGGAAAAGTTACAAAGTTTTGTCGGATTCTA

upper sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 4
attgatttcctcttatatttacgaaggtccagattcagtgtcctataaatttaactggttatgtttcttaagattttctc----gtcactattattttgtaaagAACGGAATTGGTTCCTGCCTATGTGCGGTTGCTTCGAGACAATGAAGCTGAAGTACGGATTGCAGCTGCTGGGAAAGTGACCAAGTTTTGCCGGATATTA
  | || ||   || |  |  |  |  ||  ||||   | || |      ||   |  || | ||| ||    |||| |     || |||  |||  | | ||||||||| |||||||| || ||| ||||||| |||||||| ||||| ||||||||||| || ||||||||||| ||||| || || || || | ||| |||
--taatctcaagttttcctggctta--tcttgatttcctttctttctttctttctttctttttttttttttttttttttttgtggtgactgatatcattttaagAACGGACTTGGTTCCCGCTTATATGCGGTTACTTCGAGATAATGAGGCTGAAGTACGAATAGCAGCTGCTGGCAAAGTAACTAAATTCTGTCAGATCTTA

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|192325432|gb|FK017188.1|FK017188
EST:     GCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAG                         AACGGAATTGGTTCCTGCCTATGTGCGGTTGCTTCGAGACA
genomic: GCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAGgtattatgtt ... ttttgtaaagAACGGAATTGGTTCCTGCCTATGTGCGGTTGCTTCGAGACA
EST: gi|7146818|gb|AW508740.1|AW508740
EST:     GCAAATCAATTGTATGAGCTGTGTGAAGCTGTAGGCCCTGAACCTACCAG                         AACGGAATTGGTTCCTGCCTATGTGCGGTTGCTTCGAGACAATGAAGCTGA
genomic: GCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAGgtattatgtt ... ttttgtaaagAACGGAATTGGTTCCTGCCTATGTGCGGTTGCTTCGAGACAATGAAGCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatttaactggttatgtttcttaagattttctcgtcactattattttgtaaagAACGGAATTGGTTCCTGCCTATGTGCGGTTGCTTCGAGACAATGAAGCTGAAGTACGGATTGCAGCTGCTGGGAAAGTGACCAAGTTTTGCCGGATATTA
   atttaac  putative branch site (score: 3)
                                          ttatttt  putative PPT
                                      actattattttgtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgatttcctcttatatttacgaaggtccagattcagtgtcctataaatttaactggttatgtttcttaagattttctcgtcactattattttgtaaagAACGGAATTGGTTCCTGCCTATGTGCGGTTGCTTCGAGACAATGAAGCTGAAGTACGGATTGCAGCTGCTGGGAAAGTGACCAAGTTTTGCCGGATATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - -ttcagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - -actggtt