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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttttcttttgttcttacaatgaaatgttgtaacagcatgttaggatctgattgcaaggtatgagacttgagttcattatttgtctgtcaattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGATA

Basic information

species Glycine max
transcript GLYMA08G13560.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 12
ttcttttcttttgttcttacaatgaaatgttgta-acagcatgttaggatctgattgcaaggtatgagacttgagttcattatt--tgtctgtcaattg---atagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGATA
        |   ||   ||    | |  |  ||  |  || | ||    | |||| |  |  |||||    |    |  |||||  || |||  || |    | ||||||| || || || |||||||||||| | ||||| ||||| ||  ||||||| |  |||||||| |||||||||||||| || |||||||||||||| |
------cataaagtggctattgagcatcgaagtgcattgcttttttcattttgatggttatttatgaattctattatggttattcttgactggaaacttgttacagGTTGTAAAAAGTTTTTCATCTGGTAAACGGGAAGGGGGAGATTTCCTTGCAGCTTCCGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA

upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 12
ttcttttcttttgttcttacaatgaaatgttgtaacagcatgttagg-atctgattgcaaggtatgagacttgagttcattatttgtctgtcaattgat---agGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGATA
   ||  |    | | |   |   ||     |  |    || | ||  || | | ||  |  | |    ||||   | || |||    ||  ||||  |   ||||||||||||| |||||||| |||||  ||||||| ||||| ||||||||||| |  |||||||| |||||||||||||| || |||||||||||||| |
--tttaacaaaggctgtagaagataagcaaggcgaggatatctcagccatttaactgttatttctagtgcttgg--ttatgattgccttgaaaatttgtttcagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCAGCTTCAGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA

upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 13
lower sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 13
ttcttttcttttgttcttacaatgaaatgttgtaacagcatgttaggatctgattgcaaggtatgagacttgagttcattatttgtctg--tcaattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGATA
        |    |||   ||| |   |  || ||     ||| |   ||       ||  || ||   || |  |  || | | |  |  ||  ||   ||||||||||||| |||||||| ||||| || ||||| ||||| ||||| ||||| ||||| ||  | |||||||| ||||| |||||  | || ||||| |
-------gtaaatttccagcaacggtctcctgcaaatcagtgtcattgtcatgcca-aaactaagattgttcacatgcttctatattggaatccttttgcagGTTGTGAAGAGTTTCTCATCCGGTAATAGGGAAGGAGGAGATTTTGTAGCAGCATGTGTATCTACAAAAGGAGATTGGATATACTGCATCGGCGAAGACA

upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 13
---ttcttttcttttgttcttacaatgaaatgttgtaacagcatgttaggatctg-attgcaaggtatgagacttgagttcattatttgtctgtcaattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGATA
      |   |    |    ||| || | |  | ||       | | |   | ||   |||| | ||     |   |    |  |  ||| ||| |      ||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||||||||| ||||| ||||||||||||||||| |||||||||||||| |
ggtgcgtaaccaaggggaactacgatcaga-atggttgtgatttctaaatgtttgtgatgcaggttacttatcaaaaaaaaaaaaaatgtttgtgat---gcagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCAGCCTGTGTCTCACCCAAAGGAGAATGGATTTATTGTGTTGGTGAAGACA

upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 13
lower sequence: EFJ30597 (Selaginella moellendorffii), 3'ss of exon 11
ttcttttcttttgttcttacaatgaaatgttgtaacagcatgttaggatctgattgcaaggtatgagacttgagttcattatttgtctgtcaattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGATA
                                         ||     |||  || |    | || | ||    ||     |  | || |  ||||  ||||||| ||||||||||| ||||| |||||||| || || || || || || ||||| || || || |||||||| |||||||| || ||||| ||||| |
-----------------------------------------gtgcatttctcctttcc---tttgtgcctgatttttcccttccggctttgcattggcagGTTGTCAAGAGCTTCTCGTCTGGCAAAAGAGAGGGTGGCGATTTCGTCGCGGCCTGCGTCTCGCCAAAAGGAGACTGGATTTATTGCGTTGGAGAAGACA

upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 13
lower sequence: EFJ15973 (Selaginella moellendorffii), 3'ss of exon 11
ttcttttcttttgttcttacaatgaaatgttgtaacagcatgttaggatctgattgcaaggtatgagacttgagttcattatttgtctgtcaattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGATA
                                         ||     |||  ||      | || | ||    ||     |  | || |  ||||  ||||||| ||||||||||| ||||| |||||||| || || || || || || ||||| || || || |||||||| |||||||| || ||||| ||||| |
-----------------------------------------gtgcatttctccttttc---tttgtgcctgatttttcccttccggctttgcattggcagGTTGTCAAGAGCTTCTCGTCTGGCAAAAGAGAGGGTGGCGATTTCGTCGCGGCCTGCGTCTCGCCAAAAGGAGACTGGATTTATTGCGTTGGAGAAGACA

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|208155709|gb|GD958470.1|GD958470
EST:     TTGTTTGTAACAAAACGTCATCCATATATATCATGACACTTCAAGGACAG                         GTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCA
genomic: TTGTTTGTAACAAAACGTCATCCATATATATCATGACACTTCAAGGACAGgtataccgaa ... caattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCA
EST: gi|209710369|gb|BW681268.1|BW681268
EST:     TTGTTTGTAACAAAACGTCATCCATATATATCATGACACTTCAAGGACAG                         GTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCA
genomic: TTGTTTGTAACAAAACGTCATCCATATATATCATGACACTTCAAGGACAGgtataccgaa ... caattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatctgattgcaaggtatgagacttgagttcattatttgtctgtcaattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGATA
  atctgat  putative branch site (score: 4)
                             ttcattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttttcttttgttcttacaatgaaatgttgtaacagcatgttaggatctgattgcaaggtatgagacttgagttcattatttgtctgtcaattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA