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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaattatggatcttattattatcatcttagtattaaatttttcttaatttatgttatgtatgcttcgtaagattcaaaactttactcatacttgaacagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG

Basic information

species Glycine max
transcript GLYMA03G33000.6
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33000.4 (Glycine max), 3'ss of exon 7
lower sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 5
acaatta-tggatcttattattatcatcttagtattaaatttttcttaatttatgttatgtatgcttcgtaagattcaaaactttactcatacttga-acagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG
  ||| | |  |   ||| |  ||||||  || ||   | | |   | ||||   |  |  |     | |   ||   || |||     ||| ||   |||||| |||||  | ||||| |||||||||||||||||||| |||||||| ||||| ||||||||||||
ttaatcaatcaagtctataagcatcatc--agcatctcagtctgtcttatttgactggtagaaaacacatctcatgtgaatcttgttgaatattttctacagGAACCGGTGATCCCAGGATGCTTTCTTCGGGCCAAAGCTATTGGTCTGATGCCAATGATTGATCAG

upper sequence: GLYMA03G33000.4 (Glycine max), 3'ss of exon 7
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 5
acaattatggatcttattattatcatcttagtattaaatttttcttaatttatgttatgtatg-----cttcgtaagattcaaaactttactcatacttgaacagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG
|   || |||||    |  ||    ||| | ||||  || || |  |      |||||  |||       || ||    | |   ||||  ||| || |  |||||| || ||||||||||| |||||||| ||||| ||||| |||||||||||||| ||||||||||||
aattttttggat---gtgcttggtttctgaatattccatattacaaagcaatggttataaatggaaactctcatattccttatggcttt--tcaaacatttacagGAACCAGTTCTTCCAGGATGCTTTCTCCGGGCTAAAGCTATTGGTCTCATGCCTATGATTGATCAG

upper sequence: GLYMA03G33000.4 (Glycine max), 3'ss of exon 7
lower sequence: EFJ33488 (Selaginella moellendorffii), 3'ss of exon 4
acaattatggatcttattattatcatcttagtattaaatttttcttaatttatgttatgtatgcttcgtaagattcaaaactttactcatacttgaacagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG
   |   |  ||||  || ||    | ||     |   ||| ||||| |  | | |       ||  |  |  |    ||||||  |||    |||||||||||| |||||||||||    ||||| || |||||||| || || |||||||| ||||| ||||||
gtgagcttccatctctttttttctttttt--ccctggttttgtcttagtaaacgct-------ctcggccaagt---gaacttt--tca----tgaacagGAGCCTGTTCTTCCAGGAGCGTTTCTCCGAGCCAAAGCCATCGGGCTCATGCCGATGATCGATCAG

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|193357096|gb|FK323568.1|FK323568
EST:     GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAG                         GAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAACGCAATTGGTCTCATG
genomic: GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAGgtatttatat ... acttgaacagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
EST: gi|207831666|gb|GD801720.1|GD801720
EST:     GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAG                         GAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
genomic: GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAGgtatttatat ... acttgaacagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
EST: gi|151404690|gb|EV274504.1|EV274504
EST:     GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAG                         GAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
genomic: GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAGgtatttatat ... acttgaacagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
EST: gi|298199436|gb|HO042799.1|HO042799
EST:     GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAG                         GAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
genomic: GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAGgtatttatat ... acttgaacagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
EST: gi|7925031|gb|AW831057.1|AW831057
EST:     GTACTATTTGTGAGGACAGTGATCCACTGGATGTCTTGATTATTATGCAG                         GAGCCGGTTCTTTCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
genomic: GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAGgtatttatat ... acttgaacagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
EST: gi|8827754|gb|BE211484.1|BE211484
EST:     GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAG                         GAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
genomic: GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAGgtatttatat ... acttgaacagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
EST: gi|192324459|gb|FK015810.1|FK015810
EST:     GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAG                         GAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
genomic: GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAGgtatttatat ... acttgaacagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
EST: gi|5510301|gb|AI856743.1|AI856743
EST:     GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAG                         GAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
genomic: GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAGgtatttatat ... acttgaacagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
EST: gi|10236851|gb|BE805739.1|BE805739
EST:     GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAG                         GAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
genomic: GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAGgtatttatat ... acttgaacagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
EST: gi|208275603|gb|GE078223.1|GE078223
EST:     GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAG                         GAGCCGGTTCTTCCAGGTTG
genomic: GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAGgtatttatat ... acttgaacagGAGCCGGTTCTTCCAGGTTG
EST: gi|16105384|gb|BI893124.1|BI893124
EST:     GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAG                         GAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
genomic: GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAGgtatttatat ... acttgaacagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
EST: gi|192296495|gb|FG989111.1|FG989111
EST:     GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAG                         GAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
genomic: GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAGgtatttatat ... acttgaacagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
EST: gi|207702226|gb|GD682981.1|GD682981
EST:     GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAG                         GAGCCGGTTCTTCCAGGT
genomic: GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAGgtatttatat ... acttgaacagGAGCCGGTTCTTCCAGGT
EST: gi|17022987|gb|BM094021.1|BM094021
EST:     GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAG                         GAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG
genomic: GTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAGgtatttatat ... acttgaacagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttatgttatgtatgcttcgtaagattcaaaactttactcatacttgaacagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG
 tcttaat  putative branch site (score: 3)
                               aaaacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaattatggatcttattattatcatcttagtattaaatttttcttaatttatgttatgtatgcttcgtaagattcaaaactttactcatacttgaacagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA