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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttttaaaatggataaagaaaggaaatatgaatatgagacagatgatgtggttgcatttggcatttaattgattttgttgtcaatctcattgccgtagGTCATATGGGTTGAGCACGTAGAAGTGGATGACAGAGGTGTCCATAATCTATACAAGCAGCTTGTTAGCTCGGGGCATGCATTTGGTGCAAAACGTTGGA

Basic information

species Glycine max
transcript GLYMA12G32050.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G32050.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv12s0059g02310.t01 (Vitis vinifera), 3'ss of exon 7
-------------tatttttaaaatggataaagaaaggaaatatg--aata-tgagacagatgatgtggttgc--atttggcatttaattgattttgttgtcaatctcat-tgccgtagGTCATATGGGTTGAGCACGTAGAAGTGGATGACAGAGGTGTCCATAATCTATACAAGCAGCTTGTTAGCTCGGGGCATGCATTTGGTGCAAAACGTTGGA
              ||   ||||    |  || |||  |     |  | || |||     |  |  |   | |  ||| |   | | ||| | |||  ||     ||  | |||| ||||| | |||||||||||| || ||||| |||||  ||||||| |||||| |||| |||||| | |||| ||| || | ||||||||| || ||| | ||| 
gtaaataaatgatcataactaaatgccactaaaaaactactctagccagtactgaatttcaacacattaatactaattagttctctcatttaattttctgatggccttttatgccttagGTTACATGGGTTGAGCATGTTGAAGTTGATGATCGAGGTGTTCATAATATATATAAGCAGTTAGTTAACTCTGGTCTTGCATTTGGGGCGAAAAGATGGG
















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|7327253|gb|AW620975.1|AW620975
EST:     GAAGGCCCTCAGGTTGCTTAATTCAAGAAATGCCCAATGGCTACTCTAAG                         GTCATATGGGTTGAGCACGTAGAAGTGGATGACAGAGGTGTCCATAATCTA
genomic: GAAGGCCCTCAGGTTGCTTAATTCAAGAAATGCCCAATGGCTACTCTAAGgttaggatta ... attgccgtagGTCATATGGGTTGAGCACGTAGAAGTGGATGACAGAGGTGTCCATAATCTA
EST: gi|208204360|gb|GE002363.1|GE002363
EST:     GAAGGCCCTCAGGTTGCTTAATTCAAGAAATGCCCAATGGCTACTCTAAG                         GTCATATGGGTTGAGCACG
genomic: GAAGGCCCTCAGGTTGCTTAATTCAAGAAATGCCCAATGGCTACTCTAAGgttaggatta ... attgccgtagGTCATATGGGTTGAGCACG
EST: gi|193543148|gb|FK502453.1|FK502453
EST:     GAAGGCCCTCAGGTTGCTTAATTCAAGAAATGCCCAATGGCTACTCTAAG                         GTCATATGGGTTGAGCAC
genomic: GAAGGCCCTCAGGTTGCTTAATTCAAGAAATGCCCAATGGCTACTCTAAGgttaggatta ... attgccgtagGTCATATGGGTTGAGCAC
EST: gi|208207435|gb|GE002218.1|GE002218
EST:     GAAGGCCCTCAGGTTGCTTAATTCAAGAAATGCCCAATGGCTACTCTAAG                         GTCATATGGGTTGAGCACGTAGAAGTGGATGACAGAGGTGTCCATAATCTA
genomic: GAAGGCCCTCAGGTTGCTTAATTCAAGAAATGCCCAATGGCTACTCTAAGgttaggatta ... attgccgtagGTCATATGGGTTGAGCACGTAGAAGTGGATGACAGAGGTGTCCATAATCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgtggttgcatttggcatttaattgattttgttgtcaatctcattgccgtagGTCATATGGGTTGAGCACGTAGAAGTGGATGACAGAGGTGTCCATAATCTATACAAGCAGCTTGTTAGCTCGGGGCATGCATTTGGTGCAAAACGTTGGA
                       aattgat  putative branch site (score: 4)
                                         tctcatt  putative PPT
                   atttaattgattttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttttaaaatggataaagaaaggaaatatgaatatgagacagatgatgtggttgcatttggcatttaattgattttgttgtcaatctcattgccgtagGTCATATGGGTTGAGCACGTAGAAGTGGATGACAGAGGTGTCCATAATCTATACAAGCAGCTTGTTAGCTCGGGGCATGCATTTGGTGCAAAACGTTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - -gtggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatctc