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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcccgaagatatttttattccttgaatctttggtcatttatttaaatagtttaatatatttatgtaaaatttccattttattatttgttccttctgcccttcagTGTGGGGATCAAGAGCGTTGTAGATGAGAATGAAAGAAAATCATTGGGTGGTCATCATGGTGCTGCTTGTCCTGCATGTGAGATGGCGGTTGTTTGGATG

Basic information

species Glycine max
transcript GLYMA17G01500.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G01500.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G62290.2 (Arabidopsis thaliana), 3'ss of exon 9
gtgagtcccgaagatatttttattccttgaatctttggtcatttatttaaatagtttaatatatttatgtaaaatttccattttattatttgttccttctgcccttcagTGTGGGGATCAAGAGCGTTGTAGATGAGAATGAAAGAAAATCATTGGGTGGTCATCATGGTGCTGCTTGTCCTGCATGTGAGATGGCGGTTGTTTGGATG
                |   | | |  ||| | | |   ||  ||  ||  | || || ||| |  || |    ||  | | || |    ||||   ||     || ||| |||||||  |    || || ||  || |  | | || |||||   |||||| ||  |  || | ||||||||||||||| ||||||||||| ||||| 
---------------gtaaatttccaatgattttctaaccaaataactatct-gtctattatgtacat-tggtgttctcttattgtgcggtgttgtatca--tgtttagTATGGGGATTGAATCGGTGGTGGACAAGGAAAACACAAGATCATCTAGTGGTCTTCGAGACGCGGGTTGTCCTGCATGTGAAATGGCGGTTGTGTGGATA
















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|193648227|gb|FK595308.1|FK595308
EST:     ATCTGTTCCCGAATTGGATTGTGCGCATTTGATGGGACTCATGGTGTTGA                         TGTGGGGATCAAGAGCGTTGTA
genomic: ATCTGTTCCCGAATTGGATTGTGCGCATTTGATGGGACTCATGGTGTTGAgtgagtcccg ... tgcccttcagTGTGGGGATCAAGAGCGTTGTA
EST: gi|13790574|gb|BG653165.1|BG653165
EST:     ATCTGTTCCCGAATTGGATTGTGCGCATTTGATGGGACTCATGGTGTTGA                         TGTGGGGATCAAGAGCGTTGTAGATGAGAATGAAAGAAAATCATTGGGTGG
genomic: ATCTGTTCCCGAATTGGATTGTGCGCATTTGATGGGACTCATGGTGTTGAgtgagtcccg ... tgcccttcagTGTGGGGATCAAGAGCGTTGTAGATGAGAATGAAAGAAAATCATTGGGTGG
EST: gi|207800501|gb|GD773784.1|GD773784
EST:     ATCTGTTCCCGAATTGGATTGTGCGCATTTGATGGGACTCATGGTGTTGA                         TGTGGGGATCAAGAGCGTTGTAGATGAGAATGAAAGAAAATCATTGGGTGG
genomic: ATCTGTTCCCGAATTGGATTGTGCGCATTTGATGGGACTCATGGTGTTGAgtgagtcccg ... tgcccttcagTGTGGGGATCAAGAGCGTTGTAGATGAGAATGAAAGAAAATCATTGGGTGG
EST: gi|26047831|gb|CA784491.1|CA784491
EST:     ATCTGTTCCCGAATTGGATTGTGCGCATTTGATGGGACTCATGGTGTTGA                         TGTGGGGATCAAGAGCGTTGTAGATGAGAATGAAAGAAAATCATTGGGTGG
genomic: ATCTGTTCCCGAATTGGATTGTGCGCATTTGATGGGACTCATGGTGTTGAgtgagtcccg ... tgcccttcagTGTGGGGATCAAGAGCGTTGTAGATGAGAATGAAAGAAAATCATTGGGTGG
EST: gi|37996199|gb|CF807788.1|CF807788
EST:     ATCTGTTCCCGAATTGGATTGTGCGCATTTGATGGGACTCATGGTGTTGA                         TGTGGGGATCAAGAGCGTTGTAGATGAGAATGAAAGAAAATCATTGGGTGG
genomic: ATCTGTTCCCGAATTGGATTGTGCGCATTTGATGGGACTCATGGTGTTGAgtgagtcccg ... tgcccttcagTGTGGGGATCAAGAGCGTTGTAGATGAGAATGAAAGAAAATCATTGGGTGG
EST: gi|193435291|gb|FK400323.1|FK400323
EST:     ATCTGTTCCCGAATTGGATTGTGCGCATTTGATGGGACTCATGGTGTTGA                         TGTGGGGATCAAGAGCGTTGTAGATGAGAATGAAAGAAAATCATTGGGTGG
genomic: ATCTGTTCCCGAATTGGATTGTGCGCATTTGATGGGACTCATGGTGTTGAgtgagtcccg ... tgcccttcagTGTGGGGATCAAGAGCGTTGTAGATGAGAATGAAAGAAAATCATTGGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaatatatttatgtaaaatttccattttattatttgttccttctgcccttcagTGTGGGGATCAAGAGCGTTGTAGATGAGAATGAAAGAAAATCATTGGGTGGTCATCATGGTGCTGCTTGTCCTGCATGTGAGATGGCGGTTGTTTGGATG
 gtttaat  putative branch site (score: 4)
                          ttttattatttgttcc  putative PPT
     tatatttatgtaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcccgaagatatttttattccttgaatctttggtcatttatttaaatagtttaatatatttatgtaaaatttccattttattatttgttccttctgcccttcagTGTGGGGATCAAGAGCGTTGTAGATGAGAATGAAAGAAAATCATTGGGTGGTCATCATGGTGCTGCTTGTCCTGCATGTGAGATGGCGGTTGTTTGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG