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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggagctttggttagaatgcctttgtacctttgaaaccaatatagccttggaattccatgcttgcttactcttcttccgttcttttttaattgtgatagAGCTATGGTGGATTTTGTGCAGTCACATATTTGAGTTTTGCACCACAAGGACTGAAGCAAGTCCTTATAACTGGAGGAATTCCTCCGATTGGCAGTGGAT

Basic information

species Glycine max
transcript GLYMA09G39020.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G39020.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g06820.1 (Oryza sativa), 3'ss of exon 2
---taggagcttt--ggttagaatgcctttgtacctttgaaaccaatatagccttggaattccatgcttgcttactcttcttccgttcttttttaattgtgatagAGCTATGGTGGATTTTGTGCAGTCACATATTTGAGTTTTGCACCACAAGGACTGAAGCAAGTCCTTATAACTGGAGGAATTCCTCCGATTGGCAGTGGAT
    ||||  |||   |||  | ||| | | || |||| |  | |  || | | |  |   ||||  |   |   |  ||| |  |  || ||  | |   | |||| ||||||||||||||||| || || |||||||||||||| ||| |||| |||||    || ||| | ||||| ||  |||| ||  | || ||||  |
cttcaggatattttatgttcaactgcttgtttatctttcattcgatgatggtcatctagcaccatattaattatgttgtctac--tctttcttcgact---acagAGTTATGGTGGATTTTGTGCTGTTACCTATTTGAGTTTTGCTCCAGAAGGCCTGAAATCTGTTCTTTTGACTGGGGGGCTTCCACCTCTAGGGAGTGCCT

upper sequence: GLYMA09G39020.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G075488_T02 (Zea mays), 3'ss of exon 3
--taggagctttggttagaatgcctttgtacctttgaaacca-atatagccttggaattcca-tgct-tgcttactct-tcttccgttcttttttaattgtgatagAGCTATGGTGGATTTTGTGCAGTCACATATTTGAGTTTTGCACCACAAGGACTGAAGCAAGTCCTTATAACTGGAGGAATTCCTCCGATTGGCAGTGGAT-
  |      ||| ||||   || | ||  |      ||  ||   ||    ||||  |   |   || ||||||  |  || ||      ||  ||||||    |||| ||||||||||||||||| || ||||||||||||||||| ||| |||| |||||    || ||| | ||||||||  | || || | | | ||    | 
cttgcagtttttagttat--tgtcctt-cattcacaaagtcatgcattcttttggggtagtagcactctgcttatgccatcatcgacctgttcgtaattgc---agAGTTATGGTGGATTTTGTGCCGTTACATATTTGAGTTTTGCTCCAGAAGGCCTGAAATCTGTTCTTTTGACTGGAGGGCTCCCACC-ACTAGGAGAACCTT

upper sequence: GLYMA09G39020.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G61540.1 (Arabidopsis thaliana), 3'ss of exon 3
taggagctttggttagaatgcctttgtacc-tttgaaaccaatatagccttggaattccatgcttgcttac-tcttcttccgttcttttttaattgtgatagAGCTATGGTGGATTTTGTGCAGTCACATATTTGAGTTTTGCACCACAAGGACTGAAGCAAGTCCTTATAACTGGAGGAATTCCTCCGATTGGCAGTGGAT
             ||   || |||||||   | |       || | || |  |   |      ||| ||   | ||| ||  || || || || | | | |||| |  ||||| ||||||||| | |||||| |||||||||||||  ||||||| || ||||| || ||||||||||||||||| || ||||| |  | ||
------------gtaatttgtctttgtattgtctattggtcatcttgcttcagttcttgtcatttgattttgtattcatctttttttcttcaaatct-acagAGTTTCGGTGGCTTTTGTGCACTTACATATCTGAGTTTTGCACCCGAAGGACTCAAACAAGTGCTAATAACTGGAGGAATTCCACCAATTGGTAAAGCAT

upper sequence: GLYMA09G39020.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0046g02160.t01 (Vitis vinifera), 3'ss of exon 3
taggagctttggttagaatgcctttgtacctttgaaaccaatatagccttggaattccatgctt------gcttactcttcttccgttcttttttaattgtgatagAGCTATGGTGGATTTTGTGCAGTCACATATTTGAGTTTTGCACCACAAGGACTGAAGCAAGTCCTTATAACTGGAGGAATTCCTCCGATTGGCAGTGGAT
      |     ||| |||    ||||    |  |   || || ||| ||||||||  |||  |        ||||         ||||||||||| ||     |||||| |||||| |||||||| || || |||||||||||||||||| ||||| |||| ||||||||| ||||||| ||||||||||| ||||| ||||| |
--aattcccgcattataatttgcttgtgg--tgcattgcattaaagctttggaattatatgactcataaaatttaccaaaagcttgttcttttttatttt--gcagAGCTTTGGTGGTTTTTGTGCGGTTACCTATTTGAGTTTTGCACCAAAAGGATTGAAACAAGTCCTTCTAACTGGGGGAATTCCTCCAATTGGAAGTGGCT

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|10843114|gb|BF066433.1|BF066433
EST:     GATGCTGGTCCTTGGACAATATTGGGACAG                         AGCTATGGTGGATTTTGTGCAGTCACATATTTGAGTTTTGCACCACAAGGA
genomic: GATGCTGGTCCTTGGACAATATTGGGACAGgtatttgagt ... attgtgatagAGCTATGGTGGATTTTGTGCAGTCACATATTTGAGTTTTGCACCACAAGGA
EST: gi|151394459|gb|EV264330.1|EV264330
EST:     TTCGAGTACGCCTTGTTCCAGATGCTGGTCCTTGGACAATATTGGGACAG                         AGCTATGGTGGATTTTGTGCAGTCACATATTTGAGTTTTGCACCACAAGGA
genomic: TTCGAGTACGCCTTGTTCCAGATGCTGGTCCTTGGACAATATTGGGACAGgtatttgagt ... attgtgatagAGCTATGGTGGATTTTGTGCAGTCACATATTTGAGTTTTGCACCACAAGGA
EST: gi|192301724|gb|FG997638.1|FG997638
EST:     TTCGAGTACGCCTTGTTCCAGATGCTGGTCCTTGGACAATATTGGGACAG                         AGCTATGGTGGATTTTGTGCAGTCACATATTTGAGTTTTGCACCACAAG-A
genomic: TTCGAGTACGCCTTGTTCCAGATGCTGGTCCTTGGACAATATTGGGACAGgtatttgagt ... attgtgatagAGCTATGGTGGATTTTGTGCAGTCACATATTTGAGTTTTGCACCACAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccttggaattccatgcttgcttactcttcttccgttcttttttaattgtgatagAGCTATGGTGGATTTTGTGCAGTCACATATTTGAGTTTTGCACCACAAGGACTGAAGCAAGTCCTTATAACTGGAGGAATTCCTCCGATTGGCAGTGGAT
                    cttactcttcttccgt  CT-rich tract
                                      ttttttaattgtgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taggagctttggttagaatgcctttgtacctttgaaaccaatatagccttggaattccatgcttgcttactcttcttccgttcttttttaattgtgatagAGCTATGGTGGATTTTGTGCAGTCACATATTTGAGTTTTGCACCACAAGGACTGAAGCAAGTCCTTATAACTGGAGGAATTCCTCCGATTGGCAGTGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - -gctttgg
- - - - - - - -gaatgcc
- - - - - - - - - - - - - -acctttg
- - - - - - - - - - - - - - - - - - - - - - - ccttgga