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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgaagttttttttctagccatgtgctctggattgatatttattggacctcattttgtttatttgcacaaggttttataatttatgtccaatgtgacagGCTTATCAAGACTCAACAAAAGAGAAGCGACGTGCACAAATAGCCCAAG

Basic information

species Glycine max
transcript GLYMA05G30430.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 3
tatgaagttttttttctagc-catgtgctctggattgatatttattggacctcattttgtttat---ttgcac-aaggttttataatttatgtccaatgtgacagGCTTATCAAGACTCAACAAAAGAGAAGCGACGTGCACAAATAGCCCAAG
|  || | || |||| || |  ||    |||    | ||| ||  ||  | |||||  |||| |   | |  | ||     | |    | ||||  |||||||||||||||||||| |||||||||||||| || ||||| ||||| |||||||
tgagatgattattttttatcatatcaaatctatgct-atagtttctg--cttcattgagtttgtgcttggtgctaaaaaactgtgcactgtgtc--atgtgacagGCTTATCAAGATTCAACAAAAGAGAAACGTCGTGCTCAAATTGCCCAAG

upper sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S31_68V6.1 (Physcomitrella patens), 3'ss of exon 3
tatgaagttttttttc-tagccatgtgctctggattgatatttattggacctcattttgtttatttgcacaaggttttataatttatgtccaatgtgacagGCTTATCAAGACTCAACAAAAGAGAAGCGACGTGCACAAATAGCCCAAG
 |  |  |       |  |     ||    ||   |    |  ||      |    ||    || ||      ||   |   |  ||||    ||||||||||||||||||| ||| | ||||||||  |||||||||| || || ||||
-agaatatccgggaacacaaattagtttattgcggttgcttccataaagaatagagtttgggatgtgacttttgtacgactctccatgttgtttgtgacagGCTTATCAAGAATCATCCAAAGAGAAAAGACGTGCACAGATTGCTCAAG
















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|209727601|gb|BW669925.1|BW669925
EST:     ATTTGCGTCTTGATCATCTCCTAGTTAGAACTTATATTGATCCAAATGAG                         GCTTATCAAGACTCAACAAAAGAGAAGCGACGTGCACAAATAGCCCAAG
genomic: ATTTGCGTCTTGATCATCTCCTAGTTAGAACTTATTTTGATCCAAATGAGgttagaaata ... aatgtgacagGCTTATCAAGACTCAACAAAAGAGAAGCGACGTGCACAAATAGCCCAAG
EST: gi|151408433|gb|EV278241.1|EV278241
EST:     TTGCGTCTTTGATCATCTCCTAGTTAGAACTTATTTTTGATCCAAATGAG                         GCTTATCAAGACTCAACAAAAGAGAAAGCGACGTGCACAAATAGCCCAAG
genomic: TTGCGTC-TTGATCATCTCCTAGTTAGAACTTA-TTTTGATCCAAATGAGgttagaaata ... aatgtgacagGCTTATCAAGACTCAACAAAAGAG-AAGCGACGTGCACAAATAGCCCAAG
EST: gi|208188792|gb|GD981376.1|GD981376
EST:     ATTTGCGTCATGATCATCTCCTAGTTAGAACTTATTTTGATCCAAATGAG                         GCTTATCAAGACTCAACAAAAGAGAAGCGACGTGCACAAATAGCCCAAG
genomic: ATTTGCGTCTTGATCATCTCCTAGTTAGAACTTATTTTGATCCAAATGAGgttagaaata ... aatgtgacagGCTTATCAAGACTCAACAAAAGAGAAGCGACGTGCACAAATAGCCCAAG
EST: gi|192300630|gb|FG989632.1|FG989632
EST:     ATTTGCGTCTTGATCATCTCCTAGTTAGAACTTATTTTGATCCAAATGAG                         GCTTATCAAGACTCAACAAAAGAGAAGCGACGTGCACAAATAGCCCAAG
genomic: ATTTGCGTCTTGATCATCTCCTAGTTAGAACTTATTTTGATCCAAATGAGgttagaaata ... aatgtgacagGCTTATCAAGACTCAACAAAAGAGAAGCGACGTGCACAAATAGCCCAAG
EST: gi|213609045|gb|DB958814.1|DB958814
EST:     ATTTGCGTCTTGATCATCTCCTAGTTAGAACTTATTTTGATCCAAATGAG                         GCTTATCAAGACTCAACAAAAGAGAAGCGACGTGCACAAATAGCCCAAG
genomic: ATTTGCGTCTTGATCATCTCCTAGTTAGAACTTATTTTGATCCAAATGAGgttagaaata ... aatgtgacagGCTTATCAAGACTCAACAAAAGAGAAGCGACGTGCACAAATAGCCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggacctcattttgtttatttgcacaaggttttataatttatgtccaatgtgacagGCTTATCAAGACTCAACAAAAGAGAAGCGACGTGCACAAATAGCCCAAG
                        aaggttttataattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgaagttttttttctagccatgtgctctggattgatatttattggacctcattttgtttatttgcacaaggttttataatttatgtccaatgtgacagGCTTATCAAGACTCAACAAAAGAGAAGCGACGTGCACAAATAGCCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC