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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatggttattattttgctagcatgattttccttttcagcttcaggaaatttgatggtattgtcatgtatagctagataatgtactcttgtttcctacagGCGGTTGAGATATCTAGCAATGAATACGAACCTTCTGAAAGGGACATAGTATATGCAGAAGGGGTTACTCAGGGAAATGGTTTGGCTTTCATGGAATTTT

Basic information

species Glycine max
transcript GLYMA09G34300.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G34300.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv02s0012g02570.t01 (Vitis vinifera), 3'ss of exon 6
aaatggttattattttgctagcatgattttccttttcagcttcaggaa-atttgatggtattgtcatgta-tagctagataatgtactcttgtttcctacagGCGGTTGAGATATCTAGCAATGAATACGAACCTTCTGAAAGGGACATAGTATATGCAGAAGGGGTTACTCAGGGAAATGGTTTGGCTTTCATGGAATTTT
   |       |  || |    |   ||| |  ||  | ||  |     | |       ||||  ||  | ||| ||  || | |  | || || |   ||||| |||||| | || ||||||||||| |||||||| || ||||||||| |||||||||||||||| || || || ||||||||||||||||| ||||| |
-tcttccacccaaatttcagttacagtttacgattagatctgaatattcaataagcaacattgatatcgactagttatttactttg-ttttcttcctctcagGCTGTTGAGGTCTCAAGCAATGAATATGAACCTTCAGAGAGGGACATACTATATGCAGAAGGGGTCACACAAGGGAATGGTTTGGCTTTCATAGAATTCT
















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|308098251|gb|HO759992.1|HO759992
EST:     ACTTCTTAAGCCGG                         GCGGTTGAGATATCTAGCAATGAATACGAACCTTCTGAAAGGGACATAGTA
genomic: ACTTCTTAAGCCGGgtaattgttt ... tttcctacagGCGGTTGAGATATCTAGCAATGAATACGAACCTTCTGAAAGGGACATAGTA
EST: gi|9986960|gb|BE661068.1|BE661068
EST:     AAGATGAGCTTCACTTTCTTCCAGATGTTGCCGAGTACTTCTTAAGCCGG                         GCGGTTGAGATATCTAGCAATGAATACGAACCTTCTGAAAGGGACATAGTA
genomic: AAGATGAGCTTCACTTTCTTCCAGATGTTGCCGAGTACTTCTTAAGCCGGgtaattgttt ... tttcctacagGCGGTTGAGATATCTAGCAATGAATACGAACCTTCTGAAAGGGACATAGTA
EST: gi|151395784|gb|EV265661.1|EV265661
EST:     AAGATGAGCTTCACTTTCTTCCAGATGTTGCCGAGTACTTCTTAAGCCGG                         GCGGTTGAGATATCTAGCAATGAATACGAACCTTCTGAAAGGGACATAGTA
genomic: AAGATGAGCTTCACTTTCTTCCAGATGTTGCCGAGTACTTCTTAAGCCGGgtaattgttt ... tttcctacagGCGGTTGAGATATCTAGCAATGAATACGAACCTTCTGAAAGGGACATAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatttgatggtattgtcatgtatagctagataatgtactcttgtttcctacagGCGGTTGAGATATCTAGCAATGAATACGAACCTTCTGAAAGGGACATAGTATATGCAGAAGGGGTTACTCAGGGAAATGGTTTGGCTTTCATGGAATTTT
   atttgat  putative branch site (score: 5)
                                     tactcttgtttcct  putative PPT
                            tagataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatggttattattttgctagcatgattttccttttcagcttcaggaaatttgatggtattgtcatgtatagctagataatgtactcttgtttcctacagGCGGTTGAGATATCTAGCAATGAATACGAACCTTCTGAAAGGGACATAGTATATGCAGAAGGGGTTACTCAGGGAAATGGTTTGGCTTTCATGGAATTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - gcatgat
- - - - - - - - - - - - - - - - - - cagcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - gatggta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtat