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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atattcttgttaaccgtctattttagttcttgtgggttttttttttattctatatgtttattgttttaaaataatcttatactttatgttaatattttagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTTGTCTTCCAG

Basic information

species Glycine max
transcript GLYMA10G28530.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G28530.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 3'ss of exon 3
-atattcttgttaaccgtctattttagttcttgtgggttttttttttattctatatgtttattgttttaaaataatcttatactttatgttaata-ttttagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTTGTCTTCCAG
 |||   |  |      | | |||  | | || |   ||| || |  ||  | | |    |||||||     ||||   |   | ||| || ||| ||  |||| ||||| |||||||| ||||| ||||| ||||||||||||||||||||||| || || 
tatacattaatctctaatttgttt-ggatgttctacatttattctccatgat-tgtcccaattgtttatctctaatgccaatttgtatatttataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTTGTTTTTCAA
















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|5676842|gb|AI937972.1|AI937972
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... aatattttagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|23726962|gb|BU761494.1|BU761494
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... aatattttagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|298194802|gb|HO043274.1|HO043274
EST:     GGCATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... aatattttagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|254344095|gb|GR851005.1|GR851005
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... aatattttagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|21602288|gb|BQ612619.1|BQ612619
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... aatattttagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattctatatgtttattgttttaaaataatcttatactttatgttaatattttagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTTGTCTTCCAG
                                         tgttaat  putative branch site (score: 3)
           tttattgttttaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atattcttgttaaccgtctattttagttcttgtgggttttttttttattctatatgtttattgttttaaaataatcttatactttatgttaatattttagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTTGTCTTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - -ttgtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa