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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgcatgttgattttgtaaagtctatatcttcattttatgttattacagatgtttattgtccaataatgctgtaaaattaatgatttgctgttacctagGTCCTAAGCATGATTCCAGAGGAGTCTGATGGTGAGCGTTTTGAAGATGCTCTTGCACGTGTCTGTTGTTGTGTTGGGGGTGGAAATGCAAATGATAATG

Basic information

species Glycine max
transcript GLYMA12G29270.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G29270.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G60410.4 (Arabidopsis thaliana), 3'ss of exon 12
catgcatgttgattttgtaaagtctatatc--ttcattttatgttattacagatgtttattgtccaataatgctgtaaaattaatgatttgctgttacctagGTCCTAAGCATGATTCCAGAGGAGTCTGATGGTGAGCGTTTTGAAGATGCTCTTGCACGTGTCTGTTGTTGTGTTGGGGGTGGAAATGCAAATGATAATG
||    ||||| | || |    |  | |    ||||| || |    | |        |  | |||||      | || |  || | ||||  |   | |||||| ||||   |||||||||| |||  | | || |||  ||||||||||||||||||||||||| |  | ||  |||| ||||||  || | |||||||||
cacttttgttggtgttcttgtatacagaggaattcatattgtacgttaatgatctaatgatctccaagttgcttatatatatactcattt--ttgcatctagGTTCTAAATTTGATTCCAGAAGAGGGTAAAGGGGAGACTTTTGAAGATGCTCTTGCACGTGTCCGCCGATGCATTGGAGGTGGAGGTGGAGATGATAATG

upper sequence: GLYMA12G29270.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0004g03180.t01 (Vitis vinifera), 3'ss of exon 11
--catgcatgttgattttg---taaagtctatatcttcattttatgttattacagatgtttattgtccaataatgctgtaaaattaatgatttgc-tgttacctagGTCCTAAGCATGATTCCAGAGGAGTCTGATGGTGAGCGTTTTGAAGATGCTCTTGCACGTGTCTGTTGTTGTGTTGGGGGTGGAAATGCAAATGATAATG
  |||| || |    |||    |    || | || |   |||| | || ||  |  |  || || |      |||   | |  ||| |  ||| | | ||   ||| |  ||||| |||||||  | || || ||||||||||||||||||||||| || || |||||  || ||||  |||| ||||||  ||||| ||||||||
tacatgaatttctgctttacttttgcatcaagatgtgagttttttatttttttatttccttgttat------atgtgatcatgttagttctttacatcttttgtagATTTTAAGCTTGATTCCTAAAGAATCAGATGGTGAGCGTTTTGAAGATGCGCTGGCTCGTGTTCGTCGTTGCATTGGTGGTGGAGGTGCAACTGATAATG
















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|193372278|gb|FK338295.1|FK338295
EST:     GCATATTCTGTTTAGGGGTCCGTATTGTTAAAAGACTCAGCATGCCAGAG                         GTCCTAAGCATGATTCCAGAGGAGTCTGATGGTGAGCGTTTTGAAGATGCT
genomic: GCATATTCTGTTTAGGGGTCCGTATTGTTAAAAGACTCAGCATGCCAGAGgtagattaca ... tgttacctagGTCCTAAGCATGATTCCAGAGGAGTCTGATGGTGAGCGTTTTGAAGATGCT
EST: gi|207747494|gb|GD720227.1|GD720227
EST:     GCATATTCTGTTTAGGGGTCCGTATTGTTAAAAGACTCAGCATGCCAGAG                         GTCCTAAGCATGATTCCAGAGGAGTCTGATGGTGAGCGTTTTGAAGATGCT
genomic: GCATATTCTGTTTAGGGGTCCGTATTGTTAAAAGACTCAGCATGCCAGAGgtagattaca ... tgttacctagGTCCTAAGCATGATTCCAGAGGAGTCTGATGGTGAGCGTTTTGAAGATGCT
EST: gi|207732541|gb|GD709078.1|GD709078
EST:     CATATTCTGTTTAGGGGTCCGTATTGTTAAAAGAACTCAGCATGCCAGAG                         GTCCTAAGCATGATTCCAGAGGAGTCTGATGGTGAGCGTTTTGAAGATGCT
genomic: CATATTCTGTTTAGGGGTCCGTATTGTTAAAAG-ACTCAGCATGCCAGAGgtagattaca ... tgttacctagGTCCTAAGCATGATTCCAGAGGAGTCTGATGGTGAGCGTTTTGAAGATGCT
EST: gi|193317716|gb|FK283670.1|FK283670
EST:     GCATATTCTGTTTAGGGGTCCGTATTGTTAAAAGACTCAGCATGCCAGAG                         GTCCTAAGCATGATTCCAGAGGAGTCTGATGGTGAGCGTTTTGAAGATGCT
genomic: GCATATTCTGTTTAGGGGTCCGTATTGTTAAAAGACTCAGCATGCCAGAGgtagattaca ... tgttacctagGTCCTAAGCATGATTCCAGAGGAGTCTGATGGTGAGCGTTTTGAAGATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacagatgtttattgtccaataatgctgtaaaattaatgatttgctgttacctagGTCCTAAGCATGATTCCAGAGGAGTCTGATGGTGAGCGTTTTGAAGATGCTCTTGCACGTGTCTGTTGTTGTGTTGGGGGTGGAAATGCAAATGATAATG
                               aattaat  putative branch site (score: 3)
                          tgtaaaattaatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgcatgttgattttgtaaagtctatatcttcattttatgttattacagatgtttattgtccaataatgctgtaaaattaatgatttgctgttacctagGTCCTAAGCATGATTCCAGAGGAGTCTGATGGTGAGCGTTTTGAAGATGCTCTTGCACGTGTCTGTTGTTGTGTTGGGGGTGGAAATGCAAATGATAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- -gcatgtt
- - - - - - - - - - - - - - -cttcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatttg