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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttgttatcaaagactcgatggaattttttttttatccaaaactctcacacaaaattatattgataatggccggtgattatattctgaattttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCACACCCCAAATTCGAAGTAATGGCATTGATCAAGTACAATTTACCCCTCC

Basic information

species Glycine max
transcript GLYMA01G44600.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G44600.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0041g02080.t01 (Vitis vinifera), 3'ss of exon 3
-atttgttatcaaagactcgatggaattttttttttatccaaaact--ctcacacaaaattatattgataatggccggtgattatattctgaattttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCACACCCCAAATTCGAAGTAATGGCATTGATCAAGTACAATTTACCCCTCC
 |  |  ||| |  || |   |||| ||| ||    |   |    |   |         |||||       ||     |    ||  | | || ||| | ||| ||  |||||||| || ||||| || || |||| ||| ||||||||| | ||||||||||| ||||| ||||||||||||   |  || ||  |  ||||
aagcttatatgatggaatgagtggattttattgagaaataaggtttattttctgtttggttatagctcctctgatt--tatccatcctattaacttttt-cagATTTCCAGCCAAACGGGCAAGCTCCAATCTCTTGTACAGACAAGCCATTGACACCCCAAATCCGAAGCAATGGCATTGATGTTGCCCAGTTCTCAACTCC

upper sequence: GLYMA01G44600.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0041g02020.t01 (Vitis vinifera), 3'ss of exon 3
-atttgttatcaaagactcgatggaattttttttttatccaaaact--ctcacacaaaattatattgataatggccggtgattatattctgaattttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCACACCCCAAATTCGAAGTAATGGCATTGATCAAGTACAATTTACCCCTCC
 |  |  ||| |  || |  | ||| ||| ||    |   |    |   |         |||||       ||     |    ||  | | |||||| | ||| ||  |||||||| || ||||| || || |||| ||| ||||||||| | ||||||||||| ||| | |||||||||| |   |  || ||  | |||||
aagcttatatgatggaatgaacggattttattgagaaataaggtttattttctgtttggttatagctcctctgatt--tatccatcctattaatttttt-cagATTTCCAGCCAAACGGGCAAGCTCCAATCTCTTGTACAGACAAGCCATTGACACCCCAAATCCGAGGCAATGGCATTGGTGTTGACCAGTTCTCACCTCC
















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|4303254|gb|AI443450.1|AI443450
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGGAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|6724334|gb|AW308733.1|AW308733
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|19937188|gb|BQ081188.1|BQ081188
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGCTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|21637821|gb|BM107976.1|BM107976
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAARAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|13480608|gb|BG509951.1|BG509951
EST:     GGGGGTTTTCTTCTGTCAAATTTGGCACGTGGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: GGTG-TTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|298197029|gb|HO041716.1|HO041716
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|192297056|gb|FG990327.1|FG990327
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|254345565|gb|GR851727.1|GR851727
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|13479195|gb|BG508538.1|BG508538
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|7588905|gb|AW704690.1|AW704690
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|13562349|gb|BG550569.1|BG550569
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTAACAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|192295796|gb|FG990862.1|FG990862
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|33388659|gb|CA851866.1|CA851866
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|298196403|gb|HO041146.1|HO041146
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|15814078|gb|BI786353.1|BI786353
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|33390375|gb|CA853570.1|CA853570
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|4396863|gb|AI495860.1|AI495860
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|7926222|gb|AW832248.1|AW832248
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|8284685|gb|BE022227.1|BE022227
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|19935988|gb|BQ080671.1|BQ080671
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|7638963|gb|AW733295.1|AW733295
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|8282576|gb|BE020137.1|BE020137
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|15815611|gb|BI787886.1|BI787886
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|192322649|gb|FK014986.1|FK014986
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|192324298|gb|FK018274.1|FK018274
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCGG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|14991432|gb|BI317105.1|BI317105
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|14989963|gb|BI315636.1|BI315636
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|18732748|gb|BM527225.1|BM527225
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|15000796|gb|BI321610.1|BI321610
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|7639562|gb|AW733882.1|AW733882
EST:     CGGTGTTTTCTTCTGTCA-ATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|17400292|gb|BM177074.1|BM177074
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|15815436|gb|BI787711.1|BI787711
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
EST: gi|19936789|gb|BQ081013.1|BQ081013
EST:     CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAG                         TTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA
genomic: CGGTGTTTTCTTCTGTCAGATTTGGCACGTTGGAAGAGTTTCAGATTCAGgtcttttctt ... ttttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcacacaaaattatattgataatggccggtgattatattctgaattttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCACACCCCAAATTCGAAGTAATGGCATTGATCAAGTACAATTTACCCCTCC
              tattgat  putative branch site (score: 3)
     acaaaattatattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttgttatcaaagactcgatggaattttttttttatccaaaactctcacacaaaattatattgataatggccggtgattatattctgaattttgtacagTTTATCAGCCAAATGGACAAGCACCCATATCTTCTACGGACAAGCCACTCACACCCCAAATTCGAAGTAATGGCATTGATCAAGTACAATTTACCCCTCC

- - - - - - - - - - - - - - - - - -atccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gccggtg