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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTACCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAGgtaaatatatataaccaagtgctaactggtttggttattcacatgtttgtagggaaatggatctcaagctaagttggttttgctttttcgtttggttattcag

Basic information

species Glycine max
transcript GLYMA08G23380.4
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G23380.4 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os02g08440.4 (Oryza sativa), 5'ss of exon 3
CCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTACCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAGgtaa-----atatatataaccaagtgctaactggtttggtta---ttcacatgtttgtagggaaatggatctcaagctaagttggttttgctttttcgtttggttattcag
|||||||||||| ||||| || ||||| ||||  || ||||| | ||| ||||| || ||||  ||||| ||||||||   |||||||||||| ||||||||||     ||   | |||| || | | || || ||| || |   ||   |  |||   |  || | || |              | ||  |  |||   || |  |||||
CCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAGgtaacttaaattcctctaactaattccaaagtgatttcgtaagttttgctaaatttagtgcaaattcgagcctgtttctgaactttgttcgtggttcaaatgttgtttcag

upper sequence: GLYMA08G23380.4 (Glycine max), 5'ss of exon 4
lower sequence: AT1G80840.1 (Arabidopsis thaliana), 5'ss of exon 3
CCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTACCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAGgtaaatatatataaccaagtgctaact---ggtttggttattcacatgtttgtagggaaatggatct-caagctaagttggttttgctttttcgtttggtt--attcag
 |||||||||||||||||||| || ||||| ||||| || || |  || ||||| || ||||| ||  ||| ||||||||||||  |||||||||||||||||| |    |  |  ||   || |||   | ||    |||  |   |  |      || | |||   |    |||  || ||||| |  |  ||||| ||  ||||||
TCAATGGAGGAAATATGGACAGAAAGTGACTAGAGACAATCCATCTCCAAGAGCTTACTTCAAATGTGCTTGTGCTCCAAGCTGTTCTGTCAAAAAGAAGgtaattgataaagaaaaaaaactgactctcgcttaaaatatgaattggcataatacaaatttgatagacttattaatctgattttgatcctgtgtttgtttctattcag

upper sequence: GLYMA08G23380.4 (Glycine max), 5'ss of exon 4
lower sequence: Vv09s0018g00240.t01 (Vitis vinifera), 5'ss of exon 4
CCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTACCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAGgtaaatatatataaccaagtgctaactg--gtttggttattcacatgtttgtagggaaat--ggatctcaa--gctaagttggttttgctttttcgtttg-gttattcag-----------------------
||| |||||||||||||| |||||||| |||||||| ||||| |  || ||||| || ||||| |||||||||||||| |||||||||||||| |||||||| |   || |      | | | | |||   || |  | || |     ||||    |  |  ||||   ||  |   | |  |||||||||     | |  | | ||                          
CCAGTGGAGGAAATATGGCCAAAAGGTCACCAGAGACAACCCCTCTCCGAGAGCCTACTTCAAATGCTCTTTTGCTCCTAGCTGCCCTGTCAAGAAGAAGgtgagcctaaacttgacaatcccacctgtgattcgtctttttaggaacttgtgtcaaggtccggattgaaattgtccattgagttttgcttagcattctaagctgttttctgcaatttgtttcctttcttcag

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|254318274|gb|GR832442.1|GR832442
EST:     GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAG                         -TGCAAAGAAG
genomic: GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAGgtaaatatat ... ggttattcagGTGCAAAGAAG
EST: gi|16341648|gb|BI967243.1|BI967243
EST:     GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAG                         GTGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATGAAGGG
genomic: GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAGgtaaatatat ... ggttattcagGTGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATGAAGGG
EST: gi|192300003|gb|FG991835.1|FG991835
EST:     GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAG                         -TGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATG
genomic: GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAGgtaaatatat ... ggttattcagGTGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATG
EST: gi|16345570|gb|BI971165.1|BI971165
EST:     GAGCATATTTCAAGTGCTCTNNNGCNCNNAGCTGCCCTGTCAAAAAGAAG                         GTGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATGAAGGG
genomic: GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAGgtaaatatat ... ggttattcagGTGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATGAAGGG
EST: gi|14008932|gb|BG725536.1|BG725536
EST:     GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAG                         GTGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATGAAGGG
genomic: GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAGgtaaatatat ... ggttattcagGTGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATGAAGGG
EST: gi|9819706|gb|BE555219.1|BE555219
EST:     GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAG                         GTGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATGAAGGG
genomic: GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAGgtaaatatat ... ggttattcagGTGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATGAAGGG
EST: gi|16345666|gb|BI971261.1|BI971261
EST:     GCTGCCCTGTCAAANNGAAG                         GTGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATGAAGGG
genomic: GCTGCCCTGTCAAAAAGAAGgtaaatatat ... ggttattcagGTGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATGAAGGG
EST: gi|18732673|gb|BM527178.1|BM527178
EST:     GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAG                         GTGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATGAAGGG
genomic: GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAGgtaaatatat ... ggttattcagGTGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATGAAGGG
EST: gi|254348970|gb|GR860242.1|GR860242
EST:     GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAG                         GTGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATGAAGGG
genomic: GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAGgtaaatatat ... ggttattcagGTGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATGAAGGG
EST: gi|16341647|gb|BI967242.1|BI967242
EST:     GAGCATATTTCAAGTGCTCTTTTNCTCCAAGCTGCCCTGTCAAAAAGAAG                         GTGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATGAAGGG
genomic: GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAGgtaaatatat ... ggttattcagGTGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATGAAGGG
EST: gi|254342047|gb|GR853184.1|GR853184
EST:     GAGCATATTTCAAGTGCTCTTTTGCT-CAAGCTGCCCTGTCAAAAAGAAG                         GTGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATGAAGGG
genomic: GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAGgtaaatatat ... ggttattcagGTGCAAAGAAGTGTGGATGATCATTCTGTTCTGCTTGCTACTTATGAAGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTACCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAGgtaaatatatataaccaagtgctaactggtttggttattcacatgtttgtagggaaatggatctcaagctaagttggttttgctttttcgtttggttattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG