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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATGgtatttttttttttttggttgaatctggtacttctgtccaattaagttggaattgcatgacatgcaataagttaatgtgagttgatacagatcagttgat...

Basic information

species Glycine max
transcript GLYMA09G41330.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G41330.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 5'ss of exon 4
CGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATGgtatttttttttttttggt----tgaatctggtacttctgtccaattaagttggaattgcatgacatgcaataagttaatgtgagttgataca-gatcagttgat
||||||||||| ||||| ||||| || || |||||||||||||| || || || |||||||| || || |||||||  ||    || | ||    ||| |       ||||||    || |  ||    |   |||| ||  |   |||  ||| |  ||    | |  ||| ||  
CGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATGgtatggttcaacttcttgtaccgtgactgcaaatgttctgttttgttcatctg---cttattgacttgtgaattgttt-tgttatctgtccaatggccagctgt-

upper sequence: GLYMA09G41330.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S13_321V6.1 (Physcomitrella patens), 5'ss of exon 3
CGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATGgtatttttttttttttggttgaatctggtacttctgtccaattaagttggaattgcatgacatgcaataagttaatgtgagttgatacagatcagttgat--
|||||||| |||||||| ||| | |||||||| || ||||| ||||| || ||||||||||| || || ||||||||  | |  ||         | |   |||  | | |  |  |     |||| |      |   |      | ||   |||  ||      | ||  |  
CGTTTTGCAGCTGTTATCATGCGAATCAGGGAGCCTAAAACAACTGCTCTTATTTTTGCATCCGGTAAAATGgtattgctataattcaacccc--ttttaaactagtattctctatatgcataattactaagtgtaagaattaaaactgcaggttcgtatcttctacttttttg

upper sequence: GLYMA09G41330.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S246_34V6.1 (Physcomitrella patens), 5'ss of exon 3
CGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATGgtattttt----ttttttttggttgaatctggtacttctgtccaattaagttggaattgcatgacatgcaataagtt-aatgtgagt-tgatacagatcagttgat
|||||||| |||||||||||| | || ||||| |||||||| ||||| ||||||||||||||||| || |||||||| |     |   ||||  ||| |||  | | ||      | |   | |  | ||| || || || |||| |||  |  || || | || || |  | ||   
CGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATGgtattgtcccagtcgcttttatttggatcgtgaaattgaa---attgtggctttatttggatcacctg-aataggttcgaactgggtatcatgcacactaattt--

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|254336235|gb|GR842414.1|GR842414
EST:     GGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG                         GTCTGCACTGGAGCTAAGAGTGAGCAACAGTCTAAATTGGCGGCAAGGAAG
genomic: GGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATGgtattttttt ... tcatggttagGTCTGTACTGGAGCCAAGAGTGAGCAACAGTCTAAATTGGCGGCAAGGAAG
EST: gi|254334604|gb|GR844389.1|GR844389
EST:     GGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG                         GTCTGTACTGGAGCCAAGAGTGAGCAACAGTCTAAATTGGCGGCAAGGAAG
genomic: GGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATGgtattttttt ... tcatggttagGTCTGTACTGGAGCCAAGAGTGAGCAACAGTCTAAATTGGCGGCAAGGAAG
EST: gi|19270744|gb|BM887000.1|BM887000
EST:     GGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG                         GTCTGCACTGGAGCTAAGAGTGAGCAACAGTCTAAATTGGCGGCAAGGAAG
genomic: GGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATGgtattttttt ... tcatggttagGTCTGTACTGGAGCCAAGAGTGAGCAACAGTCTAAATTGGCGGCAAGGAAG
EST: gi|21887668|gb|BQ740881.1|BQ740881
EST:     GGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG                         GTCTGCACTGGAGCTAAGAGTGAGCAACAGTCTAAATTGGCGGCAAGGAAG
genomic: GGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATGgtattttttt ... tcatggttagGTCTGTACTGGAGCCAAGAGTGAGCAACAGTCTAAATTGGCGGCAAGGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATGgtatttttttttttttggttgaatctggtacttctgtccaattaagttggaattgcatgacatgcaataagttaatgtgagttgatacagatcagttgat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG