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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTCTGGTTCGACAACCCTTCCGCCAAGTCCAAACAAGCTGCATGGGGCAGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAGgtcaagcttcgatcttttcccttccttttcccccaattttccctcttctgggtcttaacctaattgcttctttcttgattattggaagttctgacccttgtttttttgttttaaaatttgttcag

Basic information

species Glycine max
transcript GLYMA15G09630.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G09630.2 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os01g73880.1 (Oryza sativa), 5'ss of exon 1
CCTTCTGGTTCGACAACCCTTCCGCCAAGTCCAAACAAGCTGCATGGGGCAGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAGgtcaagcttcgatcttttcccttccttttcccccaattttccctcttctgggtcttaacctaattgcttctttcttgattattggaagttctgacccttgtttttttgttttaaaatttgttcag
|||||||||||||||||||    |  |||||||| || ||  | ||||| ||||||||||| |||||| |||| ||| |||||||||| || || |||||||     | | | |    ||| |||| |||      ||| |||||  |    |||  | |   |  |||| |   | | ||||| |  |||     || | | |||                   
CCTTCTGGTTCGACAACCCGCAGGGAAAGTCCAAGCAGGCAACCTGGGGAAGCTCCATCCGCCCCATCCACACCTTCTCCACCGTCGAGGACTTCTGGAGgtt----tcccaccc---cccctcctcttct-----tttcccctccacaacctctccatcccttgccttcatgaatcagtattgtagattccccatctagctgtttaacccg-------------

upper sequence: GLYMA15G09630.2 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G113096_T01 (Zea mays), 5'ss of exon 1
CCTTCTGGTTCGACAACCCTTCCGCCAAGTCCAAACAAGCTGCATGGGGCAGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAGgt-caagcttcgatcttttcccttccttttcccccaattttccctcttctgggtcttaacctaattgcttctttcttgattattggaagttctgacccttgtttttttgttttaaaatttgttcag
|||||||||||||||||||   || ||||  |||    || || ||||| |||||||||||||||||| |||| ||| ||||||| || || || ||| ||| |   |  | |||| |  |   |   | | | |   ||  |||| | |   || |  |  | |  |     |  || |      |||| | ||  |    |                       
CCTTCTGGTTCGACAACCCGCACGGCAAGAACAAGATGGCCGCCTGGGGGAGCTCCATCCGACCCATCCACACCTTCTCCACCGTAGAGGACTTCTGGGGgtgcgtccgactatctctctctgacacatgcacacctcttaacctcctttccctcctctcacactctcacaactactggt----acaagtccagattcacaata----------------------
















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|213613945|gb|DB960938.1|DB960938
EST:     AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAG                         CATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
genomic: AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAGgtcaagcttc ... atttgttcagCATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
EST: gi|298194469|gb|HO042941.1|HO042941
EST:     AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAG                         CATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
genomic: AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAGgtcaagcttc ... atttgttcagCATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
EST: gi|18735078|gb|BM528551.1|BM528551
EST:     AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAG                         CATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
genomic: AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAGgtcaagcttc ... atttgttcagCATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
EST: gi|192308366|gb|FK002794.1|FK002794
EST:     AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAG                         CATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
genomic: AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAGgtcaagcttc ... atttgttcagCATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
EST: gi|9820397|gb|BE555907.1|BE555907
EST:     AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAG                         CATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
genomic: AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAGgtcaagcttc ... atttgttcagCATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
EST: gi|15337801|gb|BI498457.1|BI498457
EST:     AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAG                         CATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
genomic: AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAGgtcaagcttc ... atttgttcagCATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
EST: gi|6846595|gb|AW348885.1|AW348885
EST:     AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAG                         CATNNACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
genomic: AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAGgtcaagcttc ... atttgttcagCATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
EST: gi|6724495|gb|AW308894.1|AW308894
EST:     TCTACACTTTCGCCACCGTCGAAGAGTTTTGGAG                         CATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
genomic: TCTACACTTTCGCCACCGTCGAAGAGTTTTGGAGgtcaagcttc ... atttgttcagCATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
EST: gi|209698255|gb|BW678026.1|BW678026
EST:     AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAG                         CATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
genomic: AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAGgtcaagcttc ... atttgttcagCATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
EST: gi|298191604|gb|HO039083.1|HO039083
EST:     AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAG                         CATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
genomic: AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAGgtcaagcttc ... atttgttcagCATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
EST: gi|8826570|gb|BE210300.1|BE210300
EST:     AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAG                         CATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
genomic: AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAGgtcaagcttc ... atttgttcagCATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT
EST: gi|298165619|gb|HO011668.1|HO011668
EST:     AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAG                         CATTTACAATAACATTCACCACCCGAGCGAGTTGGGTGTGGGGGCGGACTT
genomic: AGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAGgtcaagcttc ... atttgttcagCATTTACAATAACATTCACCACCCGAGCAAGTTGGGTGTGGGGGCGGACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTCTGGTTCGACAACCCTTCCGCCAAGTCCAAACAAGCTGCATGGGGCAGCTCCATCCGACCCATCTACACTTTCGCCACCGTCGAAGAGTTTTGGAGgtcaagcttcgatcttttcccttccttttcccccaattttccctcttctgggtcttaacctaattgcttctttcttgattattggaagttctgacccttgtttttttgttttaaaatttgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG