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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaactgtattggtttttctaatgtcttttatgaagtgtgaaaaatgaaaataaagcattttatcttatttgattttgtttccttgcaacttcatccagCCGCATACCAGGGCATTGGGTTCAGCCTCCTCCTCCAGCTAATGAGATATGGGCATCTTACTTGGTGAGACCTAAATGATTATTATTAGTTAACAAATCA

Basic information

species Glycine max
transcript GLYMA12G05400.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G05400.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g12670.1 (Oryza sativa), 3'ss of exon 8
tgcaactgtattggtttttctaatgt---cttttatgaagtgtgaaaaatgaaaataaagcattttatcttatttgattttgtt-tccttgcaacttcatccagCCGCATACCAGGGCATTGGGTTCAGCCTCCTCCTCCAGCTAATGAGATATGGGCATCTTACTTGGTGAGACCTAAATGATTATTATTAGTTAACAAATCA-
    | |  ||||   | || | |||     ||||  | |||  |  |||   | |  |||||| |  ||||||| |   ||   |  |  || || | | |||||| ||||| ||||| ||||||||||| || ||||||||| ||||  |||||||||| || || |||   || || ||   |   | | |  ||  | |  
-tttagtacattgtgctctcgattgtagtgctttaccatgtgaaacgaattcta-tgtagcattct--cttatttaacaatgcaattgtctcacctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATGGGCATCCTATTTAGTGCAGCCCAACTGTCCAA-GTAACTCCACTTAGCTG

upper sequence: GLYMA12G05400.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G058366_T01 (Zea mays), 3'ss of exon 7
tgcaactgtattggtttttctaatgtcttttatgaagtgtgaaa--aatgaaaataaagcattttatcttatttgattttgtttccttgcaacttcatccagCCGCATACCAGGGCATTGGGTTCAGCCTCCTCCTCCAGCTAATGAGATATGGGCATCTTACTTGGTGAGACCTAAATGA-TTATTATTAGT-TAACAAATCA
  |    ||||  || | || ||     ||  || ||||       || |  |||     ||  ||| ||   | ||  |   |  |||||  | |   |||||| ||||| ||||| |||||||  || || ||||||||| ||||| | ||||||||||| ||||||   |  || | | | |  ||  || | | ||||  
-acctaagtatcagtgtctcaaaatggattagtgcagtggtgtgttaaagcgaatctcatataatattttccctaatagtaagtg-ttgcacttgctcgcagCCGTATACCTGGGCACTGGGTTCCACCACCCCCTCCAGCTGATGAGGTTTGGGCATCTTATTTGGTGCAGCACAAGTAAATCACCATGGGTATGAGAAAT--
















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|7590657|gb|AW706404.1|AW706404
EST:     GTTAGAAGAGGATGGGATGCCTATATCAGACCAGGAGGAAG                         CCGCATACCAGGGCATTGGGTTCAGCCTCCTCCTCCAGCTAATGAGATATG
genomic: GTTAGAAGAGGATGGGATGCCTATATCAGACCAGGAGGAAGgtaagaaatt ... cttcatccagCCGCATACCAGGGCATTGGGTTCAGCCTCCTCCTCCAGCTAATGAGATATG
EST: gi|208204986|gb|GE004501.1|GE004501
EST:     GTTAGAAGAGGATGGGATGCCTATATCAGACCAGGAGGAAG                         CCGCATACCAGGGCATTGGGTTCAGCCTCCTCCTCCAGCTAATGAGATATG
genomic: GTTAGAAGAGGATGGGATGCCTATATCAGACCAGGAGGAAGgtaagaaatt ... cttcatccagCCGCATACCAGGGCATTGGGTTCAGCCTCCTCCTCCAGCTAATGAGATATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaaaataaagcattttatcttatttgattttgtttccttgcaacttcatccagCCGCATACCAGGGCATTGGGTTCAGCCTCCTCCTCCAGCTAATGAGATATGGGCATCTTACTTGGTGAGACCTAAATGATTATTATTAGTTAACAAATCA
                       atttgat  putative branch site (score: 5)
                                             cttcatcc  putative PPT
     aataaagcattttatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcaactgtattggtttttctaatgtcttttatgaagtgtgaaaaatgaaaataaagcattttatcttatttgattttgtttccttgcaacttcatccagCCGCATACCAGGGCATTGGGTTCAGCCTCCTCCTCCAGCTAATGAGATATGGGCATCTTACTTGGTGAGACCTAAATGATTATTATTAGTTAACAAATCA

-gcaactg
- - - - - - - - - - - - - - - - - aagtgtg
- - - - - - - - - - - - - - - - - - - - - - - - aaaataa