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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcttgagcaagcttctttaatgtttgtaatgacttggaattggaagttgtcaaaattcagtttttcttcatagctttattcttaatcatgtggacagGAATGGAGCTACCTTAGGGGTGGCCTTACAACTATTGATCGTGACTACGGATGGATCAATAACATCCACCACGACATTGGAACCCATGTCATTCATCACC

Basic information

species Glycine max
transcript GLYMA03G07570.1
intron # 6
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G07570.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 6
--ttttcttgagcaagcttctttaatgtttgt-aatgacttggaattggaagttgtcaaaattcagtttttcttcat-agctt-tattcttaatcatgtggacagGAATGGAGCTACCTTAGGGGTGGCCTTACAACTATTGATCGTGACTACGGATGGATCAATAACATCCACCACGACATTGGAACCCATGTCATTCATCACC
  ||||| |  | |   |    |   | || | ||  ||||   | |      | |   | || |  | || || || ||||   ||| |   |         |||| |||||||| ||  | || ||  | |||||  ||||||| |||||||| |||||||| ||| | ||||| |||||||||||||||||||||||||| |
cattttcctacgtagaatgaagtgcagattatcaaatacttttcacta-----ttttggagtttatatatttttaatgagctcacattttcttttgctctattagGAGTGGAGCTATCTGCGCGGAGGATTGACAACACTTGATCGGGACTACGGGTGGATCAACAACGTACACCATGACATTGGAACCCATGTCATTCATCATC

upper sequence: GLYMA03G07570.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g49310.1 (Oryza sativa), 3'ss of exon 5
ttttcttgagcaagcttctttaatgtttgtaatgactt--ggaattggaagttgtcaaaattcagttttt---cttcatagctttattc-ttaatcatgtggacagGAATGGAGCTACCTTAGGGGTGGCCTTACAACTATTGATCGTGACTACGGATGGATCAATAACATCCACCACGACATTGGAACCCATGTCATTCATCACC
     || || ||   |   ||  |     ||| |||   |||| |  || |  | | |||     ||||   |||     ||  ||   || || || || |||||||||||||||  |  |||| || || || ||  | ||  | ||||| || |||||||| ||||||||||||||||| || || ||||||||||| || |
-----tttagaaaatgttcgtag-gcagagaattactcaaggaaatccaaataataataatctcacttttgcacttttgtactgaatagattgatgatatgtacagGAATGGAGCTATTTGCGGGGAGGACTGACGACAGTGGACAGGGACTATGGGTGGATCAACAACATCCACCACGACATCGGGACACATGTCATTCACCATC

upper sequence: GLYMA03G07570.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G129209_T01 (Zea mays), 3'ss of exon 3
ttttcttgagcaagcttctttaatgtttgtaatgacttggaattggaagttgtcaaaattcag-tttttcttcatagctttattcttaatcatgtggacagGAATGGAGCTACCTTAGGGGTGGCCTTACAACTATTGATCGTGACTACGGATGGATCAATAACATCCACCACGACATTGGAACCCATGTCATTCATCACC
                                |    |  |  |  |      |   || ||| |||   || |  | | |||   ||||         ||||||||| ||| ||| |||||||||| |||||  | || || |||||||| |||||||| ||||||||||| |||||||| || |||||||| || || |
-------------------------------gtagtatatagctaaatcacagctgcatgcaggtttcagttaactgttctataactaatggacctactagGAATGGACCTATCTTCGGGGTGGCCTGACAACGCTCGACCGGGACTACGGGTGGATCAACAACATCCACCATGACATTGGGACTCATGTCATCCACCATC

upper sequence: GLYMA03G07570.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G128971_T03 (Zea mays), 3'ss of exon 2
ttttcttgagcaagcttctttaatgttt--gtaatgacttggaattggaagttgtcaaaattcagtttttcttcatagctttattcttaatcatgtggac-agGAATGGAGCTACCTTAGGGGTGGCCTTACAACTATTGATCGTGACTACGGATGGATCAATAACATCCACCACGACATTGGAACCCATGTCATTCATCACC
      | | | | |    ||||| ||   ||| |   |    |||     || | ||| |  | |  ||  | || ||   ||| ||  |  | |  |  |||| ||||| || ||  | || || || || ||  | || || ||||||||||||||||| |||||||| |||||||| ||||| |||||||| |||||||
--cagattatcgaccactgttaattttaaagtactctatccagattcttccttttgaaagtagactagttactgat-gccacattgttctttttctatattagGAGTGGAGTTATCTGCGTGGAGGACTGACGACGCTCGACCGGGACTACGGATGGATCAACAACATCCATCACGACATCGGAACTCATGTCATCCATCACC

upper sequence: GLYMA03G07570.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0105g00430.t01 (Vitis vinifera), 3'ss of exon 6
ttttcttgagcaagcttctttaatgtttgtaatgacttggaattggaagttgtcaaaattcagtttttcttcatagctttattcttaatc---atgtggacagGAATGGAGCTACCTTAGGGGTGGCCTTACAACTATTGATCGTGACTACGGATGGATCAATAACATCCACCACGACATTGGAACCCATGTCATTCATCACC
       |||  ||       |     ||| |     |    ||  ||  | | |  |||   ||  | |  | || || | | ||  |     ||||||||||||||||| || || ||||| || ||||||||  ||||||||||||| |||||||| |||||||| ||||| || |||||||| ||||| ||||| || |
--aaacagagggagaaataccaccaactgttaccttctctggtttaaacct-ttagcattgttttgatgtaaaaagtttgaattttcgttcttgtgtggacagGAATGGAGTTATCTGAGGGGAGGGCTTACAACCCTTGATCGTGACTATGGATGGATTAATAACATTCACCATGATATTGGAACACATGTGATTCACCATC

upper sequence: GLYMA03G07570.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ20170 (Selaginella moellendorffii), 3'ss of exon 6
-------ttttcttgagcaagcttctttaatgtttgtaatgacttggaattggaagttgtcaaaattcagtttttcttcatagctttattcttaatcatgtggacagGAATGGAGCTACCTTAGGGGTGGCCTTACAACTATTGATCGTGACTACGGATGGATCAATAACATCCACCACGACATTGGAACCCATGTCATTCATCACC
         | |  ||     |     ||  ||  | |   ||  | | ||    ||| | |  ||||| ||| |||  |  |   | || |  |||       ||||||||||  ||| |  | || |||||  ||||||| || || ||||| |||| | |||||||||| ||||||||||||||||| |||||| | |||||  
catggccactaccagaaagtaccatggtatcgtgggaaggtacaagtattttcctgttctgaggattca-tttctctcaaacgagctcttttacatct------cagGAATGGAATTACATCCGAGGCGGCCTATCAACTATAGACCGAGACTATGGATTGTTCAATAACATTCACCACGACATTGGAACGCATGTCGTGCATCATT

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|31461767|gb|CD403795.1|CD403795
EST:     ATTTGCATCACCATGGCCATGAAGACAAATTACCTTGGTATCCTGGAGAG                         GAATGGAGCTACCTTAGGGTTGGCCTTACAACTATTGATCGTGACTACGGA
genomic: ATTTGCATCACCATGGCCATGAAGACAAATTACCTTGGTATCGTGGAGAGgtatcctttc ... atgtggacagGAATGGAGCTACCTTAGGGGTGGCCTTACAACTATTGATCGTGACTACGGA
EST: gi|27425914|gb|CA937434.1|CA937434
EST:     ATTTGCATCACCATGGCCATGAAGACAAATTACCTTGGTATCGTGGAGAG                         GAATGGAGCTACCTTAGGGGTGGCCTTACAACTATTGATCGTGACTACGGA
genomic: ATTTGCATCACCATGGCCATGAAGACAAATTACCTTGGTATCGTGGAGAGgtatcctttc ... atgtggacagGAATGGAGCTACCTTAGGGGTGGCCTTACAACTATTGATCGTGACTACGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagttgtcaaaattcagtttttcttcatagctttattcttaatcatgtggacagGAATGGAGCTACCTTAGGGGTGGCCTTACAACTATTGATCGTGACTACGGATGGATCAATAACATCCACCACGACATTGGAACCCATGTCATTCATCACC
                                   attcttaat  putative branch site 
                                tttattcttaatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcttgagcaagcttctttaatgtttgtaatgacttggaattggaagttgtcaaaattcagtttttcttcatagctttattcttaatcatgtggacagGAATGGAGCTACCTTAGGGGTGGCCTTACAACTATTGATCGTGACTACGGATGGATCAATAACATCCACCACGACATTGGAACCCATGTCATTCATCACC

- - - - - - -gcttctt
- - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - tgacttg