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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttaaaaatcttattccaataactttgatacctaagttttctttaagattactttatagtattttcataaaaaaaattgattgcatttcttaacatatttgatcagACAAGAAGAATGAGAACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCATCCACTGCTGTTGAATCCATCCAGTACTCAAT

Basic information

species Glycine max
transcript GLYMA16G01960.1
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01960.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g36260.1 (Oryza sativa), 3'ss of exon 5
gtatccttaaaaatcttattccaataactttgatacctaagttttctttaagattactttatagtattttcataaaaaaaattgattgcatttcttaacatatttgatcagACAAGAAGAATGAGAACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCATCCACTGCTGTTGAATCCATCCAGTACTCAAT
       ||    |  |    ||     |  |||  |||  ||||  ||| | ||  |  || | |  || ||   ||    |  ||  |||  | | || | |   ||||||||||||||||||||||||||||| || || ||||| ||  | |||||  | || |||  |||| | ||||||||||| ||
------gtacgcctgcttcctcagctcatacgattgctacatttt--ttatgcttggt--attgcaccttgatttcaa----ttgttttattcttgatcaaaatctttcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCTTGCCTGCTCCGACAGCTCGTGAAGCAATCCAGTACTCTAT

upper sequence: GLYMA16G01960.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 7
gtatccttaaaaatcttattccaataactttgatacctaagttttctttaagattactttatagtattt-tcataaaaaaaattgattgcatttcttaaca-tatttgatcagACAAGAAGAATGAGAACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCATCCACTGCTGTTGAATCCATCCAGTACTCAAT
||||||| | |   | | ||   ||   ||  ||   |   | | |  ||   |      ||||||||  ||||  | | |  || ||    | ||||||| ||| |  | ||||||||||||||||||||||||||| || ||| |||  ||  | |||||   |||||||  |||  |||| |||||||| ||
gtatcctcatagtccgtttt---atggtttaaat---tgcatatcccatatagt------atagtattggtcatgcatacatctg-ttattgtccttaacaatatgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCAACACTGCTCGTGACGCCATTCAGTACTCCAT

upper sequence: GLYMA16G01960.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g64670.1 (Oryza sativa), 3'ss of exon 6
gtatccttaaaaatcttattccaataactttgatacctaagttttctttaagattactttatagtattttcataaaaaaaattgattgcatttcttaacatatttgatcagACAAGAAGAATGAGAACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCATCCACTGCTGTTGAATCCATCCAGTACTCAAT
             | |  | | | ||  | | | | |   | |    | |  | |  |||||    | ||| | |   || |   | |  ||||| ||| ||||    |||||||||||||||| ||||||||||| || || |||||  | || ||||   || |||||   ||  |||||||||| || ||
------------gtatgttcctactagttctcaaatc---gctgcactgaccaatgttttat----tcttcttcagctaactctgtag--tttctgaacttatt----cagACAAGAAGAATGAAAACAAGGAGGTCGCCGTGAATGAGGTACTGCCTGTGACCGCTGCTCGGGATGCCATCCAGTATTCCAT

upper sequence: GLYMA16G01960.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g64670.3 (Oryza sativa), 3'ss of exon 6
gtatccttaaaaatcttattccaataactttgatacctaagttttctttaagattactttatagtattttcataaaaaaaattgattgcatttcttaacatatttgatcagACAAGAAGAATGAGAACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCATCCACTGCTGTTGAATCCATCCAGTACTCAAT------------------
             | |  | | | ||  | | | | |   | |    | |  | |  |||||    | ||| | |   || |   | |  ||||| ||| ||||    |||||||||||||||| ||||||||||| || || |||||  | || ||||   || |||||   ||  |||||||||| || ||                  
------------gtatgttcctactagttctcaaatc---gctgcactgaccaatgttttat----tcttcttcagctaactctgtag--tttctgaacttatt----cagACAAGAAGAATGAAAACAAGGAGGTCGCCGTGAATGAGGTACTGCCTGTGACCGCTGCTCGGGATGCCATCCAGTATTCCATGTAAGTGATGAACTGTCC

upper sequence: GLYMA16G01960.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatccttaaaaatcttattccaataactttgatacctaagttttctttaagattactttatagtattttcataaaaaaaattgattgcatttcttaac-atatttgatcagACAAGAAGAATGAGAACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCATCCACTGCTGTTGAATCCATCCAGTACTCAAT
                        || | || | |||||       |||||   ||||| ||         | |  |    ||  ||||  |  ||||| | | |  | ||||||||||||||||||||||||| || ||||| |||||||||||||   |     ||||| ||||| |||| |||||||||||
-----------------------gtatccttaaaaccta------ttttaa---tacttgattaggaaacaaaaccatttcttttttgctatctttaaccaaaatataacagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAATGATTTTCTACAACCTGGTCCTGCTATTGAAGCCATTCAGTACTCAAT

upper sequence: GLYMA16G01960.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatccttaaaaatcttattccaataactttgatacctaagttttctttaagattactttatagtattttcataaaaaaaattgattgcatttcttaac----atatttgatcagACAAGAAGAATGAGAACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCATCCACTGCTGTTGAATCCATCCAGTACTCAAT
                        || | ||  | | | ||| ||| |    |||  | | || |  | ||  || ||  |||  ||       |||||    |||| | | |||||||||| || ||||||||||| || ||||| ||||||||||| ||  |     |||| |||||| | ||||||||||||||
-----------------------gtatccttt-ttcttcagtgttcctccttattcatctctattgatctctcaacaagtattagtttttccctttaactctaatatctta-cagACAAGAAAAACGAGAACAAGGAAGTTGCAGTGAATGATTTTCTGCCATCTGAGTCTGCGGTTGAAGCTATCCAGTACTCAAT

upper sequence: GLYMA16G01960.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S315_67V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------gtatccttaaaaatcttattccaataactttgatacctaagttttctttaagattactttatagtattttcataaaaaaaattgattgcatttcttaacatatttgatcagACAAGAAGAATGAGAACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCATCCACTGCTGTTGAATCCATCCAGTACTCAAT
                            | | | |||   ||  |       |  |  || |   | || |  ||     |     | |   |  ||  |||     |  ||| |  ||           |  ||||||||||||||||||||||||||| ||| | ||  || | || ||           ||||  || || |||||    |||| ||
gtaagtgccgagtgaggtgacgcggtgatgtgcataatggtccaagatgtggacgtgagagagggaggtgtctttgcttgtggtgatgtgtgacgtttgtaaccggcagggatgggttt-------ggggtgaatcagACAAGAAGAATGAGAACAAGGAAGTAACGGTGGATAACTTCCTGGGCCACGAAGCTGCGATTCAAGCCATCAGTCACTCCAT

upper sequence: GLYMA16G01960.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------gtatccttaaaaatcttattccaataactttgatacctaagttttctttaagattactttatagtattttcataaaaaaaattgattgcatttcttaacatatttgatcagACAAGAAGAATGAGAACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCATCCACTGCTGTTGAATCCATCCAGTACTCAAT
                            | | | |||   ||  |       |  |  || |   | || |  ||     |     | |   |  ||  |||     |  ||| |  ||           |  ||||||||||||||||||||||||||| ||| | ||  || | || ||           ||||  || || |||||    |||| ||
gtaagtgccgagtgaggtgacgcggtgatgtgcataatggtccaagatgtggacgtgagagagagaggtgtctttgcttgtggtgatgtgtgacgtttgtaaccggcagggatgggttt-------ggggtgaatcagACAAGAAGAATGAGAACAAGGAAGTAACGGTGGATAACTTCCTGGGCCACGAAGCTGCGATTCAAGCCATCAGTCACTCCAT

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|16279981|gb|BI943717.1|BI943717
EST:     TCCGCCGCTTCTTTGAAGATT                         ACAAGAAGAATGAGAACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCAT
genomic: TCCGCCGCTTCTTTGAAGATTgtatccttaa ... atttgatcagACAAGAAGAATGAGAACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttatagtattttcataaaaaaaattgattgcatttcttaacatatttgatcagACAAGAAGAATGAGAACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCATCCACTGCTGTTGAATCCATCCAGTACTCAAT
 tttcttaac  putative branch site 
        tattttcataaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccttaaaaatcttattccaataactttgatacctaagttttctttaagattactttatagtattttcataaaaaaaattgattgcatttcttaacatatttgatcagACAAGAAGAATGAGAACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCATCCACTGCTGTTGAATCCATCCAGTACTCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT