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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctcatgtaatatgtctacaaggagatattgtttaatttgtgaaagctgttaacttgggtatctaattttcttcatttctcttcatcagtttgatttgtcattttatatcacaaataatatacctccttttcccatgcagAGTATTGCAATAGAATTGCAGAGCGAGCCTAAATGGAAGCAATTGGGAGAATTAGCTATGTCTACTGGAAAG

Basic information

species Glycine max
transcript GLYMA13G43680.2
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 18
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 22
gtatgctcatgtaatatgtctacaaggagatattgtttaatttgtgaaagctgttaacttgggtatctaattttcttcatttct----cttcatcagtttgatttgtcattttatatcacaaataatatacctccttttcccatgcagAGTATTGCAATAGAATTGCAGAGCGAGCCTAAATGGAAGCAATTGGGAGAATTAGCTATGTCTACTGGAAAG
                                                           |  || | || ||||   |||||      ||| ||     ||| ||  |  | | | |      | |      || | ||      |||   |||||  ||||    || |  ||  |||||||||||||| | ||||||||||||||||| | ||| |||
----------------------------------------------------------gttagtctgtagtttttaccatttgagaagctttatttccatgacttaccgatatgttt------ttactcgattcttattttttgacagGACATTGCTGTAGAGGCACAAAATGAATCTAAATGGAAGCAACTTGGAGAATTAGCTATGTCAAGTGGGAAG

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 18
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 18
-----gtatgctcatgtaatatgtctacaaggagatattgtttaatt-tgtgaaagct-gttaacttgggtatctaattt--tcttcatttctcttc--------atcagtttgatttgtca-ttttatatcacaaataatatacctccttttcccatgcagAGTATTGCAATAGAATTGCAGAGCGAGCCTAAATGGAAGCAATTGGGAGAATTAGCTATGTCTACTGGAAAG
      |||| | || |  ||||||   |  | |||||    || || | ||| || | ||| |||||   || |||     |||| ||||   |          || |||    | || || |||||| | | | |||  ||   || | ||  | | |||   ||||| | |||| |||| || ||| | |||||||||||||||||||||||||||||||| |||||||||
gtaaattatgttgattt--tatgtcagtatagggatataaactagttctttgacagtttgttgacttgaacatttaagcacatctttattttcttctgaggaatgattagtcctctgtgacaattttatctgaaatatagcatga-tcttctttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 18
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 18
----gtatgctcatgtaa-tatgtctacaaggagatattgtttaatttgtgaaagctgttaacttgggtatctaattttcttcatttctcttcatcagtttgatttgtcattttatatcacaaataatatacctccttttcccatgcagAGTATTGCAATAGAATTGCAGAGCGAGCCTAAATGGAAGCAATTGGGAGAATTAGCTATGTCTACTGGAAAG
    | ||  | || ||  | |   ||   | | | |   || |||| |            |  |  ||   | | ||  |  |  ||   || |   ||  | ||||   |||  || |  ||  || |  || || |||   |||||   || ||   |||| | ||||| ||  | ||||||||||| |||||||||||||||||||| | |||||||
gtaagaatttttatttatctttagttaggtgtataaacc-ttcaattggcatttaacacctatgtaagtgagtgagttcatcaaaatcaactcttttcttataattgtttgtttccattatgaaagatgtttcttctcttct--tgcagGAAATAGCTTCAGAAGTACAGAGTGAAACCAAATGGAAGCAGTTGGGAGAATTAGCTATGTCCAATGGAAAG

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|298199623|gb|HO043500.1|HO043500
EST:     ACTACAGATTTGATCTAGCAATACAGCTTGGAAAACTAGATGTTGCAAAG                         AGTATTGCAATAGAATTGCAGAGCGAGCCTAAATGGAAGCAGTTGGGAGAA
genomic: ACTACAGATTTGATCTAGCAATACAGCTTGGAAAACTAGATGTTGCAAAGgtatgctcat ... tcccatgcagAGTATTGCAATAGAATTGCAGAGCGAGCCTAAATGGAAGCAATTGGGAGAA
EST: gi|151398221|gb|EV268099.1|EV268099
EST:     ACTACAGATTTGATCTAGCAATACAGCTTGGAAAACTAGATGTTGCAAAG                         AGTATTGCAATAGAATTGCAGAGCGAGCCTAAATGGAAGCAATTGGGAGAA
genomic: ACTACAGATTTGATCTAGCAATACAGCTTGGAAAACTAGATGTTGCAAAGgtatgctcat ... tcccatgcagAGTATTGCAATAGAATTGCAGAGCGAGCCTAAATGGAAGCAATTGGGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagtttgatttgtcattttatatcacaaataatatacctccttttcccatgcagAGTATTGCAATAGAATTGCAGAGCGAGCCTAAATGGAAGCAATTGGGAGAATTAGCTATGTCTACTGGAAAG
   gtttgat  putative branch site (score: 5)
                                 tatacctccttttccc  putative PPT
        atttgtcattttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctcatgtaatatgtctacaaggagatattgtttaatttgtgaaagctgttaacttgggtatctaattttcttcatttctcttcatcagtttgatttgtcattttatatcacaaataatatacctccttttcccatgcagAGTATTGCAATAGAATTGCAGAGCGAGCCTAAATGGAAGCAATTGGGAGAATTAGCTATGTCTACTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA