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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgctacaatgtttcatgaactcctattcattgccaatagttatttttgtccgtgtggatggaagcctgatgctattgtccttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAAATTTCTGCAAAATGTTAAATTCAGTTTGTTGTCAACAATGAGGAGCCAT

Basic information

species Glycine max
transcript GLYMA07G38890.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G38890.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G451672_T01 (Zea mays), 3'ss of exon 9
gtatttgctacaatgtttcatgaactcctattcattgccaatagttatttttgtccgtgtggatggaagcctgatgctattgtccttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAAATTTCTGCAAAATGTTAAATTCAGTTTGTTGTCAACAATGAGGAGCCAT
|||| |   ||| || ||||  |  | ||  |  || |   |   || || ||  | ||||     || |    | || |||           |||||||| |||||||||||||| || |||||||| |||||||| || || | ||||||||||  ||| |||   || ||||   |     || |  | | |
gtatctttcaca-tgcttcagcattttct--ttgtttctggtttatagttatgagcctgtgacacaaaac----tactgttgc----------agTTGGCAGAATGATGTATTTGTGGTTGCTGAACCCGGAGAACTTGCAGACAGATTTCTGCAATCTGTCAAAACTAGCTTGTCAACCTTGTTGCGTGGGCGT

upper sequence: GLYMA07G38890.1 (Glycine max), 3'ss of exon 14
lower sequence: AT1G61850.2 (Arabidopsis thaliana), 3'ss of exon 15
gtatttgctacaatgtttcatgaactcctat-tcattgccaat---agttatttttgtccgtgtggatggaagcctgatgctattgtccttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAAATTTCTGCAAAATGTTAAATTCAGTTTGTTGTCAACAATGAGGAGCCAT
   || |    ||  |||||    |  | || |||    || |   |   |  ||  | |  ||| || ||   |   |||| || |  ||| |||||||||||| |||||||||||||| || |||||||||||||| || ||||| || ||||| ||||  || ||| ||||| | ||||||   |||   ||  ||
--gttagtccaaacttttcagtttccaccatatcacactcagttctaaaaaggttgattctagtgaattgattacatttgctttt-tggtttcatttagTTGGCAAAATGATGTATTTGTGGTTGCTGAACCTGGAGATCTAGCTGATAAGTTTCTCCAAAGCGTCAAAGTCAGTATATTGTCAGTCATGCAAAGTAAT

upper sequence: GLYMA07G38890.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv10s0116g00830.t01 (Vitis vinifera), 3'ss of exon 15
--gtatttgctacaatgtttcatgaactcctattcattgccaatagttatttttgtccgtgtggatggaagcctgatgctattgtccttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAAATTTCTGCAAAATGTTAAATTCAGTTTGTTGTCAACAATGAGGAGCCAT
  | | || |  |  || ||| | |  | ||||||       ||  |   ||   ||    | |      ||||| || |  ||| | |   ||||||||||| || ||||||||||| || || |||||||| ||||||||||| || ||||| |||| |||||| || || ||||| |||   ||| ||  ||||
gtgaactttcccct-tggttcttcatgttctattctcctgttattatagcttcattcttaatcgtgacctgcctggtgtt--tgttcct---tttagTTGGCAAAAGGATGTATTTGTGGTTGCGGAACCTGGGGAACTCGCTGATAAGTTTCTACAAAGTGTTAAGTTTAGCTTGTTATCAGTGATGCGGGCCCAT

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|193330392|gb|FK295292.1|FK295292
EST:     GGTGTTATGCATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAG                         TTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAA
genomic: GGTGTTATACATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAGgtatttgcta ... ttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAA
EST: gi|208258572|gb|GE055019.1|GE055019
EST:     GGTGTTATACATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAG                         TTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAA
genomic: GGTGTTATACATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAGgtatttgcta ... ttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAA
EST: gi|193418668|gb|FK383074.1|FK383074
EST:     GGTGTTATGCATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAG                         TTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAA
genomic: GGTGTTATACATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAGgtatttgcta ... ttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAA
EST: gi|13481690|gb|BG511033.1|BG511033
EST:     GGTGTTATACATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAG                         TTGGCACAATGATGTATNTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAA
genomic: GGTGTTATACATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAGgtatttgcta ... ttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAA
EST: gi|193394366|gb|FK360345.1|FK360345
EST:     GGTGTTATGCATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAG                         TTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAA
genomic: GGTGTTATACATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAGgtatttgcta ... ttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAA
EST: gi|207747022|gb|GD720679.1|GD720679
EST:     TTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAG                         TTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAA
genomic: TTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAGgtatttgcta ... ttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAA
EST: gi|51335705|gb|CO979571.1|CO979571
EST:     ATGGCTTAATTGTGAG                         TTGGCACAATGATGTATTTGNNGTGGCTGAACCTGGAGAACTCGCTGAGAA
genomic: ATGGCTTAATTGTGAGgtatttgcta ... ttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAA
EST: gi|193315535|gb|FK280215.1|FK280215
EST:     GGTGTTATACATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAG                         TTGGCACAATGA
genomic: GGTGTTATACATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAGgtatttgcta ... ttttatttagTTGGCACAATGA
EST: gi|193414370|gb|FK380982.1|FK380982
EST:     GGTGTTATGCATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAG                         TTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAA
genomic: GGTGTTATACATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAGgtatttgcta ... ttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAA
EST: gi|193385972|gb|FK352370.1|FK352370
EST:     GGTGTTATACATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAG                         TTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAA
genomic: GGTGTTATACATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAGgtatttgcta ... ttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAA
EST: gi|208327957|gb|GE124635.1|GE124635
EST:     GGTGTTATACATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAG                         TTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAA
genomic: GGTGTTATACATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAGgtatttgcta ... ttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAA
EST: gi|193525516|gb|FK479257.1|FK479257
EST:     GGTGTTATACATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAG                         TTGGCACAATGATGTATTTGTTGTGG
genomic: GGTGTTATACATTTGGCTCTTCAAAATGACTCGGATGGCTTAATTGTGAGgtatttgcta ... ttttatttagTTGGCACAATGATGTATTTGTTGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagttatttttgtccgtgtggatggaagcctgatgctattgtccttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAAATTTCTGCAAAATGTTAAATTCAGTTTGTTGTCAACAATGAGGAGCCAT
                            gcctgat  putative branch site (score: 4)
                                       ttgtccttttattt  putative PPT
                                             ttttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgctacaatgtttcatgaactcctattcattgccaatagttatttttgtccgtgtggatggaagcctgatgctattgtccttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAACTCGCTGAGAAATTTCTGCAAAATGTTAAATTCAGTTTGTTGTCAACAATGAGGAGCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG