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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctgctactatgctactatgtttcatgaactcctattcattgtcaatagttatttttgcccgtgtggatggaagcctgatgctattgtccttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAGCTCGCTGAGAAATTTCTACAAAATGTTAAATTCAGTTTGTTGTCAACAATGAGGAGCCAT

Basic information

species Glycine max
transcript GLYMA17G01850.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G01850.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G451672_T01 (Zea mays), 3'ss of exon 9
gtatctgctactatgctactatgtttcatgaactcctattcattgtcaatagttatttttgcccgtgtggatggaagcctgatgctattgtccttttatt-tagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAGCTCGCTGAGAAATTTCTACAAAATGTTAAATTCAGTTTGTTGTCAACAATGAGGAGCCAT
                   ||| |||||    || |    |||| ||     || ||| ||    | | | |   |||||| ||  |     ||  | ||  |||||||| |||||||||||||| || |||||||| ||||| || || || | |||||| |||  ||| |||   || ||||   |     || |  | | |
------------------gtatctttcacatgcttcag--cattttct----ttgtttctggtt-tatagttatgagcctg-tgacacaaaactactgttgcagTTGGCAGAATGATGTATTTGTGGTTGCTGAACCCGGAGAACTTGCAGACAGATTTCTGCAATCTGTCAAAACTAGCTTGTCAACCTTGTTGCGTGGGCGT

upper sequence: GLYMA17G01850.1 (Glycine max), 3'ss of exon 15
lower sequence: AT1G61850.2 (Arabidopsis thaliana), 3'ss of exon 15
gtatctgctactatgctactatgtttcatgaactcctattcattgtcaatagttatttttgcccgtgtggatggaagcctgatgctattgtccttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAGCTCGCTGAGAAATTTCTACAAAATGTTAAATTCAGTTTGTTGTCAACAATGAGGAGCCAT
     |  | | |   |   |  || ||  |  ||  | ||| |   || |   |  ||    |  ||| || ||   |   |||| || |  ||| |||||||||||| |||||||||||||| || |||||||||||||| || ||||| || ||||| ||||  || ||| ||||| | ||||||   |||   ||  ||
---gttagtccaaacttttcagtttccaccatatcacactcagttctaaaa---aggttgattctagtgaattgattacatttgct-ttttggtttcatttagTTGGCAAAATGATGTATTTGTGGTTGCTGAACCTGGAGATCTAGCTGATAAGTTTCTCCAAAGCGTCAAAGTCAGTATATTGTCAGTCATGCAAAGTAAT

upper sequence: GLYMA17G01850.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv10s0116g00830.t01 (Vitis vinifera), 3'ss of exon 15
--gtatctgctactatgctactatgtttcatgaactcctattcattgtcaatagttatttttgcccgtgtggatggaagcctgatgctattgtccttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAGCTCGCTGAGAAATTTCTACAAAATGTTAAATTCAGTTTGTTGTCAACAATGAGGAGCCAT
  | |  | |  || || | ||   | |  |   ||||| || ||| |   |  | ||| ||   ||||         ||||| || |  ||| | |||   ||||||||| || ||||||||||| || || |||||||| || |||||||| || |||||||||| |||||| || || ||||| |||   ||| ||  ||||
gtgaactttcccct-tggttcttcatgttctattctcctgtt-attatagct--tcattcttaatcgtg-----acctgcctggtgtt--tgttccttt---tagTTGGCAAAAGGATGTATTTGTGGTTGCGGAACCTGGGGAACTCGCTGATAAGTTTCTACAAAGTGTTAAGTTTAGCTTGTTATCAGTGATGCGGGCCCAT

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|193682607|gb|FK623369.1|FK623369
EST:     GGTGTTATACATTTGGCTCTTCAAAATAACTCAGATGGCTTAATTGTTAG                         TTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAGCTCGCTGAGAA
genomic: GGTGTTATACATTTGGCTCTTCAAAATAACTCAGATGGCTTAATTGTTAGgtatctgcta ... ttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAGCTCGCTGAGAA
EST: gi|208269300|gb|GE070280.1|GE070280
EST:     GGTGTTATACATTTGGCTCTTCAAAATAACTCAGATGGCTTAATTGTTAG                         TTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAGCTCGCTGAGAA
genomic: GGTGTTATACATTTGGCTCTTCAAAATAACTCAGATGGCTTAATTGTTAGgtatctgcta ... ttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAGCTCGCTGAGAA
EST: gi|208111495|gb|GD909549.1|GD909549
EST:     GGTGTTATACATTTGGCTCTTCAAAATAACTCAGATGGCTTAATTGTTAG                         TTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAGCTCGCT
genomic: GGTGTTATACATTTGGCTCTTCAAAATAACTCAGATGGCTTAATTGTTAGgtatctgcta ... ttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAGCTCGCT
EST: gi|207755568|gb|GD730429.1|GD730429
EST:     TGTTATACATTTGGCTCTTCAAAATAACTCAGATGGCTTAATTGTTAG                         TTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAGCTCGCTGAGAA
genomic: TGTTATACATTTGGCTCTTCAAAATAACTCAGATGGCTTAATTGTTAGgtatctgcta ... ttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAGCTCGCTGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagttatttttgcccgtgtggatggaagcctgatgctattgtccttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAGCTCGCTGAGAAATTTCTACAAAATGTTAAATTCAGTTTGTTGTCAACAATGAGGAGCCAT
                            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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctgctactatgctactatgtttcatgaactcctattcattgtcaatagttatttttgcccgtgtggatggaagcctgatgctattgtccttttatttagTTGGCACAATGATGTATTTGTTGTGGCTGAACCTGGAGAGCTCGCTGAGAAATTTCTACAAAATGTTAAATTCAGTTTGTTGTCAACAATGAGGAGCCAT

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