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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTCATAAGACACGTCAAGAATTTGCTGAGTTCTACAAAAGTGCCCTTCTCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatcagaattgtcttaaatgtttttgttgattgttgccttttttgttgtctcaaatcatggctatttacttgtactttactctgattatggtgt...

Basic information

species Glycine max
transcript GLYMA01G01460.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G01460.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 5'ss of exon 2
GTTTCATAAGACACGTCAAGAATTTGCTGAGTTCTACAAAAGTGCCCTTCTCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtc--atcagaattgtcttaa--atgtttttgttgattgttgccttttttgttgtctcaaatcatggctatt-tacttgtactt-tactctgattatggtgt-------
||  |||||| | || ||||||||||||||||||||||| | ||||||||| ||| |||| |||||  | || || || |||||||| || ||||| |||||||||   ||    |       ||  |  |        ||  || |||  |    |   |  ||| |||  | ||  |  | |  ||   || ||||  ||   |       
GTACCATAAGGCTCGCCAAGAATTTGCTGAGTTCTACAAGAATGCCCTTCTGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTGgtatgttctattgttaacaatgcaattacatgacaaaaaatcatttcctcctcgcattattttaataatgtatcttgcatctatgtttaccctttgatgctgtcttgtgtcag

upper sequence: GLYMA01G01460.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os01g32800.1 (Oryza sativa), 5'ss of exon 2
GTTTCATAAGACACGTCAAGAATTTGCTGAGTTCTACAAAAGTGCCCTTCTCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtat--gtcatcagaattgtcttaaatgtttttgttgattgttgccttttttgttgtctcaaatcatggctatttact-tgtactttactctgatt-atggtgt-------------------------
||  |||||| |  | |||||||| ||||| ||||| || | ||| ||||| ||| |||| |||||  | ||||| || |||||||| ||||||||||||||||     ||   ||||   | | |         |     || |   | |  ||   |    | ||  | |  |||| || |  ||  |   ||| ||  | |                         
GTACCATAAGGCTTGCCAAGAATTCGCTGAATTCTATAAGAATGCTCTTCTTTATCTGGCCTACACTACTGTGGAGTCGCTCTCTGAGTCATTCAAGCTGgtattaacaatgccaattacataacagaaaaaaaatagcatttcctcctctcattagttagtttaataacaacatactgtgcatattgtttgtattgataatttaccctttgacactgtcatgtgtcag

upper sequence: GLYMA01G01460.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM5G868757_T04 (Zea mays), 5'ss of exon 3
GTTTCATAAGACACGTCAAGAATTTGCTGAGTTCTACAAAAGTGCCCTTCTCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgt--catcag-aattgtcttaaatgtttttgttgattgttgccttttttgtt-gtctcaaatcatggctatttacttgtactttactctgattatggtgt
 |  || ||| |  | ||||||||||| |||||||| || | ||| ||||||||| |||| |||||| | ||||| ||||| ||||| ||||||||||| ||||||  |||||  | |    ||  |  | |   | ||   |    ||   ||||  ||| |  |  || || ||| ||     || |               
ATACCACAAGGCCTGCCAAGAATTTGCAGAGTTCTATAAGAATGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttcatcatcagtaacatttgaactctaaatagaacttcagtttaaatgttcatctgatttattgactgttttctatcttttcag--------------

upper sequence: GLYMA01G01460.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G083076_T03 (Zea mays), 5'ss of exon 3
GTTTCATAAGACACGTCAAGAATTTGCTGAGTTCTACAAAAGTGCCCTTCTCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatcagaattgtcttaaatgtttttgttgattgttgccttttttgttgtctcaaatca--tggctatttacttgtactttactctgattatggtgt
 |  || ||| || | ||||||||||| |||||||| || |  || ||||||||| |||| |||||| | ||||| ||||| ||||| ||||||||||| ||||||       |   ||   ||  |||    ||           ||  ||| |   |  |||  || ||  ||   | | || ||   ||          
ATACCACAAGTCATGCCAAGAATTTGCAGAGTTCTATAAGAACGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttc----accatcaataacatttgaactgtaaaacaaaacttcagtt-taaaagttcatctgacttattgactattctatatcttgtcag------

upper sequence: GLYMA01G01460.1 (Glycine max), 5'ss of exon 2
lower sequence: AT5G45620.2 (Arabidopsis thaliana), 5'ss of exon 2
GTTTCATAAGACACGTCAAGAATTTGCTGAGTTCTACAAAAGTGCCCTTCTCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatcagaattgtcttaaatgtttttgttgattgttgccttttttgttgtctcaaatcatggctatttacttgtactttactctgatt--atggtgt------------------------------------------------------------------------------------------------
||  ||||||   |||||||||||| |||| |||||||||||||| || || ||| | |||||||| || |||||    || || || || || ||||||||||| |     |||  | |  |   | ||  |  ||| |   ||| | |   || ||   | |  | || |   |   | | | |    |||  |||   |                                                                                                
GTACCATAAGTGCCGTCAAGAATTTTCTGATTTCTACAAAAGTGCTCTGCTTTATCTTGCATACACGTCTGTGGAGGACCTTTCAGAATCGTTTAAGCTGgtatgcccctgtaatattatgtaccttgttcttatattttgttcttatgttaagtttcctgttagcgatagtggataagagtattcagaaatttgatgaaatttagaggaaactgaagaaaaaagttgcgtactagttagcttccctagagtcaccgatcaaattttgctaatgtcagatcatatctgtgtctttcag

upper sequence: GLYMA01G01460.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv02s0012g02660.t01 (Vitis vinifera), 5'ss of exon 2
GTTTCATAAGACACGTCAAGAATTTGCTGAGTTCTACAAAAGTGCCCTTCTCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatcagaattgtcttaaatgtttttgttgattgttgccttttttgttgtctcaaatcatggctatttacttgt--actttactctgat-tatggtgt
|| | ||||  | ||||||||||| || || ||||| |||||||| ||||| ||| ||||||||||||||||||| |||||||||||  |||| |||||||||||| | |  |  ||  |||| | |||      |||   | | ||| |  ||  ||| || ||   |  | ||||||  |   |  | |||  | |  |||
GTATTATAAATCTCGTCAAGAATTCGCAGAATTCTATAAAAGTGCTCTTCTATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgtta-ctcatgtgctttaattatttcaaaaaattcaagtcatttataatgattcacattatactt--tcacttgttaaggctgttttgacatctcatgt

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|151410399|gb|EV280214.1|EV280214
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|207794208|gb|GD765722.1|GD765722
EST:     GGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: GGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|151396447|gb|EV266324.1|EV266324
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|23052675|gb|BU577167.1|BU577167
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|27426218|gb|CA937738.1|CA937738
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|193679433|gb|FK621043.1|FK621043
EST:     CGTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCT
genomic: C-TATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCT
EST: gi|23052846|gb|BU577337.1|BU577337
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|151413131|gb|EV282939.1|EV282939
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|6501937|gb|AW203310.1|AW203310
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|308098687|gb|HO760428.1|HO760428
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|151397751|gb|EV267624.1|EV267624
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|15204623|gb|BI427391.1|BI427391
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|11688213|gb|BF595889.1|BF595889
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTCATAAGACACGTCAAGAATTTGCTGAGTTCTACAAAAGTGCCCTTCTCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatcagaattgtcttaaatgtttttgttgattgttgccttttttgttgtctcaaatcatggctatttacttgtactttactctgattatggtgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG