Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caagtttcctttttatagtatattagtattattgattcttttatattaattattgtcttgattttttaattaatagttaaatgtttttttcttaatgcagTTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACCCAAATGCAACTGAGCATCTGCAGAAACTAAAAAAGATGGACCGCATAGA

Basic information

species Glycine max
transcript GLYMA16G29740.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G29740.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G52660.2 (Arabidopsis thaliana), 3'ss of exon 5
-caagtttcctttttatagtatattagtattattgattcttttatattaattattgtcttgattttttaattaatagttaaatgtttttttcttaatgcagTTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACCCAAATGCAACTGAGCATCTGCAGAAACTAAAAAAGATGGACCGCATAGA
  |||  ||    ||| |   | |      | || ||  |||| | |  |  ||  |    |||| ||| |  | ||||     ||||||| ||    ||||| | || || ||| | || ||||| ||||||||||| ||||| ||||||||| |||||| | | ||||| || || || || |||||||||| ||||||
gtaagcatcg---ttacatcgtctc----ctgttaatctttttgtttgtaccatatttaccatttcttactagacagttccgcctttttttttt---tcagTTTTACCGGACTTTGCCCAAGTATACGGCTTCATTGGAAGTGTGTTTGACCCATATGCAAGTAATCATCTACAAAAGCTGAAGAAGATGGACCCCATAGA

upper sequence: GLYMA16G29740.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0050g01180.t01 (Vitis vinifera), 3'ss of exon 5
-caagtttcctttttatagtatattagtattattgattcttttatattaattattgtcttgattttttaattaatagttaaatgttttttt-cttaatgcagTTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACCCAAATGCAACTGAGCATCTGCAGAAACTAAAAAAGATGGACCGCATAGA
  | |  |  |   | |  || |    |  |    |||||| | |||    |||| | || ||  | | | ||| |  | ||| |   ||| ||| |||||||||| || || |||  |||||||||  | |||||||||||||| |||||||| ||| | ||||  ||| | ||||| |||||||||||||| |  |||||
ggacggcttataaatttcttagaaagttgcttacaattcttatctatc--ctattttgttcatactcttactaacatattaatatccctttgcttgatgcagTTCTGCCTGACTTTGTTCAGGTATACAGATTCATTGGCAGTGTTTTTGACCCTAATTCTACTGGCCATTTACAGAAGCTAAAAAAGATGGATCCAATAGA
















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|19053052|gb|BM731719.1|BM731719
EST:     GCCAGTTGGTGAATCTAATTGTCAAGGGAATAAAATCCATCCATTGAGAG                         TTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACC
genomic: GCCAGTTGGTGAATCTAATTGTCAAGGGAATAAAATCCATCCATTGAGAGgcaaggtttt ... cttaatgcagTTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACC
EST: gi|58016997|gb|CX703739.1|CX703739
EST:     GCCAGTTGGTGAATCTAATTGTCAAGGGAATAAAATCCATCCATTGAGAG                         TTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACC
genomic: GCCAGTTGGTGAATCTAATTGTCAAGGGAATAAAATCCATCCATTGAGAGgcaaggtttt ... cttaatgcagTTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACC
EST: gi|21479821|gb|BQ576504.1|BQ576504
EST:     GCCAGTTGGTGAATCTAATGGTCAAGGGAATAAAATCCATCCATTGAGAG                         TTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACC
genomic: GCCAGTTGGTGAATCTAATTGTCAAGGGAATAAAATCCATCCATTGAGAGgcaaggtttt ... cttaatgcagTTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACC
EST: gi|26049069|gb|CA785522.1|CA785522
EST:     GCCAGTTGGTGAATCTAATTGTCAAGGGAATAAAATCCATCCATTGAGAG                         TTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACC
genomic: GCCAGTTGGTGAATCTAATTGTCAAGGGAATAAAATCCATCCATTGAGAGgcaaggtttt ... cttaatgcagTTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACC
EST: gi|58016753|gb|CX703495.1|CX703495
EST:     GCCAGTTGGTGAATCTAATTGTCAAGGGAATAAAATCCATCCATTGAGAG                         TTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACC
genomic: GCCAGTTGGTGAATCTAATTGTCAAGGGAATAAAATCCATCCATTGAGAGgcaaggtttt ... cttaatgcagTTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACC
EST: gi|120528797|gb|EH256931.1|EH256931
EST:     GCCAGTTGGTGAATCTAATTGTCAAGGGAATAAAATCCATCCATTGAGAG                         TTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACC
genomic: GCCAGTTGGTGAATCTAATTGTCAAGGGAATAAAATCCATCCATTGAGAGgcaaggtttt ... cttaatgcagTTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACC
EST: gi|120531655|gb|EH259788.1|EH259788
EST:     GCCAGTTGGTGAATCTAATTGTCAAGGGAATAAAATCCATCCATTGAGAG                         TTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACC
genomic: GCCAGTTGGTGAATCTAATTGTCAAGGGAATAAAATCCATCCATTGAGAGgcaaggtttt ... cttaatgcagTTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACC
EST: gi|193546523|gb|FK501832.1|FK501832
EST:     GCCAGTTGGTGAATCTAATGGTCAAGGGAATAAAATCCATCCATTGAGAG                         TTCTTCCAGATTTTACTCAGGTATATGGCTTCATTG
genomic: GCCAGTTGGTGAATCTAATTGTCAAGGGAATAAAATCCATCCATTGAGAGgcaaggtttt ... cttaatgcagTTCTTCCAGATTTTACTCAGGTATATGGCTTCATTG
EST: gi|6666602|gb|AW278061.1|AW278061
EST:     GCCAGTTGGTGAATCTAATTGTCAAGGGAATAAAATCCATCCATTGAGAG                         TTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACC
genomic: GCCAGTTGGTGAATCTAATTGTCAAGGGAATAAAATCCATCCATTGAGAGgcaaggtttt ... cttaatgcagTTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaattattgtcttgattttttaattaatagttaaatgtttttttcttaatgcagTTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACCCAAATGCAACTGAGCATCTGCAGAAACTAAAAAAGATGGACCGCATAGA
                                    tgtttttttctt  CT-rich tract
            ttgattttttaattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caagtttcctttttatagtatattagtattattgattcttttatattaattattgtcttgattttttaattaatagttaaatgtttttttcttaatgcagTTCTTCCAGATTTTACTCAGGTATATGGCTTCATTGGCAGTGTATTTGACCCAAATGCAACTGAGCATCTGCAGAAACTAAAAAAGATGGACCGCATAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcttg