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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCACGGAGATGAAATATGCGGAGCTGTTGTGAATGTCAGAAGTAGGCAGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAGgtaacattcctatttattcagttagttttggtttgtttctttttttccctttgtttactattgtgctgcaggtgggagggagtgagggagatttatctag...

Basic information

species Glycine max
transcript GLYMA15G09630.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G09630.2 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os01g73880.1 (Oryza sativa), 5'ss of exon 3
TGATCACGGAGATGAAATATGCGGAGCTGTTGTGAATGTCAGAAGTAGGCAGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAGgtaacattcctatttattcagttagttttggtttgtttctttttttccctttgtttactattgtgctgcaggtgggagggagtgagggagatttatctag-------
 ||| | || |||||||| || ||||| ||||| | |||  |  | | |||||||| ||| ||||| |||||||| || ||| | ||||||||||||||||||  ||| |||       || ||  |   | |  ||| ||| || ||    | | |  |       |        |       |   | | || |  |        
CGATTATGGGGATGAAATTTGTGGAGCAGTTGTTAGTGTGCGTGGCAAGCAGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttcta-------agatatgtgctgctaatttatttgttacctgcagataataaccacatagttttcaacatcattaaattcaaacttttacatgtcattg

upper sequence: GLYMA15G09630.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G002616_T01 (Zea mays), 5'ss of exon 3
TGATCACGGAGATGAAATATGCGGAGCTGTTGTGAATGTCAGAAGTAGGCAGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAGgtaacattcctatttattcagttagttttggtttgtttctttttttccctttgtttactattgtgctgcaggtgggagggagtgagggagatttatctag--
 ||  | || |||||||| || || || ||||| | |||  |  | | |||||||| ||||||||||||||| || || ||| | |||||||| |||||||||      || |     |||| |  | |   |||       || | || |  |||| |  | |  | |  |            | |    ||    ||   
CGACTATGGTGATGAAATTTGTGGCGCAGTTGTCAGTGTGCGTGGGAAGCAGGAAAGAATTGCTATTTGGACAAAAAATGCTGCCAATGAAGCCGCTCAGgtatatgcgctgtagtaacagtaacctcttcattggaaacacttgtaccataatttatt--tattttccttgctaacaaataccatgccttttctcataata

upper sequence: GLYMA15G09630.2 (Glycine max), 5'ss of exon 3
lower sequence: AT4G18040.1 (Arabidopsis thaliana), 5'ss of exon 3
TGATCACGGAGATGAAATATGCGGAGCTGTTGTGAATGTCAGAAGTAGGCAGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAGgtaac--attcctatttattcagttagttttggtttgtttctttttttccctttgtttactattgtgctgcaggtggg-agggagtgagggagatttatctag
|||||| |||||||||||||| ||||| ||||| ||  | ||| | | ||| ||||  ||  ||||||||||||| || |||||||| ||||||||||||||||         |  | |    | |    |  |       | | | |   |     ||  | | |  | |  ||  | |   | ||  | ||          
TGATCATGGAGATGAAATATGTGGAGCAGTTGTCAACATTAGAGGAAAGCAAGAAAGGATATCTATTTGGACTAAAAATGCTTCAAACGAAGCTGCTCAGgtaaatagaaaagacctttctcatcaaaactcatcaaacagtctctctgtgtaaaaataagactttaattctcgtctgcatcaaatgttgcag----------

upper sequence: GLYMA15G09630.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv10s0003g02250.t01 (Vitis vinifera), 5'ss of exon 3
TGATCACGGAGATGAAATATGCGGAGCTGTTGTGAATGTCAGAAGTAGGCAGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAGgtaac--attcctatttattcagttagttttggtttgtttctttttttccctttgtttactattgtgctgcaggtgggagggagtgaggga-gatttatctag
|||||| ||||||||||| || ||||| ||  | |||||||||  ||| ||||| ||||| ||| | ||||| ||||| |||||||||||||||||||||||| |  | |  |||  ||| |  |   |||  |  | || |  |      | |||||    || |    || ||   |  ||||||     || ||||    
TGATCATGGAGATGAAATCTGTGGAGCAGTGATCAATGTCAGAGCTAGACAGGAGAAAATAGCTCTATGGACCAAGAATGCTTCAAATGAAGCTGCTCAGgtagctaaattttataaattaatctgcattttctgaggttgtcctaactattatgttttggtttatttaacatgttttaatgagtgacaattgaattatt---

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|31457012|gb|CD399040.1|CD399040
EST:     AGGAAAAAATTGCTATTTGGACTAAGTACGCTTCAAATGAAGCTGCTCAG                         GTGAGCATTGGAAAGCAGTGGAAGGAGTTTCTTGATTACAATGACACTATT
genomic: AGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAGgtaacattcc ... cttctcgcagGTGAGCATTGGAAAGCAGTGGAAGGAGTTTCTTGATTACAATGACACAATT
EST: gi|192308366|gb|FK002794.1|FK002794
EST:     AGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTACTCAG                         GTGAGCATTGGAAAGCAGTGGAAGGAGTTTCTTGATTACAATGACACAATT
genomic: AGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAGgtaacattcc ... cttctcgcagGTGAGCATTGGAAAGCAGTGGAAGGAGTTTCTTGATTACAATGACACAATT
EST: gi|9820397|gb|BE555907.1|BE555907
EST:     AGGAAAANATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAG                         GTGAGCATTGGAAAGCAGTGGGAGGAGTTTCTTGATTACAATGACACAATT
genomic: AGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAGgtaacattcc ... cttctcgcagGTGAGCATTGGAAAGCAGTGGAAGGAGTTTCTTGATTACAATGACACAATT
EST: gi|208251693|gb|GE044236.1|GE044236
EST:     AGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAG                         GTGAGCATTGGAAAGCAGTGGAAGGAGTTTCTTGATTACAATGACACAATT
genomic: AGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAGgtaacattcc ... cttctcgcagGTGAGCATTGGAAAGCAGTGGAAGGAGTTTCTTGATTACAATGACACAATT
EST: gi|213616888|gb|DB978878.1|DB978878
EST:     AGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAG                         GTGAGCATTGGAAAGCAGTGGAAGGAGTTTCTTGATTACAATGACACAATT
genomic: AGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAGgtaacattcc ... cttctcgcagGTGAGCATTGGAAAGCAGTGGAAGGAGTTTCTTGATTACAATGACACAATT
EST: gi|6846595|gb|AW348885.1|AW348885
EST:     AGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAG                         GTGAGCATTGGAAAGCAGTGGAAGGAGTTTCTTGATTACAATGACACAATT
genomic: AGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAGgtaacattcc ... cttctcgcagGTGAGCATTGGAAAGCAGTGGAAGGAGTTTCTTGATTACAATGACACAATT
EST: gi|207826521|gb|GD798652.1|GD798652
EST:     AGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAG                         GTGAGCATTGGAAAGCAGTGGAAGGAG
genomic: AGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAGgtaacattcc ... cttctcgcagGTGAGCATTGGAAAGCAGTGGAAGGAG
EST: gi|31470645|gb|CD412673.1|CD412673
EST:     AGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAG                         GTGAGCATTGGAAAGCAGTGGAAGGAGTTTCTTGATTACAATGACACAATT
genomic: AGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAGgtaacattcc ... cttctcgcagGTGAGCATTGGAAAGCAGTGGAAGGAGTTTCTTGATTACAATGACACAATT
EST: gi|209698256|gb|BW678027.1|BW678027
EST:     AGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAG                         GTGAGCATTGGAAAGCAGTGGAAGGAGTTTCTTGATTACAATGACACAATT
genomic: AGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAGgtaacattcc ... cttctcgcagGTGAGCATTGGAAAGCAGTGGAAGGAGTTTCTTGATTACAATGACACAATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATCACGGAGATGAAATATGCGGAGCTGTTGTGAATGTCAGAAGTAGGCAGGAAAAAATTGCTATTTGGACTAAGAACGCTTCAAATGAAGCTGCTCAGgtaacattcctatttattcagttagttttggtttgtttctttttttccctttgtttactattgtgctgcaggtgggagggagtgagggagatttatctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggaggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgaggg