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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcaactattttcctcctttgatttgaatttttgtctttgttatctaaattcttccttgctgctctctttgcctaaagtagttgaatttttctttttcagGGTTAAAACCAACATTAGATTTCATGTTGGGGATGTCGAAGTGGCAGCAGTTCCATGTGGCTTTGGACGTGCTATTGGCAATAAG

Basic information

species Glycine max
transcript GLYMA20G36090.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G36090.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g32440.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------atcaactattttcc-tcctttgatttgaatttttgtctttgttatctaaat---tcttccttgctgctctctttgcctaaagtagttgaatttttctttttcagGGTTAAAACCAACATTAGATTTCATGTTGGGGATGTCGAAGTGGCAGCAGTTCCATGTGGCTTTGGACGTGCTATTGGCAATAAG
                                      |  |   ||||    ||   | ||   || || | |  ||  ||  || ||   |   | ||   |     |||   | |  | ||  |  ||  |||||  ||||  | ||  | | |||      ||||||| ||||| ||||  || ||||| |||||||| |||||||||||||| |||||||||
gtattgtgtcttgtcatgacttagctgatttggtttacactataaatttcttgtcacataatgataacttgtttaatttataattagatgaattaccattctcgtgtaatttattttacat-gtaaacattaacttttcaagGGCAAGAAAGAGCCTTAAGCCATATGTTGGTGATGTGGAAGCTGCTGCAGTGCCATGTGGTTTTGGACGTGCTATCGGCAATAAG

upper sequence: GLYMA20G36090.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g41270.2 (Oryza sativa), 3'ss of exon 5
-----------------------------atcaactattttcctcctttgatttgaatttttgtctttgttatctaaattcttccttgctgctctctttgcctaaagtagttgaatttttct--ttttcagGGTTAAAACCAACATTAGATTTCATGTTGGGGATGTCGAAGTGGCAGCAGTTCCATGTGGCTTTGGACGTGCTATTGGCAATAAG
                              | ||  ||||| ||  | | || | |||| |  | ||| ||    |  ||  | |||    |   |  |   ||  | |  |  ||  |  |  |||  ||||  |  |   || |||     |||||||| ||||| || |  || ||||| |||||||||||||| |||||||||||||| |||
gtactggtttatcttaaaaccatttcttagtgaaacatttttctgttattatat-aattatcattttttttgc--acttttgtacttttctcatacgatatgtatggcatgtacatcatgataatttcaagGGCAAGGAAGGACCTTAAGCCACATGTTGGTGATGTTGATGCTGCTGCAGTACCATGTGGCTTTGGGCGTGCTATTGGCAACAAG

upper sequence: GLYMA20G36090.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G329909_T01 (Zea mays), 3'ss of exon 4
------atcaactattttcctcctttgatt--------tgaatttttgtctttgt---tatctaaatt--cttccttgctgctctctttgcctaaagtagttgaatttt---------tctttttcagGGTTAAAACCAACATTAGATTTCATGTTGGGGATGTCGAAGTGGCAGCAGTTCCATGTGGCTTTGGACGTGCTATTGGCAATAAG---------------
      |  ||  ||  || |   || ||         || |||| |||     |    ||   ||||  | |  |   | || |  | | || |  |      ||  |         |  | |  ||||  |  |   || |||     |||||||| ||||| || |  || ||||| ||||||||||||||||||||||||||||| |||               
gtactgactaatcataatcatttcttaataaaacatcgtgcatttctgttcacatgagcattacaatttgcattttccgtacttttctcgtctcatatttccacatcctacgtcatgattatctgaagGGCAAGGAATGACCTTAAGCCACATGTTGGTGATGTTGATGCTGCTGCAGTGCCATGTGGCTTTGGACGTGCTATTGGCAACAAGGTAAGCGATTGTCAA

upper sequence: GLYMA20G36090.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G318949_T01 (Zea mays), 3'ss of exon 3
-------------atcaactattttcc--tcctttgatttgaatttttgtct---ttgttatctaaatt----cttccttgctgctctctt-tgcctaaagtagttgaatttttctttttcagGGTTAAAACCAACATTAGATTTCATGTTGGGGATGTCGAAGTGGCAGCAGTTCCATGTGGCTTTGGACGTGCTATTGGCAATAAG
             || ||  ||||     |       | | ||||| |||     |  ||||   | ||    ||||| |  |  || | | |  | | | |  |||   |  |  | |  ||||  |  |   || ||||    |||||||| ||||| || |   | ||||| |||||||||||||| |||||||||||||| |||
gtactgactaatcatgaatcatttcttaatgacacattataaatttatgttcacatgattattacagtttgcgcttccatatttatcccatatttccacattctttgtcatgattatctgaagGGCAACGAATGACCTTAGGCCACATGTTGGTGATGTTGATGCTACTGCAGTGCCATGTGGCTTTGGGCGTGCTATTGGCAACAAG

upper sequence: GLYMA20G36090.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G065225_T01 (Zea mays), 3'ss of exon 4
-------------atcaactattttcc--tcctttgatttgaatttttgtct---ttgttatctaaatt----cttccttgctgctctctt-tgcctaaagtagttgaatttttctttttcagGGTTAAAACCAACATTAGATTTCATGTTGGGGATGTCGAAGTGGCAGCAGTTCCATGTGGCTTTGGACGTGCTATTGGCAATAAG
             |  ||  ||||     |       | | ||||| |||     |  ||||   | ||    ||||| | ||  || | | |  | | | |   ||   |  |  |||  ||||  |  |   || ||||    |||||||| ||||| ||    || ||||| |||||||||||||| |||||||||||||| |||
gtactgattaatcacgaatcatttcttaatgacacattataaatttctgttcacatgattattacagtttgcgcttccatacttatcccatatttccacattctgtgtcatgattatttgaagGGCAACGAATGACCTTAGGCCACATGTTGGTGATGTTGATACTGCTGCAGTGCCATGTGGCTTTGGGCGTGCTATTGGCAACAAG

upper sequence: GLYMA20G36090.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G423567_T01 (Zea mays), 3'ss of exon 4
-------------atcaactattttcctcct-ttgatttgaatttttgtctttg------------ttatctaaattcttccttgct-gctctctttgcctaaagtagttgaatttttctttttcagGGTTAAAACCAACATTAGATTTCATGTTGGGGATGTCGAAGTGGCAGCAGTTCCATGTGGCTTTGGACGTGCTATTGGCAATAAG
              | || || |||| |    || |  | ||  | |||  |              ||    || ||  |  ||||| | |  | || | | |  | |   |  ||  |||||  ||||  | ||  | | ||| |    ||||||| ||||| ||||  || ||||| || |||||  |||||||||||||||||||||||
gtattagtttattgtgaattagtttcttagaattaaactaaaaatctgttatcacatagtgataacttcctcaatttactgtttgcttggttacctttcttgacatggaaaatattaacttttcaagGGCAAGAAAGAGCCTTAAACCATATGTTGGAGATGTTGAAGCTGCTGCAGTGCCGTGTGGTCTTGGACGTGCTATTGGCAATAAG

upper sequence: GLYMA20G36090.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G422045_T01 (Zea mays), 3'ss of exon 4
--------------------------------atcaactattttcctcctttgatttgaatttttgtcttt--gttatctaaattcttccttgctgctctctt------tgcctaaagtagttgaatttttctttttcagGGTTAAAACCAACATTAGATTTCATGTTGGGGATGTCGAAGTGGCAGCAGTTCCATGTGGCTTTGGACGTGCTATTGGCAATAAG
                                 | |||||     ||  | | |  |||   |  ||  ||   ||| ||   |  ||  || |   |||| |      ||| | |  | |   |  ||  |||||  ||||  | ||  | | | | |    ||||||| ||||| ||||  || ||||| || |||||  |||||||||||||||||||||||
gtattagcttgttgtgaattagtttcttagaattaaactacaaatctgttatcacatgatgataagttgttcaattaactgtttgtttaattacctttctcatgtgatatgcatgacatggaaaatattaacttttcaagGGCAAGAAAGAGCCTAAAACCATATGTTGGAGATGTTGAAGCTGCTGCAGTGCCGTGTGGTCTTGGACGTGCTATTGGCAATAAG

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|7692411|gb|AW760518.1|AW760518
EST:     TTTGAACGTATTGGATCCAGGCAACTTGCTGGCTTGGTCATTGCTGTGTG                         GGTTAAAACCAACATTAGATTTCATGTTGGGGATGTCGAAGTGGCAGCAGT
genomic: TTTGAACGTATTGGATCCAGGCAACTTGCTGGCTTGGTCATTGCTGTGTGgtgagtatct ... tctttttcagGGTTAAAACCAACATTAGATTTCATGTTGGGGATGTCGAAGTGGCAGCAGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaattcttccttgctgctctctttgcctaaagtagttgaatttttctttttcagGGTTAAAACCAACATTAGATTTCATGTTGGGGATGTCGAAGTGGCAGCAGTTCCATGTGGCTTTGGACGTGCTATTGGCAATAAG
                         gcctaaa  putative branch site (score: 3)
                                         tttttctttttc  putative PPT
                                    ttgaatttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcaactattttcctcctttgatttgaatttttgtctttgttatctaaattcttccttgctgctctctttgcctaaagtagttgaatttttctttttcagGGTTAAAACCAACATTAGATTTCATGTTGGGGATGTCGAAGTGGCAGCAGTTCCATGTGGCTTTGGACGTGCTATTGGCAATAAG

- - - - - ttcctcc
- - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - -gtctttg