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'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accgacacctttcatttctgactttgtttgggggatttcttcttgtatgttataaattcttaaagcttcatctcatttcactaatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG

Basic information

species Glycine max
transcript GLYMA13G42800.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 9
accgacacctttcatttctgactttgtttgggggatttcttcttgtat--gttataaatt-cttaaagcttcatctcatttcactaatgacttgttttgt-cagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG
    ||   | |   |||||    || ||     | | | | |  |||  ||  || | | ||| ||   ||||   | | |  |  |   ||  ||| | ||||| ||||| || || |||||||||||||| |||||||||||||| |||||||| ||||||||||| |||
--aaacttttatatattctgcagctgattctaatactacgtatcatataagtggtatactgcttgaaatgtcatt--agtccgttgctccttttctttcttcagTTATGGGATATAAACATGGATTCAGGCCCAGTTGCAACTTTCCAAGTTCATGAATATTTAAGACCTAAG

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 9
accgacacctttcattt-ctgactttgtttgggggatttcttcttgtatgttataaattcttaaagcttcatctcatttcactaatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG
   ||    |   |||| |||      |   || | | | ||  || | | | | | |||       ||    |||| | | |  |  | | || |  ||| | ||||| ||||| ||| | || || || |||||||| ||||||||||||||||||||||| ||||||
ggtgatttatactattttctgtagccatagaggtgttatttttctgca-gctgttacttcgatgtttttgtgttcatataaattttttccttttgttccagCTTTGGGATATTAACATGAACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAG

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 9
--------accgacacctttcatttctgactttgtttgggggatttcttcttgtatgttataaattcttaaagcttcatctcatttcactaatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG
         |  |       ||| | |||||| |||     | |   || | |       ||||     | |  ||  | | | || | ||      | |||  |||| | |||||  | || ||||||||||| || ||| |||| ||||||||||||||  ||||||| ||||||
tttgcatggcttatgatgagcatatttgactt-gttaataaggtaaattttag------gtaaagcggaataatttggtttgagtttaatatctgtct-tttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G069631_T01 (Zea mays), 3'ss of exon 9
accgacacctttcatttctgactttgtttgggggatttcttcttgtatgttataaattcttaaa-gcttcatctcatttca-ctaatgact--tgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG
        |||| |      |     ||| || | | |   ||| | || || | ||  |||   |||  |  | |||| |  |||    |  |||||   |||||||||||  | || |||||||||||||| ||||||||||| ||||||||||| || ||| | || |||
----tagactttgaggatcaaggaacttttggtgctctgcccttttgtgataaatatgtttatctgctagaaataattttagttaaccgtttttgtttctccagTTGTGGGATCTAAACATGGATTCAGGCCCAGTTGCAACTTTTCAGGTTCATGAATACTTACGTCCTAAG

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G51690.2 (Arabidopsis thaliana), 3'ss of exon 9
---------------accgacacctttcatttctgactttgtttgggggatttc--ttcttgtatgttataaattcttaaagcttcatctcatttcac-taatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG
                    || | |||| |  |||  |    | |  | | ||  |   ||  |   ||   ||| |  |   | | || |   ||  | |||  ||   | | ||||| |||||||| || |||||  |||| || || |||||||||||||||||||| ||||| | ||| |||
gtccatattttcactgttttcatcattcaata-tgatatcccctcgaagttatcagtggctggtttcgatttgttcgtgtaaggtaaactgaccccatgttatgttttacat-gccagTTATGGGACATCAACATGGACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAG

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 9
accgacacctttcatttct--gactttgtttgggggatttcttcttgtatgtta---taaattcttaaagct-tcatctcatttcactaatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG
       | || |||  |   || ||  | ||    |||| |  || |   |||   ||    ||| ||    |||    | ||   |  | ||||| ||| |||||| ||||||||||||||||| |||||||| ||| |||| |||||||||||||| ||||||||||| |||
---aggtctttgcatcacaaggaattgatatgtactatttgtctttctggcttaagttagggccttgaactaatcactggaatttgtt--ttacttgcttt-tcagTTATGGGACATTAATATGGACTCAGGCCCAGTTTCAACCTTCCAGGTTCATGAATATTTAAGACCTAAG

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|7686354|gb|AW757002.1|AW757002
EST:     TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAG                         TTGTGGGACATTAATATGGATTCAGGCACCGTTGCAACTTTGCAGGTTCAT
genomic: TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAGgtttgaaatt ... gttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCAT
EST: gi|18730643|gb|BM525996.1|BM525996
EST:     TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAG                         TTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCAT
genomic: TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAGgtttgaaatt ... gttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCAT
EST: gi|5770902|gb|AI974076.1|AI974076
EST:     TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAG                         TTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCAT
genomic: TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAGgtttgaaatt ... gttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCAT
EST: gi|193711274|gb|FK646095.1|FK646095
EST:     TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAG                         TTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACCTTCCAGGTTCAT
genomic: TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAGgtttgaaatt ... gttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCAT
EST: gi|21887329|gb|BQ740542.1|BQ740542
EST:     TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAG                         TTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACT
genomic: TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAGgtttgaaatt ... gttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgttataaattcttaaagcttcatctcatttcactaatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG
                                 cactaat  putative branch site (score: 2)
                                          cttgtttt  putative PPT
     tataaattcttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accgacacctttcatttctgactttgtttgggggatttcttcttgtatgttataaattcttaaagcttcatctcatttcactaatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG

- cgacacc
- - - - - - - -ttctgac
- - - - - - - - - - - - - - -gggggat
- - - - - - - - - - - - - - - - - - - - - -tgtatgt