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'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttctgtgagggtgagttggtgttggtctgtttgcttgggcattattggagtaatttgaattttgacagatccttatttacttgtaccttccctttagGTTGGTGATTTTGGGCTTTCCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCTGCTGCCGGGACT

Basic information

species Glycine max
transcript GLYMA03G34890.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G34890.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 11
--gttttctgtgagggtgagttggtgttggtctgtttgcttgggcattattggagtaatttgaattttgacagatccttatttacttgtaccttccctttagGTTGGTGATTTTGGGCTTTCCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCTGCTGCCGGGACT
  | |   |   |   |  ||| |  |   | |  |   |  |   ||  |  || |||||   ||||       ||| ||  |  |||    ||| || ||||| |||||||||| ||||| ||  | ||||||||||||||||| |||||||| || || || ||||| 
aagatcatttccaaaatttgtttgcttaatttttctcattgagttcttcatttagaaattttccttttagtttggcctgat--atctgtggtgtccattcagGTTTGTGATTTTGGTCTTTCACGGTTCAAGGCAAATACATTTCTTTCATCCAAATCGGCGGCAGGGACG
















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|193725665|gb|FK661975.1|FK661975
EST:     GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG                         GTTGGTGATTTTGGGCTTTCCCGACTAAAGGCAAATACATTTCTCTCATCC
genomic: GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAGgtaagaatgg ... ttccctttagGTTGGTGATTTTGGGCTTTCCCGACTAAAGGCAAATACATTTCTCTCATCC
EST: gi|193517192|gb|FK473432.1|FK473432
EST:     GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG                         GTTGGTGATTTTGGGCTTTCCCGACTAAAGGCAAATACATTTCTCTCAT
genomic: GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAGgtaagaatgg ... ttccctttagGTTGGTGATTTTGGGCTTTCCCGACTAAAGGCAAATACATTTCTCTCAT
EST: gi|207837906|gb|GD809442.1|GD809442
EST:     GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG                         GTTGGTGATTTTGGGNTTTCCCGACTAAAGGCAAATACATTTCTCTCATCC
genomic: GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAGgtaagaatgg ... ttccctttagGTTGGTGATTTTGGGCTTTCCCGACTAAAGGCAAATACATTTCTCTCATCC
EST: gi|193648544|gb|FK598355.1|FK598355
EST:     GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG                         GTTGGTGATTTTGGGCTTTCCCGACTAAAGGCAAATACATTTCTCTCATCC
genomic: GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAGgtaagaatgg ... ttccctttagGTTGGTGATTTTGGGCTTTCCCGACTAAAGGCAAATACATTTCTCTCATCC
EST: gi|193597983|gb|FK552847.1|FK552847
EST:     GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG                         GTTGGTGATTTTGGGCTTTCCCGACTAAAGGCAAATACATTTCTCTCATCC
genomic: GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAGgtaagaatgg ... ttccctttagGTTGGTGATTTTGGGCTTTCCCGACTAAAGGCAAATACATTTCTCTCATCC
EST: gi|207735805|gb|GD713084.1|GD713084
EST:     GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG                         GTTGGTGATTTTGGGCTTTCCCGACTAAAGGCAAATACATTT
genomic: GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAGgtaagaatgg ... ttccctttagGTTGGTGATTTTGGGCTTTCCCGACTAAAGGCAAATACATTT
EST: gi|254324292|gb|GR840609.1|GR840609
EST:     GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG                         GTTGGTGATTTTGGGCTTTCCCGACTAAAGGCAAATACATTTCTCTCATCC
genomic: GAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAGgtaagaatgg ... ttccctttagGTTGGTGATTTTGGGCTTTCCCGACTAAAGGCAAATACATTTCTCTCATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattggagtaatttgaattttgacagatccttatttacttgtaccttccctttagGTTGGTGATTTTGGGCTTTCCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCTGCTGCCGGGACT
                 ttttgac  putative branch site (score: 3)
                                     cttgtaccttcccttt  putative PPT
      agtaatttgaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttctgtgagggtgagttggtgttggtctgtttgcttgggcattattggagtaatttgaattttgacagatccttatttacttgtaccttccctttagGTTGGTGATTTTGGGCTTTCCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCTGCTGCCGGGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- -ttctgtg
- - - - - -gggtgag
- - - - - - - - - - -gtgttgg
- - - - - - - - - - - - - - - tgtttgc
- - - - - - - - - - - - - - - - - - - - ggcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgtac