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

gtaacttccgttgtagcatacatactatttgaattgtagtgttaataccttattgttattgttcatatgttccctcattgattgtctcaaactattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTGAGGAGAGGTACAACGGATTATTGAGTCGCCAAGTTGT

Basic information

species Glycine max
transcript GLYMA09G30910.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g02680.t01 (Vitis vinifera), 3'ss of exon 4
gtaacttccgttgtagcatacatactatttgaattgtagtgttaataccttattgttattgttcatatgttcc-ctcattgattgtctcaaactattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTGAGGAGAGGTACAACGGATTATTGAGTCGCCAAGTTGT
               | | |  | | |    ||||  | | ||     | |  |   ||||  ||||  ||   | ||    || |     | | ||||||| ||||| ||||||||||||||||| || ||||| |||||||| ||||||||| |||  ||||| || |||||||||  |  ||| ||
---------------gtaaattttccaacaaaattaaaatctt----tcatgctaa-attgaacataatttgagcccacaagttat-----atttttgtagGCATTACCCCATATGCAAATCTCTATCACTATGACCTTCCTTTGGCACTTGAGAAGAAATACAATGGGTTATTGAGTTACAGAGTAGT
















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|209710515|gb|BW662051.1|BW662051
EST:     GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAG                         GTATTACTCCATATG
genomic: GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATG
EST: gi|208097652|gb|GD891343.1|GD891343
EST:     GTTGATCAATTACTTTGCTAGAGAAAG                         GTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTGGCACTTG
genomic: GTTGATCAATTAC-TTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
EST: gi|208218049|gb|GE017873.1|GE017873
EST:     GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAGG                         GTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
genomic: GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
EST: gi|213619687|gb|DB965633.1|DB965633
EST:     GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAG                         GTATTACTCCATATGCAAATCTCTACCATT
genomic: GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTCTACCATT
EST: gi|193500052|gb|FK463933.1|FK463933
EST:     GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAG                         GTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
genomic: GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
EST: gi|207704606|gb|GD685995.1|GD685995
EST:     AAAGGTGTAGCATACTTACAATAGGTTGATCAATTACTTGCTAGAGAAAG                         GTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
genomic: AAAGGTGTAGCATAC-TACAATAGGTTGATCAATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
EST: gi|208023473|gb|GD821693.1|GD821693
EST:     GTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAG                         GTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
genomic: GTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
EST: gi|193383973|gb|FK351378.1|FK351378
EST:     GAAAGGCGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAG                         GTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
genomic: GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
EST: gi|193623175|gb|FK574609.1|FK574609
EST:     GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAG                         GTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
genomic: GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
EST: gi|193694750|gb|FK628662.1|FK628662
EST:     TTGATCAATTACTTGCTAGNGAAAG                         GTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
genomic: TTGATCAATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
EST: gi|193638232|gb|FK585844.1|FK585844
EST:     GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAG                         GTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
genomic: GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
EST: gi|193389816|gb|FK353581.1|FK353581
EST:     GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAG                         GTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
genomic: GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
EST: gi|193341034|gb|FK305476.1|FK305476
EST:     AATTACTTGCTAGAGAAAG                         GTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
genomic: AATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
EST: gi|193660704|gb|FK606428.1|FK606428
EST:     GAAAGGTGTAGCATACTACAATAGGTTGATCGATTACTTGCTAGAGAAAG                         GTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCA
genomic: GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCA
EST: gi|208139389|gb|GD934235.1|GD934235
EST:     GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAG                         GTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
genomic: GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
EST: gi|192332517|gb|FK025622.1|FK025622
EST:     GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAG                         GTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
genomic: GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
EST: gi|298166439|gb|HO009878.1|HO009878
EST:     GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAG                         GTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCT
genomic: GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCT
EST: gi|208117295|gb|GD918209.1|GD918209
EST:     GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAG                         GTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
genomic: GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
EST: gi|207745315|gb|GD715417.1|GD715417
EST:     GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAG                         GTATTACTCCATATGCAAATCTCTACCATTATAGAATAACTTCCTTTAGCA
genomic: GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTCTACCATTAT-GA-T--CTTCCTTTAGCA
EST: gi|209718599|gb|BW674725.1|BW674725
EST:     GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAG                         GTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
genomic: GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTG
EST: gi|208092374|gb|GD885491.1|GD885491
EST:     GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAG                         GTATTACTCCATATGCAAATCTC
genomic: GAAAGGTGTAGCATACTACAATAGGTTGATCAATTACTTGCTAGAGAAAGgtaacttccg ... actattgtagGTATTACTCCATATGCAAATCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccttattgttattgttcatatgttccctcattgattgtctcaaactattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTGAGGAGAGGTACAACGGATTATTGAGTCGCCAAGTTGT
                              cattgat  putative branch site (score: 4)
     tattgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttccgttgtagcatacatactatttgaattgtagtgttaataccttattgttattgttcatatgttccctcattgattgtctcaaactattgtagGTATTACTCCATATGCAAATCTCTACCATTATGATCTTCCTTTAGCACTTGAGGAGAGGTACAACGGATTATTGAGTCGCCAAGTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG