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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgacatgtactgatttgagtatggtcacgagggtggaagatctatgtatttttgcatgtggttagcatgattgatttagagttattttgaaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTACAGTGTGGAAAGTATTATTTGGAAAGG

Basic information

species Glycine max
transcript GLYMA18G03480.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G03480.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G58030.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------ttgacatgtactgatttgagtatggtcacgagggtggaagatctatgtatttttgcatgtggtta-gcatgattgatttagagtt-----------------------attttgaaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTACAGTGTGGAAAGTATTATTTGGAAAGG
                                 |    |||  ||  |  |  |  |  |  |     |||  | |   || || |   | || | | | | ||   ||  ||||||                        |||     || |||||||||||||||||||||||| |  ||   ||||| ||||| || |||||||| ||||||||||| || ||||||||| 
gtacatcttatttttgcaatctgatattcttacttgtgtgttttgcctcaaaaactggaaaaaaaaaagaacgtttccatacttctagttttgttcatggaagagcaatgcagagttcaatcatgtcttatggatatattgtttcattgtttcagGGAAACAGAAGAGAGACACGGTTACTGGGAATTCTGTCTTTCGTTCACAGTACTGTGTGGAAAGTGTTGTTTGGAAAG-

upper sequence: GLYMA18G03480.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0037g00110.t01 (Vitis vinifera), 3'ss of exon 3
---ttgacatgtactgatttgagtatggtcacgagggtggaagatctatgtatttttgcatgtggttagcatgattgatttagagttattttgaaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTACAGTGTGGAAAGTATTATTTGGAAAGG
          ||  ||  ||   |    ||| | | |    | ||  |     | ||||||||  | ||||||    |  |     | || |||    ||||||||||||||| |||||||| || |||  ||||||||||||||||||||||||||| ||||| || |||||||| ||| 
actccagtgggttttggcttatatgaattca-gtgtgaactacattgacaatctcttgcatgta-tgagcatgcaataagtgttacttttctgatgccacagGGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGTACAGTATGGAAGGTGTTATTTGGGAAG-
















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|298197159|gb|HO041902.1|HO041902
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|208197894|gb|GD998009.1|GD998009
EST:     TATGCGGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: TATGC-GGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|192302735|gb|FG993755.1|FG993755
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|208109910|gb|GD906228.1|GD906228
EST:     TTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: TTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|5606114|gb|AI900212.1|AI900212
EST:     TATGCGGTTGGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: TATGCGGTT-GGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|193662323|gb|FK603923.1|FK603923
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|254342930|gb|GR859092.1|GR859092
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|254334110|gb|GR849028.1|GR849028
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|192304323|gb|FG996449.1|FG996449
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|193445949|gb|FK413530.1|FK413530
EST:     TTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: TTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|298194561|gb|HO043033.1|HO043033
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|193403751|gb|FK365693.1|FK365693
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|21676489|gb|BQ628840.1|BQ628840
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|151411324|gb|EV281135.1|EV281135
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|31309603|gb|CD394806.1|CD394806
EST:     GGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: GGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|192302734|gb|FG993754.1|FG993754
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|254342931|gb|GR859093.1|GR859093
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|192297468|gb|FG992696.1|FG992696
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGACTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|51334757|gb|CO978623.1|CO978623
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|193607147|gb|FK557424.1|FK557424
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|254334109|gb|GR849027.1|GR849027
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|298178531|gb|HO024266.1|HO024266
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTCCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|298163034|gb|HO011767.1|HO011767
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|208178433|gb|GD977014.1|GD977014
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|298176675|gb|HO026796.1|HO026796
EST:     ATACGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|6567248|gb|AW234859.1|AW234859
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|192323071|gb|FK017012.1|FK017012
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|192304324|gb|FG996450.1|FG996450
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
EST: gi|193430306|gb|FK397270.1|FK397270
EST:     ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGG                         GAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA
genomic: ATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggct ... aaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatttttgcatgtggttagcatgattgatttagagttattttgaaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTACAGTGTGGAAAGTATTATTTGGAAAGG
                        gattgat  putative branch site (score: 4)
                             atttagagttattttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgacatgtactgatttgagtatggtcacgagggtggaagatctatgtatttttgcatgtggttagcatgattgatttagagttattttgaaattacaggGAAACAGAAGAGAGACACGGCTGTTGAATATTCTTTCTTTTGTACACAGTACAGTGTGGAAAGTATTATTTGGAAAGG

- - catgtac
- - - - - -tgatttg
- - - - - - - - - - - - - - - -gggtgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgat