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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgaatggatgcattaatattatcaatattgtaattgaaataacatctttgcaatttactgaagtgttaacaatattggttggcttcattttccacagAACTGATGGTATTGGTCTCTCAGCACCCCAATTAGGAATTAATGTTCAACTTATGGTGTTCAATCCAGTAGGTGAGCATGGTGAAGGAGAGGAAATTGTT

Basic information

species Glycine max
transcript GLYMA19G14000.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G14000.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g44980.1 (Oryza sativa), 3'ss of exon 2
atatgaatggatgcattaatattatcaatattgtaattgaaataacatct-ttgcaatttactgaagtgttaacaatattgg----ttggcttcattttccacagAACTGATGGTATTGGTCTCTCAGCACCCCAATTAGGAATTAATGTTCAACTTATGGTGTTCAATCCAGTAGGTGAGCATGGTGAAGGAGAGGAAATTGTT
 |||  |   ||  |    |  ||||| | ||  ||  |   |   ||||  |     |     |  | ||      ||||     |||| |||  || | |||| |||||||| ||||||||||| ||||| ||| | ||  | ||||| ||||||||||| || |||||||  |||| | | || ||||||||||| ||||| 
-tatccaatcatatacct-tgctatcatttttagaaa-ggcttgctatctactattgctcgagaagatattcctccaattgaaccattggtttc--ttgctacagGACTGATGGAATTGGTCTCTCTGCACCACAAGTTGGGGTGAATGTACAACTTATGGTATTTAATCCAGCTGGTGTGAAGGGAGAAGGAGAGGAGATTGTC

upper sequence: GLYMA19G14000.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G179693_T02 (Zea mays), 3'ss of exon 2
atatgaatggatgcattaatattatcaatattgtaattgaaataacatctttgca-atttactgaagtgttaacaatattggttggcttca---ttttccacagAACTGATGGTATTGGTCTCTCAGCACCCCAATTAGGAATTAATGTTCAACTTATGGTGTTCAATCCAGTAGGTGAGCATGGTGAAGGAGAGGAAATTGTT
 |||  |   ||  | ||    |  |  |  || | || | |||  |   |  || ||||| |  |   |  ||    |  |||      |   ||||  |||| || ||||| ||||||||||||||||| ||| | ||| | ||||| || |||||||| |||||||| |  || | | | || ||||||||||| ||||||
-tatttaccaat--aatagggctgcccgtggtg-atttcagatataactatgccagatttattagaagctgtactgcttaagttaaaaagaggtttttgtacagGACCGATGGCATTGGTCTCTCAGCACCACAAGTTGGAGTCAATGTGCAGCTTATGGTATTCAATCCTGCTGGGGTGAAGGGGGAAGGAGAGGAGATTGTT

upper sequence: GLYMA19G14000.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G14660.1 (Arabidopsis thaliana), 3'ss of exon 2
atatgaatggatgcattaatattatcaatattgtaattgaaataacatctttgcaatttactgaagtgttaacaatattggttggcttcattttccacagAACTGATGGTATTGGTCTCTCAGCACCCCAATTAGGAATTAATGTTCAACTTATGGTGTTCAATCCAGTAGGTGAGCATGGTGAAGGAGAGGAAATTGTT
               | | |  |    ||| ||||| | |  ||  | |||   ||   | |||     | |  | ||    |||||     ||  ||||||| ||||| ||||| ||||||||||| ||| ||||  | ||||||||||| |||||||| |||||||  || |||| ||| |||||| | |||||||| 
--------------gtaagtcctccttataatgtaagtaacttagta-cttaataacagagtgatactgtgattacat---atggcta----ttggacagAACGGATGGCATTGGGCTCTCAGCACCACAAGTAGGTCTCAATGTTCAACTCATGGTGTTTAATCCAGCTGGAGAGCCTGGAGAAGGAAAAGAAATTGTC

upper sequence: GLYMA19G14000.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0066g01070.t01 (Vitis vinifera), 3'ss of exon 4
--atatgaatggatgcattaatattatcaatattgtaattgaaataacatctttgcaatttactgaagtgttaacaatattggttggcttcattttccacagAACTGATGGTATTGGTCTCTCAGCACCCCAATTAGGAATTAATGTTCAACTTATGGTGTTCAATCCAGTAGGTGAGCATGGTGAAGGAGAGGAAATTGTT
   || || | |||  |||    |||  | ||||        |  |  ||  |||| |||||| | ||||| ||||||| | ||||||||| ||||||||||||||||||||||||| ||||||||||||||| ||||||| ||||||||||| ||||| || ||||| || ||||| | ||||||||||||||||||||||
ttttaggattagatctatt--ctttaaaattattaggtgcttataagaatgcttgccatttacaggagtgtgaacaatacttgttggcttccttttccacagAACTGATGGTATTGGGCTCTCAGCACCCCAAGTAGGAATCAATGTTCAACTCATGGTTTTTAATCCGGTTGGTGAACGTGGTGAAGGAGAGGAAATTGTT

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|193322589|gb|FK290365.1|FK290365
EST:     TGTAATGTACAA                         AACTTGATGGTATTGGTCTCTCAGCACCCCAATTAGGAATTAATGTTCAAC
genomic: TGTAATGTACAAgtaagctttc ... ttttccacagAAC-TGATGGTATTGGTCTCTCAGCACCCCAATTAGGAATTAATGTTCAAC
EST: gi|21678014|gb|BQ630365.1|BQ630365
EST:     GATGATAGTCTGAAGAAGCTTGTCCACGAAATGTTTGATGTAATGTACAA                         AACTGATGGTATTGGTCTCTCAGCACCCCAATTAGGAATTAATGTTCAACT
genomic: GATGATAGTCTGAAGAAGCTTGTCCACGAAATGTTTGATGTAATGTACAAgtaagctttc ... ttttccacagAACTGATGGTATTGGTCTCTCAGCACCCCAATTAGGAATTAATGTTCAACT
EST: gi|20813414|gb|BQ297892.1|BQ297892
EST:     GATGATAGTCTGAAGAAGCTTGTCCACGAAATGTTTGAT--AA----C--                         ---TGATGGTATTGGTCTCTCAGCACCCCAATTAGGAATTAATGTTCAACT
genomic: GATGATAGTCTGAAGAAGCTTGTCCACGAAATGTTTGATGTAATGTACAAgtaagctttc ... ttttccacagAACTGATGGTATTGGTCTCTCAGCACCCCAATTAGGAATTAATGTTCAACT
EST: gi|193314898|gb|FK281398.1|FK281398
EST:     GATGATAGTCTGAAGAAGCTTGTCCACGAAATGTTTGATGTAATGTACAA                         AACTGATGGTATTGGTCTCTCAGCACCCCAATTAGGAAATTAATGTTCAAC
genomic: GATGATAGTCTGAAGAAGCTTGTCCACGAAATGTTTGATGTAATGTACAAgtaagctttc ... ttttccacagAACTGATGGTATTGGTCTCTCAGCACCCCAATTAGGAA-TTAATGTTCAAC
EST: gi|51336558|gb|CO980424.1|CO980424
EST:     TCCACGAAATGTTTGATGTAATGTACAA                         AACTGATGGTATTGGTCTCTCAGCACCCCAATTAGGAATTAATGTTCAACT
genomic: TCCACGAAATGTTTGATGTAATGTACAAgtaagctttc ... ttttccacagAACTGATGGTATTGGTCTCTCAGCACCCCAATTAGGAATTAATGTTCAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catctttgcaatttactgaagtgttaacaatattggttggcttcattttccacagAACTGATGGTATTGGTCTCTCAGCACCCCAATTAGGAATTAATGTTCAACTTATGGTGTTCAATCCAGTAGGTGAGCATGGTGAAGGAGAGGAAATTGTT
                     tgttaac  putative branch site (score: 2)
                                        cttcattttcc  putative PPT
                       ttaacaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatgaatggatgcattaatattatcaatattgtaattgaaataacatctttgcaatttactgaagtgttaacaatattggttggcttcattttccacagAACTGATGGTATTGGTCTCTCAGCACCCCAATTAGGAATTAATGTTCAACTTATGGTGTTCAATCCAGTAGGTGAGCATGGTGAAGGAGAGGAAATTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA