Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctttgttgcaaatttgtctaacctatgctttagagaagtctggtcatccttcattagaataagctaattgcaatcctttttattttctctttgtgcagCTGGGCAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCACAAGGAATAATTATGG

Basic information

species Glycine max
transcript GLYMA14G26690.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G26690.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g15090.t01 (Vitis vinifera), 3'ss of exon 3
ctctttgttgcaaatttgtctaacctatgctttagagaagtctggtcatccttcattagaataa--gctaattgcaat--cctttttattttctctttgtgcagCTGGGCAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCACAAGGAATAATTATGG
  | ||  |  | ||    |   ||| ||  |  |||| ||  |   |    |    | || |   | ||||     |   || | || || |||||  ||||||||| ||||| || ||||||||||||||||||||||| ||||||||||| || ||  |||| ||||
--ccttccttaagatgcagccttcctttgtct--gagatgttagaaaaattgtgggaaaaacagatgttaataatggtaatctctatacttcctcttcatgcagCTGGACAGGAGAGATTTAGAACACTTACTAGTTCATACTACAGAGGAGCTCAGGGCGTAATAATGG

upper sequence: GLYMA14G26690.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ26280 (Selaginella moellendorffii), 3'ss of exon 2
ctctttgttgcaaatttgtctaacctatgctttagagaagtctggt-catccttcattagaataagctaattgcaatcctttttattttctc---tttgtgcagCTGGGCAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCACAAGGAATAATTATGG
                                     || | | |  || |  ||  | | || || |  |||  |   ||||| ||||||     | | | ||||||||||||||| ||||||||||| || |||||||| ||  |||||||||||||  | ||| | |
-----------------------------------gtaactttagcacagctgtctcttgtatgagtt--ttgagagttttttttttttcttgatctcgcgtagCTGGGCAGGAAAGATTTAGAACACTCACGAGTTCATACTATCGAGGAGCACAAGGCGTCATTCTTG

upper sequence: GLYMA14G26690.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ14579 (Selaginella moellendorffii), 3'ss of exon 2
ctctttgttgcaaatttgtctaacctatgctttagagaagtctggtcatccttcattagaataagctaattgcaatcctttttattttctctttgtgcagCTGGGCAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCACAAGGAATAATTATGG
                                  |  |  |  |  || |  ||  | | || || |  |   | |  ||||| | ||    | | | ||||||||||||||| ||||||||||| || |||||||| ||  ||||||| |||||  | ||| | |
----------------------------------gtaacttgagcacagctatctcttgtatgagttt-tgagagttttttttttcttgatctcgcgtagCTGGGCAGGAAAGATTTAGAACACTCACGAGTTCATACTATCGAGGAGCTCAAGGCGTCATTCTTG

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|58017830|gb|CX704572.1|CX704572
EST:     ATATGTTACAATTGGAGGGAAAAAGTTAAAACTTGCTATTTGGGACACAG                         CTGGGCAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCAC
genomic: ATATGTTACAATTGGAGGGAAAAAGTTAAAACTTGCTATTTGGGACACAGgtaatctgaa ... ctttgtgcagCTGGGCAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCAC
EST: gi|58018302|gb|CX705044.1|CX705044
EST:     ATATGTTACAATTGGAGGGAAAAAGTTAAAACTTGCTATTTGGGACACAG                         CTGGGCAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCAC
genomic: ATATGTTACAATTGGAGGGAAAAAGTTAAAACTTGCTATTTGGGACACAGgtaatctgaa ... ctttgtgcagCTGGGCAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCAC
EST: gi|51336316|gb|CO980182.1|CO980182
EST:     ATATGTTACAATTGGAGGGAAAAAGTTAAAACTTGCTATTTGGGACACAG                         CTGGGCAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCAC
genomic: ATATGTTACAATTGGAGGGAAAAAGTTAAAACTTGCTATTTGGGACACAGgtaatctgaa ... ctttgtgcagCTGGGCAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCAC
EST: gi|58024481|gb|CX711222.1|CX711222
EST:     ATATGTTACAATTGGAGGGAAAAAGTTAAAACTTGCTATTTGGGACACAG                         CTGGGCAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCAC
genomic: ATATGTTACAATTGGAGGGAAAAAGTTAAAACTTGCTATTTGGGACACAGgtaatctgaa ... ctttgtgcagCTGGGCAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCAC
EST: gi|192325663|gb|FK019519.1|FK019519
EST:     ATATGTTACAATTGGAGGGAAAAAGTTAAAACTTGCTATTTGGGACACAG                         CTGGGCAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCAC
genomic: ATATGTTACAATTGGAGGGAAAAAGTTAAAACTTGCTATTTGGGACACAGgtaatctgaa ... ctttgtgcagCTGGGCAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCAC
EST: gi|192294546|gb|FG986395.1|FG986395
EST:     ATATGTTACAATTGGAGGGAAAAAGTTAAAACTTGCTATTTGGGACACAG                         CTGGGCAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCAC
genomic: ATATGTTACAATTGGAGGGAAAAAGTTAAAACTTGCTATTTGGGACACAGgtaatctgaa ... ctttgtgcagCTGGGCAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatccttcattagaataagctaattgcaatcctttttattttctctttgtgcagCTGGGCAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCACAAGGAATAATTATGG
                  agctaat  putative branch site (score: 3)
                              tcctttttattttctc  putative PPT
                                 tttttattttctcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctttgttgcaaatttgtctaacctatgctttagagaagtctggtcatccttcattagaataagctaattgcaatcctttttattttctctttgtgcagCTGGGCAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCACAAGGAATAATTATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - -tgttgca
- - - - - - - - - - - -cctatgc
- - - - - - - - - - - - - - - - - - - - - - - - tccttca