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

gtaagcataaaattaagaaaaaccatatactcaaactcgtgaactggacaattcagttctattcactctctccttagttagcgaacctaattattcagttctatcaacaaataatgatttcttcttttgttcacaaatatagGGAGCTCTTCTTCTACCACACTTCAATTCAAAGGCCATAGTGATACTAGTGATTAATGAAGGAGATGCAAACATTGAACTTGTTGGCATTAAAGAACAAC

Basic information

species Glycine max
transcript GLYMA20G28640.1
intron # 4
splice site 3'
intron type U2

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|6915933|gb|AW397463.1|AW397463
EST:     CACAGCTTCGGGACTTGGATATCTTCCTCAGTTCTGTGGATATCAACGAA                         GGAGCTCTTCTTCTACCACACTTCAATTCAAAGGCCATAGTGATACTAGTG
genomic: CACAGCTTCGGGACTTGGATATCTTCCTCAGTTCTGTGGATATCAACGAAgtaagcataa ... acaaatatagGGAGCTCTTCTTCTACCACACTTCAATTCAAAGGCCATAGTGATACTAGTG
EST: gi|5342773|gb|AI795057.1|AI795057
EST:     CACAGCTTCGGGACTTGGATATCTTCCTCAGTTCTGTGGATATCAACGAA                         GGAGCTCTTCTTCTACCACACTTCAATTCANAGGCCATAGTGATACTAGTG
genomic: CACAGCTTCGGGACTTGGATATCTTCCTCAGTTCTGTGGATATCAACGAAgtaagcataa ... acaaatatagGGAGCTCTTCTTCTACCACACTTCAATTCAAAGGCCATAGTGATACTAGTG
EST: gi|7145659|gb|AW507581.1|AW507581
EST:     CACAGCTTCGGGACTTGGATATCTTCCTCAGTTCTGTGGATATCAACGAA                         GGAGCTCTTCTTCTACCACACTTCAATTCAAAGGCCATAGTGATACTAGTG
genomic: CACAGCTTCGGGACTTGGATATCTTCCTCAGTTCTGTGGATATCAACGAAgtaagcataa ... acaaatatagGGAGCTCTTCTTCTACCACACTTCAATTCAAAGGCCATAGTGATACTAGTG
EST: gi|298164587|gb|HO014232.1|HO014232
EST:     CACAGCTTCGGGACTTGGATATCTTCCTCAGTTCTGTGGATATCAACGAA                         GGAGCTCTTCTTCTACCACACTTCAATTCAAAGGCCATAGTGATACTAGTG
genomic: CACAGCTTCGGGACTTGGATATCTTCCTCAGTTCTGTGGATATCAACGAAgtaagcataa ... acaaatatagGGAGCTCTTCTTCTACCACACTTCAATTCAAAGGCCATAGTGATACTAGTG
EST: gi|298199439|gb|HO042802.1|HO042802
EST:     CACAGCTTCGGGACTTGGATATCTTCCTCAGTTCTGTGGATATCAACGAA                         GGAGCTCTTCTTCTACCACACTTCAATTCAAAGGCCATAGTGATACTAGTG
genomic: CACAGCTTCGGGACTTGGATATCTTCCTCAGTTCTGTGGATATCAACGAAgtaagcataa ... acaaatatagGGAGCTCTTCTTCTACCACACTTCAATTCAAAGGCCATAGTGATACTAGTG
EST: gi|209726538|gb|BW658092.1|BW658092
EST:     CACAGCTTCGGGACTTGGATATCTTCCTCAGTTCTGTGGATATCAACGAA                         GGAGCTCTTCTTCTACCACACTTCAATTCAAAGGCCATAGTGATACTAGTG
genomic: CACAGCTTCGGGACTTGGATATCTTCCTCAGTTCTGTGGATATCAACGAAgtaagcataa ... acaaatatagGGAGCTCTTCTTCTACCACACTTCAATTCAAAGGCCATAGTGATACTAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattattcagttctatcaacaaataatgatttcttcttttgttcacaaatatagGGAGCTCTTCTTCTACCACACTTCAATTCAAAGGCCATAGTGATACTAGTGATTAATGAAGGAGATGCAAACATTGAACTTGTTGGCATTAAAGAACAAC
 acctaat  putative branch site (score: 3)
                              tttcttcttttgttca  putative PPT
                  aacaaataatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcataaaattaagaaaaaccatatactcaaactcgtgaactggacaattcagttctattcactctctccttagttagcgaacctaattattcagttctatcaacaaataatgatttcttcttttgttcacaaatatagGGAGCTCTTCTTCTACCACACTTCAATTCAAAGGCCATAGTGATACTAGTGATTAATGAAGGAGATGCAAACATTGAACTTGTTGGCATTAAAGAACAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC