Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtgtgatgtgattattctgaatgaatgaatccctaatccctaatcccctcttgtctcgcagATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTACTGGACAAGAGCAAACATCTGGCCAGATTGAACATGAAGGAAGGCGGGAA

Basic information

species Glycine max
transcript GLYMA20G39320.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G39320.3 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g19470.1 (Oryza sativa), 3'ss of exon 1
--------------------------gtatgtgtgtgatgtg-attattctgaatgaatgaatccctaa---tccctaatcccct---cttgtctcgcagATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTACTGGACAAGAGCAAACATCTGGCCAGATTGAACATGAAGGAAGGCGGGAA
                           | ||| | |  | |  ||| ||  || || |    ||   ||   |||| | ||   |    || |     |||||||||||||||||||||||| || ||||| || |||| |||  ||||||| |||||||  ||||||||  | ||  | ||  ||||||| |  || ||
ccattttttaagtttaaggaacatgattttgtatttagtatctattgttgagactgtaactgtctggaaatttccccattctgatgtgtttattctaaagATACCCAATTGCAGAAAATGCCAAAGAGGAAGACTGACAGAGCACATGTACTAGACAAGAAAAAACATCTCTCAAGGCTAAATGTGAAGGAGGCAGGAAA

upper sequence: GLYMA20G39320.3 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g19470.2 (Oryza sativa), 3'ss of exon 1
------------gtatgtgtgtgatgtg-attattctgaatgaatgaatccctaa---tccctaatcccct---cttgtctcgcagATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTACTGGACAAGAGCAAACATCTGGCCAGATTGAACATGAAGGAAGGCGGGAA--------------
             | ||| | |  | |  ||| ||  || || |    ||   ||   |||| | ||   |    || |     |||||||||||||||||||||||| || ||||| || |||| |||  ||||||| |||||||  ||||||||  | ||  | ||  ||||||| |  || ||              
taaggaacatgattttgtatttagtatctattgttgagactgtaactgtctggaaatttccccattctgatgtgtttattctaaagatacccaattgcagAAAATGCCAAAGAGGAAGACTGACAGAGCACATGTACTAGACAAGAAAAAACATCTCTCAAGGCTAAATGTGAAGGAGGCAGGAAAGGTCCTGTTGAAAC

upper sequence: GLYMA20G39320.3 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g01530.t01 (Vitis vinifera), 3'ss of exon 1
--------------------------------gtatgtgtgtgatgtgattattct---gaatgaatgaatccctaatccctaatcccctcttgtctcgcagATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTACTGGACAAGAGCAAACATCTGGCCAGATTGAACATGAAGGAAGGCGGGAA
                                  |    ||  |    |||  ||    |  | ||  |||   | || |  ||     | || | |   ||||||||||||||||||| ||||||| |||||||| |||| | |||||||  ||||||| |  || ||||| || ||  | || || || ||||  || ||
tttttagctattactttttgtgcaaacgagttcaacagttgctaaagcattcctcaatggtgtaaacaaattagtcatactaaaatattttttttat--aagATACCCAATTGCAGAAAGTGCCTAAGAGGAAAACTGACAGATCTTATGTGTTGGACAAAACGAAGCATCTTGCAAGGCTAAATATCAATGAAGCAGGAAA

upper sequence: GLYMA20G39320.3 (Glycine max), 3'ss of exon 1
lower sequence: PP1S121_20V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------gtatgtgtgtg-atgtgattattctgaatgaatgaatccctaatccctaatcccctcttgtctcgcagATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTACTGGACAAGAGCAAACATCTGGCCAGATTGAACATGAAGGAAGGCGGGAA
                                ||   |||| | ||||  |  || |   |    | |  | | |         |  | | |||| |||||||| ||  |||||||||||||||| ||||||||||||| ||| |||||| ||||    | ||| || ||   | || | ||  |    || |  || ||
atttgcatataagcgttgtggaatacaaaaatgtcgttgtgcgtatgttctcgttttaggttttagcagacgtgacggtagcgtcaatttggtcttgcagATACTCAGCTGCAGAAAATGCCTAAGAGGAAAACCGACAGAGCATATGTATTGGATCGTAACAAGCACCTCAGCCGACTTAATGTTGTAGAGGCTGGCAA

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|192299668|gb|FG990021.1|FG990021
EST:     TCTCTTTGTATATTACTGCAAACATTGCGGATCCCATGTCCTCATAACAG                         ATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGCCAAAGCTTATGTAC
genomic: TCTCTTTGTATATTACTGCAAACATTGCGGATCCCATGTCCTCATAACAGgtatgtgtgt ... tgtctcgcagATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTAC
EST: gi|15815879|gb|BI788154.1|BI788154
EST:     TCTCTTTGTATATTACTGCAAACATTGCGGATCCCATGTCCTCATAACAG                         ATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTAC
genomic: TCTCTTTGTATATTACTGCAAACATTGCGGATCCCATGTCCTCATAACAGgtatgtgtgt ... tgtctcgcagATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTAC
EST: gi|193699770|gb|FK641653.1|FK641653
EST:     TCTCTTTGTATATTACTGCAAACATTGCGGATCCCATGTCCTCATAACAG                         ATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTAC
genomic: TCTCTTTGTATATTACTGCAAACATTGCGGATCCCATGTCCTCATAACAGgtatgtgtgt ... tgtctcgcagATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTAC
EST: gi|213593083|gb|DB969881.1|DB969881
EST:     TCTCTTTGTATATTACTGCAAACATTGCGGATCCCATGTCCTCATAACAG                         ATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTAC
genomic: TCTCTTTGTATATTACTGCAAACATTGCGGATCCCATGTCCTCATAACAGgtatgtgtgt ... tgtctcgcagATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTAC
EST: gi|298181842|gb|HO026017.1|HO026017
EST:     TCTCTTTGTATATTACTGCAAACATTGCGGATCCCATGTCCTCATAACAG                         ATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTAC
genomic: TCTCTTTGTATATTACTGCAAACATTGCGGATCCCATGTCCTCATAACAGgtatgtgtgt ... tgtctcgcagATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTAC
EST: gi|193313069|gb|FK279626.1|FK279626
EST:     TCTCTTTGTATATTACTGCAAACATTGCGGATCCCATGTCCTCATAACAG                         ATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTAC
genomic: TCTCTTTGTATATTACTGCAAACATTGCGGATCCCATGTCCTCATAACAGgtatgtgtgt ... tgtctcgcagATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTAC
EST: gi|151399174|gb|EV269045.1|EV269045
EST:     TCTCTTTGTATATTACTGCAAACATTGCGGATCCCATGTCCTCATAACAG                         ATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTAC
genomic: TCTCTTTGTATATTACTGCAAACATTGCGGATCCCATGTCCTCATAACAGgtatgtgtgt ... tgtctcgcagATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgattattctgaatgaatgaatccctaatccctaatcccctcttgtctcgcagATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTACTGGACAAGAGCAAACATCTGGCCAGATTGAACATGAAGGAAGGCGGGAA
                               ccctaat  putative branch site (score: 3)
                              tccctaatcccctctt  CT-rich tract
     ttattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtgtgatgtgattattctgaatgaatgaatccctaatccctaatcccctcttgtctcgcagATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTACTGGACAAGAGCAAACATCTGGCCAGATTGAACATGAAGGAAGGCGGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA