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'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttaatcagttttagtatcattctttgcaagtttcagttttcaaattgtagtggagcatcacttatccttgtttgaattattcttttgttgcatccagTTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAGTTCCATGGTAAAGGACCTGGAAAAATGAAGCAAGAAAAGCGTATGAAGCAATATTACGAAG

Basic information

species Glycine max
transcript GLYMA08G24660.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G24660.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv11s0078g00440.t01 (Vitis vinifera), 3'ss of exon 10
---tttttaatcagttttagtatcattctttgcaagtttcagttttcaaattgtagtggagcatcacttatccttgtttgaattattcttttgttgcatc--cagTTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAGTTCCATGGTAAAGGACCTGGAAAAATGAAGCAAGAAAAGCGTATGAAGCAATATTACGAAG
   | | || ||  | || ||| ||   | || |||  | |  || |||| | ||||| ||||| ||||       |    | | |||||   |||| |    || |||| || |||||||||||||||||||| |||||||| || ||||| ||||| || || |||||||||||||||||||| |||||||||||  | ||||
ctttctatagtccatattggtaaca---tatgtaagact-atgttacaaaatatagtgaagcattactttgtaaaataatgagt-ttcttggcttgctttaatagATGACCCCCAAGGAAGCCTTTCGGATGATTTCTCATAAATTTCATGGGAAAGGGCCCGGCAAAATGAAGCAAGAAAAGCGCATGAAGCAATACCAGGAAG

upper sequence: GLYMA08G24660.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S99_235V6.1 (Physcomitrella patens), 3'ss of exon 10
tttttaatcagttttagtatcattctttgcaagtttcagttttcaaattgtagtgga-gcatcacttatcctt-gtttgaattattcttttg-ttgcatccagTTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAGTTCCATGGTAAAGGACCTGGAAAAATGAAGCAAGAAAAGCGTATGAAGCAATATTACGAAG
|   | |||| ||||     || | ||   |||| | |  |      ||  |||  | |     || |      |||||  | |    | || ||| |   || |||| || |||||||| || || | | |||||||||||||||| || |||||||||||||| ||||||||||| ||| |   ||| |||||  | || |
taagttatcatttttcaatgcactttt---aagtcttatgtagatggtttaagtctatgtgatgctgacgagaagtttggttgacatatatgcttgaaaatagATGACACCCAAGGAAGCTTTCCGAAAGCTCTCTCATAAGTTCCACGGCAAAGGACCTGGAAAGATGAAGCAAGAGAAGAGGCAGAAACAATACCAGGAGG
















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|254316977|gb|GR828514.1|GR828514
EST:     AGAAGACAAGGGAAATTCGCATTGAAAGGACAGATGAATTTGGGAGAATT                         TTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAGTTCCATGGTAAA
genomic: AGAAGACAAGGGAAATTCGCATTGAAAGGACAGATGAATTTGGGAGAATTgtaagttttc ... ttgcatccagTTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAGTTCCATGGTAAA
EST: gi|207838463|gb|GD812001.1|GD812001
EST:     AGAAGACAAGGGAAATTCGCATTGAAAGGACAGATGAATTTGGGAGAATT                         TTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAGTTCCATGGTAAA
genomic: AGAAGACAAGGGAAATTCGCATTGAAAGGACAGATGAATTTGGGAGAATTgtaagttttc ... ttgcatccagTTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAGTTCCATGGTAAA
EST: gi|151410856|gb|EV280671.1|EV280671
EST:     AGAAGACAAGGGAAATTCGCATTGAAAGGACAGATGAATTTGGGAGAATT                         TTGACTTCTAAGGAAGCCTTTCGGATGATCTCTCATAAGTTCCATGGTAAA
genomic: AGAAGACAAGGGAAATTCGCATTGAAAGGACAGATGAATTTGGGAGAATTgtaagttttc ... ttgcatccagTTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAGTTCCATGGTAAA
EST: gi|298174867|gb|HO014784.1|HO014784
EST:     AGAAGACAAGGGAAATTCGCATTGAAAGGACAGATGAATTTGGGAGAATT                         TTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAGTTCCATGGTAAA
genomic: AGAAGACAAGGGAAATTCGCATTGAAAGGACAGATGAATTTGGGAGAATTgtaagttttc ... ttgcatccagTTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAGTTCCATGGTAAA
EST: gi|192296695|gb|FG991263.1|FG991263
EST:     AGAAGACAAGGGAAATTCGCATTGAAAGGACAGATGAATTTGGGAGAATT                         TTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAGTTCCATGGTAAA
genomic: AGAAGACAAGGGAAATTCGCATTGAAAGGACAGATGAATTTGGGAGAATTgtaagttttc ... ttgcatccagTTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAGTTCCATGGTAAA
EST: gi|16348613|gb|BI974208.1|BI974208
EST:     AGAAGACAAGGGAAATTCGCATTGAAAGGACAGATGAATTTGGGAGAATT                         TTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAGTTCCATGGTAAA
genomic: AGAAGACAAGGGAAATTCGCATTGAAAGGACAGATGAATTTGGGAGAATTgtaagttttc ... ttgcatccagTTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAGTTCCATGGTAAA
EST: gi|254321939|gb|GR837353.1|GR837353
EST:     AGAAGACAAGGGAAATTCGCATTGAAAGGACAGATGAATTTGGGAGAATT                         TTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAGTTCCATGGTAAA
genomic: AGAAGACAAGGGAAATTCGCATTGAAAGGACAGATGAATTTGGGAGAATTgtaagttttc ... ttgcatccagTTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAGTTCCATGGTAAA
EST: gi|254338240|gb|GR849765.1|GR849765
EST:     AGAAGACAAGGGAAATTCGCATTGAAAGGACAGATGAATTTGGGAGAATT                         TTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAG
genomic: AGAAGACAAGGGAAATTCGCATTGAAAGGACAGATGAATTTGGGAGAATTgtaagttttc ... ttgcatccagTTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgtagtggagcatcacttatccttgtttgaattattcttttgttgcatccagTTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAGTTCCATGGTAAAGGACCTGGAAAAATGAAGCAAGAAAAGCGTATGAAGCAATATTACGAAG
                                     ttcttttgtt  CT-rich tract
                            tttgaattattctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttaatcagttttagtatcattctttgcaagtttcagttttcaaattgtagtggagcatcacttatccttgtttgaattattcttttgttgcatccagTTGACTCCTAAGGAAGCCTTTCGGATGATCTCTCATAAGTTCCATGGTAAAGGACCTGGAAAAATGAAGCAAGAAAAGCGTATGAAGCAATATTACGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - -tgcaagt
- - - - - - - - - - - - - - - - - - - - - - - - -gtagtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtttg