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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcaagcattcattgttattcttggtattgcatgtgatataggatccatgtgcatttaaaaaaaaattaagtaatagtttttctttctgatatattcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG

Basic information

species Glycine max
transcript GLYMA03G25740.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G002687_T01 (Zea mays), 3'ss of exon 5
atgcaagcattcattgtt--attcttggtattgc--atgtgatataggatccatgtgcatttaaaaaaaaattaagtaatagtttttctttctgatatattcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG
|||   || ||  |  ||  | | |    | | |  ||    | |   |    | ||  | |     ||| ||    | ||| ||||  ||||    | | ||||||||||||||||| ||||| |||||||||||||||| ||| ||||  || || ||| |  ||||||||||   ||| || || ||  | |||
atgtttgcctttttctttgaagtttgaccaataccaatacattttgatacatctttgtgtgtctttcaaattttgagagtagatttttcttct----tctgcagGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG

upper sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G04600.3 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------------------------------------------------------------atgcaagcattcattgttattcttggtattgcatgtgatataggatccatgtgcatttaaaaaaaaatta--agtaatagtt-tttctttctgatat-attcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG
                                                                                      ||| |||||    |  |    |   || |   | |  | || | |     || ||   |     | |||  |  |||  || ||||||| || | |  |||||||||| |||||||||||||| |||||||| || ||     | || |    |||||| ||| ||||||| |||  ||| || || || || |||
gtgtgctgttttcttactttttatattaacctgtttgcctttttaaaagattaataacttcccattggtataaaaatgtctgtgactgcgagcatgtgatacttccatccataatcagtttcttttatgttttccatgtatcacatttgtatttataaccaatctttctttctttttggttttgttcagGATCCTTATTTTAGAATGACTCGTGATGTCGCACCCCGGTTAGGCTATAGCAAGCCCGCCCTGATTGAGTCAACATTTTTTCCTGCGTTGCAG

upper sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G04600.2 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------------------------------------------------------------atgcaagcattcattgttattcttggtattgcatgtgatataggatccatgtgcatttaaaaaaaaatta--agtaatagtt-tttctttctgatat-attcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG----
                                                                                      ||| |||||    |  |    |   || |   | |  | || | |     || ||   |     | |||  |  |||  || ||||||| || | |  |||||||||| |||||||||||||| |||||||| || ||     | || |    |||||| ||| ||||||| |||  ||| || || || || |||    
gtgtgctgttttcttactttttatattaacctgtttgcctttttaaaagattaataacttcccattggtataaaaatgtctgtgactgcgagcatgtgatacttccatccataatcagtttcttttatgttttccatgtatcacatttgtatttataaccaatctttctttctttttggttttgttcagGATCCTTATTTTAGAATGACTCGTGATGTCGCACCCCGGTTAGGCTATAGCAAGCCCGCCCTGATTGAGTCAACATTTTTTCCTGCGTTGCAGGCAA

upper sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 6
atgcaagcattcattgttattcttggtattgcatgtgatataggatcc-atgtgcatttaaaaaaaaattaa-gtaatagtttttctttc--tgatatattcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG
    |     ||||  || |        || |||    | | | |||  ||||  || ||| ||  | || | |  || |  ||| ||||  | || | |||||||||| ||||| ||||||||||| ||||||||||||   || || |  |||||||| || ||||||||||||||||||||||| ||  | |||
---aatattgtcatcatt-tatccaactttacattcatttttgcatctgatgtcaatgtaataattattttatggtattgcctttgtttccttaatttgttcagGATCCTTATTTCAGAATGACACGGGATGTTGCTCCTCGGATAGGATATCACAAGCCCGCATTGATTGAATCATTATTCTTCCCTGCCCTTCAG

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|112361194|gb|EE400179.1|EE400179
EST:     TTTCTGGAAANGAGAATCTTCGTTGTTTAATTCCTTGTGCAATTGACCAG                         GATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCAC
genomic: TTTCTGGAAAAGAGAATCTTCGTTGTTTAATTCCTTGTGCAATTGACCAGgtccgttggt ... atatattcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCAC
EST: gi|7686161|gb|AW756809.1|AW756809
EST:     TTTCTGGAAAAGAGAATCTTCGTTGTTTAATTCCTTGTGCAATTGACCAG                         GATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGG-TTTCCAC
genomic: TTTCTGGAAAAGAGAATCTTCGTTGTTTAATTCCTTGTGCAATTGACCAGgtccgttggt ... atatattcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCAC
EST: gi|20811614|gb|BQ296092.1|BQ296092
EST:     TTCTGGAAAAGAGAATCTTCGATGTTTAATTCCTTGTGGCA-TTGACCAG                         GATCCATATTTTAGAATGACACGTGATGCTGCTCCTAANATGGGTTTCCAC
genomic: TTCTGGAAAAGAGAATCTTCGTTGTTTAATTCCTTGTG-CAATTGACCAGgtccgttggt ... atatattcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCAC
EST: gi|26047670|gb|CA784386.1|CA784386
EST:     TTTCTGGAAAAGAGAATCTTCGNTGTTTAATTCCTTGTGCAATTGACCAG                         GATCCATATTTTAGAATG
genomic: TTTCTGGAAAAGAGAATCTTCGTTGTTTAATTCCTTGTGCAATTGACCAGgtccgttggt ... atatattcagGATCCATATTTTAGAATG
EST: gi|18039483|gb|BM307777.1|BM307777
EST:     TTTCTGGAAAAGAGAATCTTCGTTGTTTAATTCCTTGTGCAATTGACCAG                         GATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCAC
genomic: TTTCTGGAAAAGAGAATCTTCGTTGTTTAATTCCTTGTGCAATTGACCAGgtccgttggt ... atatattcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatgtgcatttaaaaaaaaattaagtaatagtttttctttctgatatattcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG
                                        ttctgat  putative branch site (score: 3)
                                 tttttctttctgat  CT-rich tract
         atttaaaaaaaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcaagcattcattgttattcttggtattgcatgtgatataggatccatgtgcatttaaaaaaaaattaagtaatagtttttctttctgatatattcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG

- - - gcattca
- - - - - - - - - - - - - - -tgcatgt
- - - - - - - - - - - - - - - - - - - - - - atccatg
- - - - - - - - - - - - - - - - - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa