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'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAGgtctctgatacaaacttaatctgcggttcaatcgccgttggaattgtttatcctgcatcttacgattttgtttcacttgttgacag

Basic information

species Glycine max
transcript GLYMA15G02640.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 11
CTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAGgtct--ctgatacaaacttaatctgcggttcaatcgccgttggaattgtttatcctgcatcttacgattttgtttcacttgttgacag
|| ||||||||||||||||||||||| || || |||||||| || || |||| ||| || ||||||||||| |||||||||||||||||||||| |  ||  | |  |  | |  |  ||| |     | ||     |  | |   ||   | ||| | |  ||| |    | |      
CTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAGgtgttgcttttgctcatctcagttatggtactgct-cggtctccttcatgtgaactaattgtta-gttgatgtatgctctttcag---

upper sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 11
CTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAGgtctctgatacaaacttaatctgcggttcaatcgccgttgga-attgtttatcctgcatcttacg-attttgtttcacttgttgacag------------
|| |||||| ||||||||||||||||||| || || || || ||||||||||| ||||| |||||| | || || |||||||| |||||||||| |||| |     || | | || | | | |  |||| |    ||| |||    || | ||     || ||   || | |  ||                
CTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAGgtatctgct-tgttctcattatgagttaccaatgccgctaactattattttatttggaactactatatgttaactctccttgtggtgccttcaactgcag

upper sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G142334_T02 (Zea mays), 5'ss of exon 11
CTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAGgtc-tctgatacaaacttaatctgcggttcaatcgccgttggaattgtttatcctgcatcttacgattttgtttcacttgttgacag
 | |||||||||||||||||||| ||||| ||||| || || || ||||||| |||||||||||||||  | |||||||||||||| |||||||  ||| |||    ||    | |  ||   |  ||  ||||     || |  | | | || || |  |  ||    |  |      
TTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctcatatg--ctcgtccagttgtaatacagc--ttggctccattaa--caggaactaactagctgtttgtgatcttcag---

upper sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 11
CTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAGgtc-tctgatacaaacttaatctgcggttcaatcgccgttggaattgtttatcctgcatcttacgattttgtttcacttgttgacag
 | |||||||||||||||||||| ||||| || || || || || ||||||| |||||||||||||||  | |||||||||||||| |||||||  |||||||     ||  | | | |||  |   | | | |   |  ||  |  | |         | | | |||  |   |    
TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgata-----ttcttgttcagttgtaatacggcttggcctcattgacaggaactgactagctatttgtcatcttcag----

upper sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G452572_T01 (Zea mays), 5'ss of exon 1
CTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAGgtc-tctgatacaaacttaatctgcggttcaatcgccgttggaattgtttatcctgcatcttacgattttgtttcacttgttgacag
           |   |||||||| ||||| ||||| || || || ||||||| |||||||||||||||  | |||| ||||||||| |||||||  ||| |||      |||||  | |||  |   | | | |  |   ||| |  | | || || |  |  ||    |  |      
---------ACACGCGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGAAACTGGTTCCTACAGgtagtctcatatg---ctaatc--cagttgtaatacagcttggctccattaacaggaa-ctaactagctgtttgtgatcttcag---

upper sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 11
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 13
CTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAGgtctct---gatacaaa----cttaatctgcggttca-atcgccgttgga--attgtttatcctgcatcttacg-attttgtttcacttg-ttgacag
|| ||||||||||||||||||||||| ||||| || |||||||| |||||| |||||||  |||| ||||| | ||| || ||||||||||||| |     ||  || |    |||| | ||   |||  ||   ||   ||  ||  ||  |  |  |  | |    ||  ||||||     ||  |||
CTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAGgtatgccaagaagcagagcatcttattttgttattcgcattttcgaatgactatgattccttgtataaatcatttgttcggtttcatacactttccag

upper sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 11
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 11
CTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAGgtc--tctgatacaaacttaatctgcggttcaatcgcc-gttggaattgtttatcctgcatcttacgattttgtttcacttgttgacag---------
|| || ||| ||||||||||||| || ||||| ||||| || || |||||||| ||||| ||||||||| | |||||||| |||||||||||||     || |       |  ||   | |  | |   | ||      |    |     |   | || | ||| ||  ||||  |  | |         
CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgcttgtcttctggtcattgctgtacttttctgtcttgtataaggaataaactaatgaccaatttattatacttaatctccggtgaaccag

upper sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 11
CTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAGgtctctgatacaaacttaatctgcggttcaatcgccgttggaattgtttatcctgcatcttacgattttgtttcacttgttgacag
 | ||||||||||||||||||||||||||||| ||||| || ||||||||||| |||||||||||| |||| ||||| || ||||||||||||||  |  |  ||| ||  | |      || | |    | |||   | || | ||  |  ||  ||    ||  |  || |  |||
TTGTGTGATTTATATGAAAATGATTCAATCTTTGATAAATTTGAATGTTGTCTGAGTGGTGATGGAATGCGTGTAGCTACAGGTTCTTACAGgtccgttttttaaattttctttatccacca-ttgtttcttgaaccctctaccatgagtactaacataaaattg-atgtgatcccag

upper sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 11
lower sequence: PP1S425_2V6.3 (Physcomitrella patens), 5'ss of exon 11
CTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAGgtctctgat-----acaaacttaatctgcggttcaatcgccgttggaat------tgtttatc------ctgcatcttacgat---tttgtttcacttgttgacag------------------------------------------------
|| |||||| | ||||| || |||||||||||||||||||| || |||||| | ||||| |||||  |||| |||||||||||||| |||||||   | ||     |   || || | ||   |   ||      || |||      |||  |||       || |||| |  ||   | |  ||   || |||  ||                                                
CTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAGgtacgtcattgctcagccacatattttggcatcttataagtcctgtaatgaagcatgtgaatcaggaacttgtatctaaacatatgtcttcttagatttttgttagtactcttccaagtgtggtaccgaattgaattattcttctttgtcacag

upper sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 11
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 5'ss of exon 11
CTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAGgtctctgataca--aacttaatc---tgcggt--tcaatcgccgttggaat-tgtttatcctgcatcttacgattttgtttcacttgttgacag-------------------------------------------------------
||||||||| | ||||| || || || |||||||| ||||| ||||||||||| ||||| |||||  |||| || ||||||||||| ||||||| |   ||     | ||||||    |||  |  |||||  | |  ||||  |||      |    |||   |||       || | |    ||                                                       
CTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAGgtattgtatttctcagcttaattgtttgctatattcaatgtctggaggaaagtgtgggaattaagacttgt-attggacaatacatctcattagatttttatgatttctcttttaactaagaaaactaatttaagtgtgcttggtacag

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|193343412|gb|FK308190.1|FK308190
EST:     AATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAAG                         TAATCTATTTCGT
genomic: AATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACA-Ggtctctgata ... ttgttgacagTAATCTATTTCGT
EST: gi|17519644|gb|BM188686.1|BM188686
EST:     GAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAG                         TAATCTATTTCGTGTGTTTGGTTGTGCCCCTGGAAGTGCTGAGGCTACAAC
genomic: GAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAGgtctctgata ... ttgttgacagTAATCTATTTCGTGTGTTTGGTTGTGCCCCTGGAAGTGCTGAGGCTACAAC
EST: gi|26057605|gb|CA800519.1|CA800519
EST:     GAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAG                         TAATCTATTTCGTGTGTTTGGTTGTGCCCCTGGAAGTGCTGAGGCTACAAC
genomic: GAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAGgtctctgata ... ttgttgacagTAATCTATTTCGTGTGTTTGGTTGTGCCCCTGGAAGTGCTGAGGCTACAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAGgtctctgatacaaacttaatctgcggttcaatcgccgttggaattgtttatcctgcatcttacgattttgtttcacttgttgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA