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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTTCTCTTAGAGTCAAGGGAAAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTGGACATGGGAGCATCATGgtaaagctacttctctttatctgcttattatgagaatgtaaaatttcttccatttttttatttgtttttttagtactaaaagttacacatttttcag

Basic information

species Glycine max
transcript GLYMA08G41570.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G41570.3 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os04g53190.1 (Oryza sativa), 5'ss of exon 4
GTTGTTCTCTTAGAGTCAAGGGAAAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTGGACATGGGAGCATCATGgtaaagctacttctctttatctgcttattatgaga-atgtaaaatttcttccatttttttatttgtttttttagtactaaaagttacacatttttcag---------
||||||||  |||| ||  | || || || |||||  ||||||||||||||||||| ||||| |||||||| ||  |||||||||| |||| | | |    |||| |  |    | || |||   || | ||||     | |   |||   | |     ||| |  |||        ||||||             
GTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTGgtgaggtt---cctctctgacaatattttctgaattatttgaaatggtggcaaaagtttatctggaaccattatttttaatccacttccattttgtgtgagcatcag

upper sequence: GLYMA08G41570.3 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os04g53195.1 (Oryza sativa), 5'ss of exon 3
GTTGTTCTCTTAGAGTCAAGGGAAAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTGGACATGGGAGCATCATGgtaaagctacttctctttatctgcttattatgaga-atgtaaaatttcttccatttttttatttgtttttttagtactaaaagttacacatttttcag
||||||||  |||| ||  | || || || |||||  ||||||||||||||||||| ||||| |||||||| ||  |||||||||| |||| | | |    |||| |  |    | || |||   || | ||||     | |                                             
GTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTGgtgaggtt---cctctctgacaatattttctgaattatttgaaatggtggcaaaag------------------------------------------

upper sequence: GLYMA08G41570.3 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G396856_T02 (Zea mays), 5'ss of exon 4
GTTGTTCTCTTAGAGTCAAGGGAAAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTGGACATGGGAGCATCATGgtaaagctacttctctttatctgcttattatgagaatgtaaaatt-tcttccatttttttatt---tgtttttttagtactaaaagttacacatttttcag
||| ||||  | || ||  | || |||||||||||| || |||||||||| ||||| ||||| ||||| || ||  |||||||||| |||| |      |||| || | ||  | |  ||| |     ||  |  ||||  |    |  |||   |||||||||  |  |     ||    |        
GTTATTCTTCTGGAATCTCGTGATAGAATTGGTGGCAGAGTTCACACTGACTACTCTTTTGGGTTTCCAGTCGATTTGGGAGCATCTTGgtgagttccattcttttgaact-ttcaccatgtgcccaaaagttcatcttgaaggaatgcattgagtgtttttttcatcatttctattgagaag-------

upper sequence: GLYMA08G41570.3 (Glycine max), 5'ss of exon 3
lower sequence: AT3G59050.1 (Arabidopsis thaliana), 5'ss of exon 2
-----------GTTGTTCTCTTAGAGTCAAGGGAAAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTGGACATGGGAGCATCATGgtaaagctacttctctttatctgcttattatgagaatgtaaaatttcttccatttttttatttgtttttttagtactaaaagttacacatttttcag---
           |||||| | || |||||  | || ||||||||||| ||| |||||||||||||||||||||||||||| || ||  | || ||||| ||||||    |   ||| ||  |  | |||  |    |  | |    | ||    | |||| |      |   |  |||||    ||  | ||||       
CTTCCTTTCAGGTTGTTGTATTGGAGTCTCGTGACAGAATTGGTGGACGAGTTCACACTGATTACTCATTTGGTTTTCCAGTTGATCTCGGTGCATCTTGgtaatatcatggctcctt--caacctatctttttcac-tgattgctgtttggatcttttgtcatcgatgcca--actaagcaatat-cgttttgtgacag

upper sequence: GLYMA08G41570.3 (Glycine max), 5'ss of exon 3
lower sequence: AT2G43020.1 (Arabidopsis thaliana), 5'ss of exon 3
GTTGTTCTCTTAGAGTCAAGGGAAAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTGGACATGGGAGCATCATGgtaaagctacttctcttt-atctgcttattatgagaatgtaaaatttcttccatttttttatttgttttt--ttagtactaaaagttacacatttttcag
||| |  |  | |||||  | || ||||||||||| ||| ||||||||||||||||||||||||||||||| ||  | || ||||||||||||    ||  |||||| |||   | |||| ||  ||||    ||  ||    |||||  ||   |||    ||  ||   ||  |    || |  |||
GTTATGGTACTGGAGTCCCGTGACAGAATTGGTGGACGAGTTCACACTGATTACTCATTTGGTTTTCCTGTTGATCTTGGTGCATCATGgtaatctcacggctctttcatcctgtcatta-gatgatgtt---ttggttttggtttttggttaactttaggctaacacagcaacatcgttatgtcacag

upper sequence: GLYMA08G41570.3 (Glycine max), 5'ss of exon 3
lower sequence: Vv12s0028g01120.t01 (Vitis vinifera), 5'ss of exon 3
GTTGTTCTCTTAGAGTCAAGGGAAAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTGGACATGGGAGCATCATGgtaaagctacttctctttatctgcttattatgagaatgtaaaatttcttccatttttttatttgtttttttagtactaaaagttacacatttttcag
|||||||| || || ||  | || ||||||||||| ||  |||| |||||||||||||||||||||||||| ||| ||||||||||||||||||  |   ||| ||    | ||| ||   | ||  |     | | ||| | |      |  ||    |     | ||| ||  ||    |  ||
GTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATGgtaaacttttatcttttagctttctttttgctaaaacctgtggatacctcc-tgtcaactctaattaaaatctctttcaaaattgtac----tcaag

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|298163510|gb|HO012243.1|HO012243
EST:     ATTCACACTGATTACTCATTTGGTTTTCCTGTGGACATGGGAGCATCATG                         GTTGCATGGAGTTTCCAATGAAAATCCACTGGCTTCGGTGATTGGGAGGCT
genomic: ATTCACACTGATTACTCATTTGGTTTTCCTGTGGACATGGGAGCATCATGgtaaagctac ... catttttcagGTTGCATGGAGTTTCCAATGAAAATCCACTGGCTTCGGTGATTGGGAGGCT
EST: gi|120530787|gb|EH258920.1|EH258920
EST:     ATTCACACTGATTACTCATTTGGTTTTCCTGTGGACATGGGAGCATCATG                         GTTGCATGGAGTTTCCAATGAAAATCCACTGGCTTCGGTGAT
genomic: ATTCACACTGATTACTCATTTGGTTTTCCTGTGGACATGGGAGCATCATGgtaaagctac ... catttttcagGTTGCATGGAGTTTCCAATGAAAATCCACTGGCTTCGGTGAT
EST: gi|7673728|gb|AW160135.1|AW160135
EST:     ACACTGATTACTCATTTGGTTTTCCTGTGGACATGGGAGCATCATG                         GTTGCCATGGAGTTTCCAATGAAAATCCACTGGCTTCGGTGATTGGGAGGC
genomic: ACACTGATTACTCATTTGGTTTTCCTGTGGACATGGGAGCATCATGgtaaagctac ... catttttcagGTTG-CATGGAGTTTCCAATGAAAATCCACTGGCTTCGGTGATTGGGAGGC
EST: gi|17153134|gb|BM143067.1|BM143067
EST:     ATTCACACTGATTACTCATTTGGGTTTCCTGTGGACATGGGAGCATCATG                         GTTGCATGGAGTT
genomic: ATTCACACTGATTACTCATTTGGTTTTCCTGTGGACATGGGAGCATCATGgtaaagctac ... catttttcagGTTGCATGGAGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTTCTCTTAGAGTCAAGGGAAAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTGGACATGGGAGCATCATGgtaaagctacttctctttatctgcttattatgagaatgtaaaatttcttccatttttttatttgtttttttagtactaaaagttacacatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA