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'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgaactcttttcattccaagcattgcaatctcccgtgaaaatttccgttttatttttctatgatttacttatgttcgttcataattccaaaatttcagTCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGACAGACTATTTAATCTTTACTCTTCGGGAAAGCTAAAG

Basic information

species Glycine max
transcript GLYMA02G15070.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G15070.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os09g28570.2 (Oryza sativa), 3'ss of exon 15
-----agtgaactcttttcat--tccaagcattgcaatctcccgtgaaaatttccgttttatttttctatgatttacttatgttcgttcataattccaaaatttcagTCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGACAGACTATTTAATCTTTACTCTTCGGGAAAGCTAAAG-------------
     ||  ||    ||  ||   |||   ||||  || | |    |  |||     |  | | | |||  | | ||    |||| ||| |  |     || ||||| |||| ||||||||  | || |||| ||||||||||||||| |||||||||| ||| ||| | || ||  | || ||||||||||||             
tgtcaagcaaatgaattgtatgagccagtgattgtgatgtactaatacgattctt-ctggaatgtcctaacactaac--gagttctttccttgtc----aacttcagGCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGGTATGCCTCGAGC

upper sequence: GLYMA02G15070.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os09g28570.1 (Oryza sativa), 3'ss of exon 15
-----agtgaactcttttcat--tccaagcattgcaatctcccgtgaaaatttccgttttatttttctatgatttacttatgttcgttcataattccaaaatttcagTCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGACAGACTATTTAATCTTTACTCTTCGGGAAAGCTAAAG
     ||  ||    ||  ||   |||   ||||  || | |    |  |||     |  | | | |||  | | ||    |||| ||| |  |     || ||||| |||| ||||||||  | || |||| ||||||||||||||| |||||||||| ||| ||| | || ||  | || ||||||||||||
tgtcaagcaaatgaattgtatgagccagtgattgtgatgtactaatacgattctt-ctggaatgtcctaacactaac--gagttctttccttgtc----aacttcagGCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG

upper sequence: GLYMA02G15070.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G479068_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------------agtgaactcttttcattccaagcattgcaatc-----------------tcccgtgaaaatttccgttttatttttctatga----tttacttatgttcgttcataattccaaaatttcagTCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGACAGACTATTTAATCTTTACTCTTCGGGAAAGCTAAAG
                                                                           |  | || ||| ||  |  ||  |   ||| |                 | |  | ||||   ||  |  |       ||||    |  | |||||     ||||  ||| ||  |||||| |||||||||||||||| |||||||  ||| |||||||||| |||||||| | ||| ||||| || || || || ||||||||||||
gtatgttcgtgctgaataacaccaaatctaaaaggacgcttttacacagatcgtagttatcacacactgaatctaaaaggacgcttctcgctt-aactaccacaaccagaactagaaaaagaagtgcttttaaaagagccactgcaaggacaaatgaagcctaaaattatgagatatcatctttctaa--tttcagGCTGGCTTTTTCCTGGTCCAATATGCGCACCTGTGGCAAGACCATCTTGAAAAACTGTTTAACCTGTATTCCTCTGGAAAGCTAAAG

upper sequence: GLYMA02G15070.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G147191_T02 (Zea mays), 3'ss of exon 15
agtgaactcttttcattccaagcattgcaatctcccgtgaaaatttccgttttatttttctatg--atttacttatgttcgttc--ataattcca----aaatttcagTCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGACAGACTATTTAATCTTTACTCTTCGGGAAAGCTAAAG
         | |  |   |||  ||||   |     |  | |  ||   | | || || | |    |||   || |   | ||   | | |||||    ||||| ||| |||| |||||||| || || |||| ||||||||||||||| |||||| ||| ||| ||| | || ||  | || ||||||||||||
--------gtatataggacaactattgagctacattggtagatgttggatctaatattccaaaagcattctgttgtagcctttgaaacatttccatttcaaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG

upper sequence: GLYMA02G15070.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv03s0063g00610.t01 (Vitis vinifera), 3'ss of exon 15
--agtgaactcttttcattccaagcattgcaatctcccgtgaaaatttccgttttatttttctatgatttacttatgttcgttcataattccaaaatttc-agTCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGACAGACTATTTAATCTTTACTCTTCGGGAAAGCTAAAG
    || ||           ||     |     ||  | |||  |      || ||||    |||  |||   |   |    | | ||| | ||  |||  || |||||||||||||||||||||||| |||||| |||||||||||| | ||||| || ||| |||||| ||| | ||||||||| |||
tgtatggaccaaaccagggacagattcttttcactttcatgattaagcatattatattg---tatcctttttgtgcttcttataacaatgctaatgtttttagGCTGGCTTTTTCCTGGTGCAATATGCTCACTTATGGCAAGAACATTTGGACAGGCTTTTTCATCTTTTCTCCTTGGGAAAGCTTAAG

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|213602767|gb|DB968937.1|DB968937
EST:     CAAAATACCCTGGACTATTGGAGAAGCTCTTAGCAAAGAGCCAAACAGTG                         TCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGAC
genomic: CAAAATACCCTGGACTATTGGAGAAGCTCTTAGCAAAGAGCCAAACAGTGgtatgtagca ... aaaatttcagTCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGAC
EST: gi|37997225|gb|CF808814.1|CF808814
EST:     CAAAATACCCTGGACTATTGGAGAAGCTCTTAGCAAAGAGCCAAACAGTG                         TCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGAC
genomic: CAAAATACCCTGGACTATTGGAGAAGCTCTTAGCAAAGAGCCAAACAGTGgtatgtagca ... aaaatttcagTCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGAC
EST: gi|4395823|gb|AI494820.1|AI494820
EST:     ACTATTGGAGAAGCTCTTAGCAAAGAGCCAAACAGTG                         TCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGAC
genomic: ACTATTGGAGAAGCTCTTAGCAAAGAGCCAAACAGTGgtatgtagca ... aaaatttcagTCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGAC
EST: gi|4290814|gb|AI441672.1|AI441672
EST:     CAAAATACCCTGGACTATTGGAGAAGCTCTTAGCANAGAGCCAAACAGTG                         TCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGAC
genomic: CAAAATACCCTGGACTATTGGAGAAGCTCTTAGCAAAGAGCCAAACAGTGgtatgtagca ... aaaatttcagTCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGAC
EST: gi|6200887|gb|AW152987.1|AW152987
EST:     CAAAATACCCTGGACTATTGGAGAAGCTCTTAGCAAAGAGCCAAACAGTG                         TCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGAC
genomic: CAAAATACCCTGGACTATTGGAGAAGCTCTTAGCAAAGAGCCAAACAGTGgtatgtagca ... aaaatttcagTCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgttttatttttctatgatttacttatgttcgttcataattccaaaatttcagTCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGACAGACTATTTAATCTTTACTCTTCGGGAAAGCTAAAG
     tttatttttctatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgaactcttttcattccaagcattgcaatctcccgtgaaaatttccgttttatttttctatgatttacttatgttcgttcataattccaaaatttcagTCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGACAGACTATTTAATCTTTACTCTTCGGGAAAGCTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
agtgaac
- - - - - - -cattcca
- - - - - - - - - - - cattgca
- - - - - - - - - - - - - - - -ctcccgt