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'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaaaactctttctcttccttcctttgctaaacatttcccatttttttcattatctttgctgcttatttctttattaaaaatgtttctttctggtgcagGCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT

Basic information

species Glycine max
transcript GLYMA03G39290.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
ttgaaaactctttctcttccttcctttgctaaacatttcccatttttttcattatctttgctgctta--tttctttattaaaaatgtttctttctggtgcagGCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT
   |  | | ||    ||||||     |   |  || |   |||   |     || |   ||    |  | |  ||    || ||| | | ||||| |  ||||||||| |||| || || || |||||||| |||||||||||||| || || || || ||||| || ||||| ||||| ||||| ||  |  |||| || 
--aactaatgttctatttccttgtcacgactattatgttggattcaatggtacatttggtctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC

upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
ttgaaaactctttctcttccttcctttgctaaacatttcccatt-tttttcattatctttgctgct-tatttctttattaaaaatgtttctttctggtgcagGCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT
   |    | ||   |  | ||| |||     | |  |   |||   | |       | | || ||  || |  | |||    |  |  | || || || ||||||||| |||| || ||||| |||||||||||||||||||| ||||| || || || ||||| || ||||| || || ||||  |||||  |||| || 
--aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctgatattctactacatgtaataattccctacttcacattgtgttgtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC

upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G116506_T01 (Zea mays), 3'ss of exon 1
ttgaaaactctttctcttccttcctttgctaaacatttcccatttttttcattatctttgctgcttatttctttattaaaaatgtttctttctggtgcagGCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT
    |   |||  | | | |||   |  |  ||      | || | |    | || ||      | || |  | |||    |  |  | || || || ||| ||||| |||| || ||||| ||||||||||||||||||||||| |  || |  || ||||| || ||||| || || ||||| |||||  |||| || 
actgatgttctcccacgttcttttatcccagaaatggaactatctgtgcgttgatattctactataatgtagtaattccctacttcacattgtgttgtagGTTTGAGCAAGAGTCGGGGTTCTTCTTCAATATGAAGTACTTTGAAGCGAAGGGCCATGCTGGGGACTGGGATGAGGTGGAGAAATACTTGTCAGGTTTC

upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 1
ttgaaaactctttctcttccttcctttgctaaacatttcccatttttttcattatctttgctgcttatttctttattaaaaatgtttctttctggtgcagGCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT
        |  |    ||   |  |||| |     ||      |       | |  ||||    | | |  ||| | |        | | |    |  |||||||||||||| || || || ||||||||||  ||||| ||||| || ||||| |  ||||| |||||||| || ||||||| ||| ||  |||| |||
------gttagtctatttatatggtttgttttgtgttgtgttgtgagaggctgaattttgggattgactgatttgtaa--------tttgttaaatatagGCTTGAGAAAGAGTCAGGATTCTTCTTCAATACCAAGTATTTTGATGAGAAAGTTCTAGCTGGAGAATGGGATGATGTTGAGACGTATTTGTCAGGTTTT

upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 1
ttgaaaactctttctcttccttcctttgctaa---acatttcccatttttttcattatctttgctgcttatttcttt--attaaaaatgtttctttctggt--gcagGCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT
        | ||| | ||   | |||| | ||   ||| || |       ||   | |  ||  |   | ||  |||  |   ||| | ||| ||  || |  | |||||||||||||| || |||||||||||||||||||||||||||||||| ||||||||||| || |||||||| |||||||||||||| ||| | || | |
-------tttttttttttttcttcttttccaatttacactttcttggaagtttggtgtagttaattaatcttaatttgaacggaaattattttttggtgttttgtagGCTTGAGAAAGAGTCAGGGTTTTTCTTCAATATGAAGTACTTTGAGGAGAAAGTACAGGCAGGAGAATGGGATGAAGTTGAGAAGTATTTATCCGGATAT

upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 1
----------ttgaaaactctttctcttccttcctttgctaaacatttcccatttttttcattatctttgctgcttatttctttattaaaaatgtttctttctggtgcagGCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT
           ||||     | ||  || |    | |||  |          ||| ||     |||| | |||  |  || | || ||         | ||||    |||| | ||| ||||||| || || ||||||||||||||||||||||| ||  |||| || | |||||| ||||| || || ||    || ||| | ||||| 
tctgcgttacgtgaagctggtgtcattttcaaaatgtgcatacagacgtttgtttcttctgcaatctgtactgactggttttataata---------ccttctaac-cagGTTGGAGCAAGAATCAGGATTCTTCTTCAATATGAAGTACTTTGAAGACCAAGTTCAAGGTGGTGAGTGGGAGGAGGTGGAACGATATTTATCTGGGTTC

upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ37833 (Selaginella moellendorffii), 3'ss of exon 1
ttgaaaactctttctcttccttcctttgctaaacatttcccatttttttcattatctttgctgcttatttctttattaaaaatgtttctttctggtgcagGCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT
                                   |       ||| |   || |  ||| || |   |      | |    ||| |  || ||  ||||||| ||| |||||||||| || | |||||| |||||||||||||| ||  | || |||  ||| || ||||| || || |||| ||||||  | || || 
----------------------------------gtgagaagatttgtggtttgttcttgttggtggat-----gtaagtgttgtgtgattttg--gcagGCTGGAGCAAGAATCTGGCTTCTACTTCAACATGAAGTACTTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC

upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 1
ttgaaaactctttctcttccttcctttgctaaacatttcccatttttttcattatctttgctgcttatttctttattaaaaatgtttctttctggtgcagGCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT
                                   |       ||| |   || |  ||| || |   |      | |    |||    || ||  ||||||| ||| |||||||||| || | |||||| |||||||||||||| ||  | || |||  ||| || ||||| || || |||| ||||||  | || || 
----------------------------------gtgagaagatttgtggtttgttcttgttggtggat-----gtaagtgttgtgcgattttg--gcagGCTGGAGCAAGAATCTGGCTTCTACTTCAACATGAAGTACTTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC

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|209726114|gb|BW675288.1|BW675288
EST:     CTGATACTCCAATTTTTGGAGGAGGAGAAGTTCAAGGAGTCGGTGCACAA                         GCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAA
genomic: CTGATACTCCAATTTTTGGAGGAGGAGAAGTTCAAGGAGTCGGTGCACAAgtaagcaagt ... tctggtgcagGCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAA
EST: gi|209697859|gb|BW670102.1|BW670102
EST:     CTGATACTCCAATTTTTGGAGGAGGAGAAGTTCAAGGAGTCGGTGCACAA                         GCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAA
genomic: CTGATACTCCAATTTTTGGAGGAGGAGAAGTTCAAGGAGTCGGTGCACAAgtaagcaagt ... tctggtgcagGCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAA
EST: gi|213590590|gb|DB968126.1|DB968126
EST:     CTGATACTCCAATTTTTGGAGGAGGAGAAGTTCAAGGAGTCGGTGCACAA                         GCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAA
genomic: CTGATACTCCAATTTTTGGAGGAGGAGAAGTTCAAGGAGTCGGTGCACAAgtaagcaagt ... tctggtgcagGCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcattatctttgctgcttatttctttattaaaaatgtttctttctggtgcagGCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT
                                     tgtttctttct  CT-rich tract
                   ttatttctttattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaaaactctttctcttccttcctttgctaaacatttcccatttttttcattatctttgctgcttatttctttattaaaaatgtttctttctggtgcagGCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - -ctcttcc
- - - - - - - - - - - cctttgc
- - - - - - - - - - - - - - - - - -tttccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attaaaaa