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

gttattattgtttaggtttaactttgttaactggggtcagtgtgcatagttggtcaatggcagaaatattaacttatagtttttatttctgttgttgaagCATATATGGTCCAGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA

Basic information

species Glycine max
transcript GLYMA12G01340.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G01340.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g03220.1 (Oryza sativa), 3'ss of exon 2
-------------------gttattattgtttaggtttaactttgttaactggggtcagtgtgcatagttggtcaatggcagaaatattaacttatagtttttatttctgttgttgaagCATATATGGTCCAGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA
                     |     | || | || |    ||   |  | ||  || |    | | ||  | ||||  |    | ||  ||| |   | || | |  |       ||||| |||||    || ||||| ||| | |||||||||||| ||||||| |||||||||||||| ||||| |  || | | |||| |||||||| ||||| 
gtatcacatgttccaccatagtgcccctattgatgtgtcttgtttcaatattggagcatttcata-atttaatgaatgcaatctgttttggcttgtttgtgttgtgtggggacaaccagCATGTATGGGATGGTGCAAGATGTGCGTATCCCATACCAGGAGAAGCGCATGTTTGGTTTTGTCACCTTCGCCTACCAAAAGACAGTGAAGCTAATTCTT

upper sequence: GLYMA12G01340.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g21160.1 (Oryza sativa), 3'ss of exon 2
--------gttattattgtttaggtttaactttgttaactggggtcagtgtgcatagttggtcaa-tggcagaaatattaac-ttatagtttttatttctgt----tgttgaagCATATATGGTCCAGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA
             | |||    | |    |||  ||   |   | | |  |   |||   |  |  ||   |  || ||  | ||   ||| ||      |      | || ||||| || || || || || |||||| | ||||| |||||||||||||| ||||| || || || ||||| ||||| || ||||| |||||||| ||  | 
gtatataatgcgatgttgcaatgatgcttcttccttctttcatggcgggctcggtaggacgcgatctgattggcatttttgcattgctgttcttggcaacgcgccgcgctgcagCATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTTTACCCGGAGACGGTGAAGCTGATCTTG

upper sequence: GLYMA12G01340.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g48410.2 (Oryza sativa), 3'ss of exon 2
gttattattgtttaggtttaactttgttaactggggtcagtgtgcatagttggt-caatggcagaaatattaacttatagtttttatttctgttgttgaagCATATATGGTCCAGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA
                    | | |  ||  |     ||  |  ||  ||     | ||| || |  | | | || ||  |      |       ||||||||| || || || ||||| |||||  | ||||| |||||||||||||| ||||| || || || ||||| || || || ||||| |||||||| ||||| 
------------------gtagtatacta--taatcccaccgcccaccgtcaccgccatgccatagctttaatctgatgatgccctctca----attgaagCATCTACGGCCCCGTCCACGACGTTCGCATCCCGTACCAGCAGAAGCGCATGTTCGGCTTCGTCACCTTCGTCTACCCGGAGACGGTGAAGCTGATTCTC

upper sequence: GLYMA12G01340.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G819035_T01 (Zea mays), 3'ss of exon 3
gttattattgtttaggtt-taactttgttaactggggtcagtgtgcatag----ttggtcaatggcagaaatattaacttatagtttttatttctgttgttgaagCATATATGGTCCAGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA
  |||   ||   |     |||  |  |   |     |  | || | |||      | |   | ||   | |     ||     || |||    ||  || | ||||| || |||||||| || |||||| | ||||| |||||||||||||| ||||| || || || ||||| || |||||||||||||||||||| || || 
-gtatgcatgcacacacggtaatgtgatgctccaatctttgcgtccgtagaaacccgtttggttgcgtgacttgaccctcgcgcttcttagcaatgcggt-gtagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTATCCAGAGACCGTGAAGCTCATCCTG

upper sequence: GLYMA12G01340.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G003424_T01 (Zea mays), 3'ss of exon 2
gttattattgtttaggtt-taactttgttaactggggtcagtgtgcatag----ttggtcaat-ggcagaaatattaacttatagtttttatttctgttgt--tgaagCATATATGGTCCAGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA
  |||   ||   |     |||  |  |   |     |  |  | | |||      | |   | ||| ||  |    | |     || || ||     ||   || ||||| || |||||||| || |||||| | ||||| |||||||||||||| ||||| || || || ||||| || || |||||||| |||||||| || || 
-gtatgcatgcacacacggtaatgtgatgctccaatctttgcttccgtagaaccccgtttggttggctgacttgacca-tcgcgcttcttgttggcaatgcggtgcagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTACCCAGAGACGGTGAAGCTCATCCTG

upper sequence: GLYMA12G01340.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G086614_T01 (Zea mays), 3'ss of exon 2
----gttattattgtttaggt-ttaactttgttaa--ctggggtcagtgtgc--atagttggtcaatggcagaaatattaacttatagtttttatttctgt-tgttgaagCATATATGGTCCAGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA
    | |||   ||   |  | ||||  |  || |  |||   ||  ||      |||  |  |   |   |     || ||        ||  |  |  |  |  | ||||| || |||||||| || |||||| | || || |||||||||||||| ||||| || || || ||||| || || |||||||| |||||||| || || 
gtatgctatgcatgcacacatgttaatgtgattgatgctgcaatctttgcttcggtagaagaaccccgtttggttggttgaccctcgcgcttcttggcaatgcggcgcagCATCTACGGTCCAGTTCACGACGTGCGCATTCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCAGAGACGGTGAAGCTCATCCTG

upper sequence: GLYMA12G01340.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0158g00370.t01 (Vitis vinifera), 3'ss of exon 3
------------gttattattgtttaggt-ttaactttgttaactggggtcagtgtgcatagttggtcaatggcag--aaatattaacttatagtttttatttctgttgttgaagCATATATGGTCCAGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA
             || | ||   ||   | ||   |||||  | | |  |   ||||   |||||     |  | |     |  ||| |    |||||   || |||||||||||||| |  |||||||| ||||| |||||||||||||| ||||||||| | ||||| || ||||| ||||| |||||||||||||| |||||||| ||| | 
gttttgaccacaattttcatgaattgtttcttggttttgtgcaattgaat---tgtgggaagttgagagctttcggttggtttctaaatcgctgttttg--ttttgttgttgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG

upper sequence: GLYMA12G01340.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S31_251V6.1 (Physcomitrella patens), 3'ss of exon 2
gttattattgtttaggtttaactttgttaactggg-gtcagtgtgcatagttggtcaatggcagaaatattaacttatagtttttatttctgttgttgaagCATATATGGTCCAGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA
|| |    ||     |  | ||| |  |   ||    |     | | | |  | ||       ||   || || ||     |||        |   || ||    || |||||||||||||| ||  ||||||| || ||||||||||| |||||||||||||| || ||||| ||| |||| || || ||    ||| | 
gtcaacggtgac--agccttactgtactttttgcatattgaaatacttgga-gatcctcttatgaccaatcaattttctcatttgtgcgggatgaatgcagGGCTTACGGTCCAGTCCAAGATGTTCGGATCCCCTATCAGCAGAAGCGGATGTTTGGTTTTGTGACTTTTGTATATTCAGAAACTGTTAAAGCAATTTTG

upper sequence: GLYMA12G01340.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ13340 (Selaginella moellendorffii), 3'ss of exon 3
gttattattgtttaggtttaactttgttaactggggtcagtgtgcatagttggtcaatggcagaaatatta-acttatagtt--tttatttctgttgttgaagCATATATGGTCCAGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA
                                        ||||  |     |  ||| |||  | | ||  | | ||  ||  ||| |||   ||| | | |    |  || || || |||||||||||||| || |||||||| ||| |||||||||| || || ||||||   ||  | ||||||||   |   || || 
-------------------------------------gtatgtgattgagaagaaaatcgcatcattgttttattcatgattcttttcttttcattgctca-gTTCTTTCGGGCCCGTACAAGACGTGAGGATTCCTTACCAGCAAAAGAGAATGTTTGGCTTCGTCACCTTTACGTACTCGGAGACCGTACGGACAATCCTG

upper sequence: GLYMA12G01340.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ24679 (Selaginella moellendorffii), 3'ss of exon 3
gttattattgtttaggtttaactttgttaactggggtcagtgtgcatagttggtcaatggcagaaatattaacttata-gtttttatttctgttgttgaagCATATATGGTCCAGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA
                                        ||||  |     |  ||| |||     |||   || |   |  || |||  |||| | | |    |  || || || |||||||||||||| || |||||||| ||| |||||||||| || || ||||||   ||  | ||||||||   |   || || 
-------------------------------------gtatgtgattgagaagaaaatcgcatgg-cattgttttgtttatggttcttttcgttgctca-gTTCTTTCGGGCCCGTACAAGACGTGAGGATTCCTTACCAGCAAAAGAGAATGTTTGGCTTCGTCACCTTTACGTACTCGGAGACCGTACGGACGATCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagttggtcaatggcagaaatattaacttatagtttttatttctgttgttgaagCATATATGGTCCAGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA
                     tattaac  putative branch site (score: 1)
                                  tttttatttctgtt  putative PPT
                  aaatattaacttatag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttattattgtttaggtttaactttgttaactggggtcagtgtgcatagttggtcaatggcagaaatattaacttatagtttttatttctgttgttgaagCATATATGGTCCAGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC