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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctctcaaaacttctgtttttgtaatcaggaagtgagcaaatataatccatttaggtataaacagacttgctgtgttcccatttttgcagGATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAG

Basic information

species Glycine max
transcript GLYMA20G34940.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os10g17990.1 (Oryza sativa), 3'ss of exon 9
gtatgctctcaaaacttctgtttttgtaatcaggaagtgagcaaatataatccatttaggtataaacagacttgctgtgttcccatttttgcagGATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAG
                |  |  | | | |||     |  |  ||||||       ||   |||  | |  |||  |  ||    | |||| ||||||||||||||||| || || || ||||||||| |||| ||||| |||||||| || 
---------------gtacgcatctattatcttttggaaaaaaaatat-------ttcaatatcga-aatcttattcagtgtatactttt-cagGATTTTGGTGATAGCATACCTGGCCATGGTGGATTTACTGACAGGATGGATTGTCAA

upper sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G452529_T02 (Zea mays), 3'ss of exon 9
gtatgctctcaaaacttctgtttttgtaatcaggaagtgagcaaatataatccatttaggtataaacagacttgctgtgttcccatttttgcagGATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAG
|||| | |     |||||  | |||| |         | |  ||   |  |  | | |  |  | | |   ||  |   || | |    || ||||||||||||| || || || || |||||||||||||| |||||||||||||| || 
gtatacacc----acttcgttgtttgca---------tcaataatattgttttactcaaattgatatatctttttt---ttacaaaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA

upper sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 9
gtatgctctcaaaacttctgtttttgtaatcaggaagtgagcaaatataatccatttaggtataaacagacttgctgtgttcccatttttgcagGATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAG
|||| | |      ||||  | |||| |         | |  ||   |     | | |   ||  | | |  | || | || | |    || ||||||||||||| || || || || |||||||||||||| || |||||||||||||| 
gtatacacc----gcttcattgtttgca---------tcaataatattgtcttactcaa--attgatatatcttcttttttacaaaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA

upper sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G22340.3 (Arabidopsis thaliana), 3'ss of exon 8
gtatgctctcaaaacttctgtttttgtaatcaggaagtgagcaaatataatccatttaggtataaacagacttgctgt-----gttc-ccatttttgcagGATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAG
                |  ||||  |     |   |||    ||  | |||  || || | | | |  || |  ||||     |||| |||   |||||||| ||||||||||||||||| |||||||| |||||||| || ||||||||||| |||
---------------gtgggtttcagatgatattcagtataaaaccacaat--atctatgca-acattgattcactgttaaatgttctccaaccttgcagGACTTTGGTGATAGTATTCCCGGACATGGCGGAATTACAGATAGAATGGATTGTCAG

upper sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G62430.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgctctcaaaacttctgtttttgtaatcaggaagtgagcaaatataatccatttaggtataaacaga--cttgctgtgttc---ccatttttgcagGATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAG
||  |   |||| || ||    | || |  || |   | |      |||   ||| ||      |||| |  ||||||         || |  | |||||| |||||||||||||||||||||||||||||||| || || |||||||| ||||||
gtcagtaatcaatacctccaaatatg-agccaagct-tcactttccata-cgcatctaacctctaacaaaaccttgcttgacaaaaaccgtaatcgcagGACTTTGGTGATAGTATTCCAGGACATGGTGGAATCACAGATAGAATGGACTGCCAG

upper sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 9
gtatgctctcaaaacttctgtttttgtaatcaggaagtga-gcaaatataatccatt-taggtataaaca-----gacttgctgtgt-----tcccattt-ttgcagGATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAG
||   ||||    | |  ||  || || |   |    |||     ||  ||  | |    | | |  |||     |  ||  | | |     ||| |||| || ||||| ||||| ||||||||||| ||||| ||||||||||| || ||||||||||| |||
gttcactctggttattgttgacttagttaagtgatgctgatatgcatggaaagcttcactgttgttgacactgttggttttttatttctttttccgatttgttacagGACTTTGGCGATAGTATTCCTGGACACGGTGGAATTACTGATAGAATGGATTGTCAG

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|6483173|gb|AW202361.1|AW202361
EST:     CTTTTGGAGGCTTCTTTGCAAGTGGTTTTAAAAGGGCTTTTAAAATAAAG                         GATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGAT
genomic: CTTTTGGAGGCTTCTTTGCAAGTGGTTTTAAAAGGGCTTTTAAAATAAAGgtatgctctc ... atttttgcagGATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGAT
EST: gi|151412323|gb|EV282135.1|EV282135
EST:     CTTTTGGAGGCTTCTTTGCAAGTGGTTTTAAAAGGGCTTTTAAAATAAAG                         GATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGAT
genomic: CTTTTGGAGGCTTCTTTGCAAGTGGTTTTAAAAGGGCTTTTAAAATAAAGgtatgctctc ... atttttgcagGATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGAT
EST: gi|10252704|gb|BE820470.1|BE820470
EST:     TGCAAGTGGTTTTAAAAGGGCTTTTAAAATAAAG                         NANNNTNGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGAT
genomic: TGCAAGTGGTTTTAAAAGGGCTTTTAAAATAAAGgtatgctctc ... atttttgcagGATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcaaatataatccatttaggtataaacagacttgctgtgttcccatttttgcagGATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAG
                                        ttcccattttt  CT-rich tract
     atataatccattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctctcaaaacttctgtttttgtaatcaggaagtgagcaaatataatccatttaggtataaacagacttgctgtgttcccatttttgcagGATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA