Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATCGTCTTCTTCGATGTCACCATCGGTAACATTCCCGCCGGTCGAATCAAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgtttctactcttaaagcgtgcgttttcttcttttagtgcttagttagactgcaccttgcctttaagcattgctaccaacttgcgcatgaact...

Basic information

species Glycine max
transcript GLYMA09G11960.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G11960.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os03g59700.1 (Oryza sativa), 5'ss of exon 1
CCATCGTCTTCTTCGATGTCACCATCGGTAACATTCCCGCCGGTCGAATCAAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctac-----gtttctactc---ttaaagcgtgcgttttcttcttttagtgcttagttagactgcaccttgcctttaagcattgctaccaacttgcg-catgaact-------------
|  | || |||||||| || ||||||||   ||| |||||||| || ||||||||||| ||||||||||| || | |||||| || || ||||| ||| ||||   ||     |      |||   ||||| | |  |||   |   |||| | ||   |  || ||    |||| ||| |    |   ||  | |||   |||    |             
CGGTGGTGTTCTTCGACGTGACCATCGGGTCCATCCCCGCCGGCCGCATCAAGATGGAGCTCTTCGCCGACATCGTCCCCAAGACGGCGGAGAACTTCCGgtactgacccagagccctcgctcgccttaaaccctaggttccatctgtttaatcctgcttctga-tgtgt-ttgcttttgatggatctcactgatttgtttcatctgtttgtttggtttcag

upper sequence: GLYMA09G11960.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G057329_T01 (Zea mays), 5'ss of exon 1
CCATCGTCTTCTTCGATGTCACCATCGGTAACATTCCCGCCGGTCGAATCAAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgta----tctacgttt----ctactcttaaagcgtgcgttttcttcttttagtgcttagttagactgcaccttgcctttaagcattgctaccaacttgcgcatgaact----------------
|| | || |||||||| || ||||||||   |||  ||||||| || ||||||||||| ||||||||||| || |||||||| || || ||||| ||| |||      |||    |    |||  | |||| | |  ||||  ||  | |  | |||  ||   | ||    ||  ||| | || |   |   |  |      |   |                
CCGTGGTGTTCTTCGACGTGACCATCGGGTCCATCGCCGCCGGCCGCATCAAGATGGAGCTCTTCGCCGACATCGCCCCCAAGACCGCGGAGAACTTCCGgtgatggcctaaaccttcaactaaccataaaccctaggtttcattggtattattctttcttctgccgc-tgatgtatttga-cacttggatagatctctaatcgtgttgctttgtttgtttcag

upper sequence: GLYMA09G11960.1 (Glycine max), 5'ss of exon 1
lower sequence: AT2G38730.1 (Arabidopsis thaliana), 5'ss of exon 1
CCATCGTCTTCTTCGATGTCACCATCGGTAACATTCCCGCCGGTCGAATCAAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgta--tctacgtttctactcttaaagcgtgcgttttcttc--ttttagtgcttagttagactgcaccttgcctttaagcattgc----taccaacttgcgcatgaact----------------
                        | |||   || ||||||||||| ||||||||||| ||||||||||| ||||| |||||||| || || || |||||| |  |||    |  |   || |     |   || | ||   ||||| || ||| |      |   ||     ||      |||    ||     ||| |  |||| |                
------------------------TTGGTGGTATCCCCGCCGGTCGTATCAAGATGGAGCTCTTCGCCGACATTGCTCCCAAAACCGCTGAAAACTTCAGGCAGTTCTGTACTGGTGAACTCAGgtactcgattctgtttctttttaatgtttactccattcgattctctatcttcgttcctgcatcttattcgtttgaggttgaatttacgatttagtatttg

upper sequence: GLYMA09G11960.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv13s0084g00620.t01 (Vitis vinifera), 5'ss of exon 1
CCATCGTCTTCTTCGATGTCACCATCGGTAACATTCCCGCCGGTCGAATCAAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgtttctactctta-aagcgtgcgttttcttct---tttagtg-----cttagtt---agactgcaccttgcctttaagcattgctaccaacttgcgcatgaact------------
                        |||| | ||| ||||||||||| ||||||||||| |||||| |||| || ||||||||||| || || ||||||||| |  |  |      |   || | |  |   || | ||||   || | |      |||| ||    ||      | |    ||   | ||  |   |  |   | ||  | |            
------------------------TCGGCACCATCCCCGCCGGTCGCATCAAGATGGAGCTCTTCTCCGACATCGCCCCCAAAACCGCTGAAAATTTCAGGCAGTTCTGCACTGGCGAGTACAGgtttttattcttttctaacttcactcattttcttattttcaggatgatttccttttctttttctttcttcttatttgatgaatacaataatgatttgcag

upper sequence: GLYMA09G11960.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ31848 (Selaginella moellendorffii), 5'ss of exon 1
CCATCGTCTTCTTCGATGTCACCATCGGTAACATTCCCGCCGGTCGAATCAAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgtttctactcttaaagcgtgcgttttcttcttttagtgcttagttagactgcaccttgcctttaagcattgctaccaacttgcgcatgaact
|| |||||||||||||  |||| ||||| |     || || || || ||||||||||| ||||||||||| ||||  ||||| || |||||||| |||||||||      |||||||       ||||  | || |  ||       ||| ||        | ||| |                                
CCGTCGTCTTCTTCGACATCACAATCGGGACGGCGCCTGCTGGGCGGATCAAGATGGAGCTCTTCGCCGACATTGTTCCCAAGACGGCCGAGAACTTCAGgtattag---ttctactt------cgtgtctgttttgtttcagagatttattt---tctttctttggcag------------------------------

upper sequence: GLYMA09G11960.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ38013 (Selaginella moellendorffii), 5'ss of exon 1
CCATCGTCTTCTTCGATGTCACCATCGGTAACATTCCCGCCGGTCGAATCAAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgtttctactcttaaagcgtgcgttttcttcttttagtgcttagttagactgcaccttgcctttaagcattgctaccaacttgcgcatgaact
|| |||||||||||||  |||| ||||| |     || || || || ||||||||||| ||||||||||| ||||  ||||| || |||||||| |||||||||      |||||||       ||||  | || || ||| || | ||  ||   |    | ||| |                                
CCGTCGTCTTCTTCGACATCACAATCGGGACGGCGCCTGCTGGGCGGATCAAGATGGAGCTCTTCGCCGACATTGTTCCCAAGACGGCCGAGAACTTCAGgtattag---ttctactt------cgtgtctgtttttgtttcagagatttattt--cctttctttggcag------------------------------

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|6719223|gb|AW306870.1|AW306870
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAATACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAGTACAG
EST: gi|151409781|gb|EV279589.1|EV279589
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAGTACAG
EST: gi|192325817|gb|FK018039.1|FK018039
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAATACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAGTACAG
EST: gi|298167097|gb|HO010536.1|HO010536
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAGTACAG
EST: gi|15286510|gb|BI470401.1|BI470401
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAATACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAGTACAG
EST: gi|298172912|gb|HO019896.1|HO019896
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAGTACAG
EST: gi|15814116|gb|BI786391.1|BI786391
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCATTTCTGCACTGGGGAATACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAGTACAG
EST: gi|193315557|gb|FK281777.1|FK281777
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAGTACAG
EST: gi|192320580|gb|FK011990.1|FK011990
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAATACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAGTACAG
EST: gi|298182560|gb|HO031295.1|HO031295
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAGTACAG
EST: gi|208255556|gb|GE052243.1|GE052243
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAGTACAG
EST: gi|298195597|gb|HO043988.1|HO043988
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAGTACAG
EST: gi|17023477|gb|BM094511.1|BM094511
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAATACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAGTACAG
EST: gi|298188736|gb|HO035429.1|HO035429
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAGTACAG
EST: gi|10847406|gb|BF070093.1|BF070093
EST:     AGATGGAACTCTTCGCCGATATTGCCCCCAAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAATACAG
genomic: AGATGGAACTCTTCGCCGATATTGCCCCC-AAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAGTACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATCGTCTTCTTCGATGTCACCATCGGTAACATTCCCGCCGGTCGAATCAAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgtttctactcttaaagcgtgcgttttcttcttttagtgcttagttagactgcaccttgcctttaagcattgctaccaacttgcgcatgaact

- - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA