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

GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagttattttttgggaaaataattcatagggttggattggttactggtgatttttacattaaatttttttttgctttcacaatcaatgtttggc...

Basic information

species Glycine max
transcript GLYMA03G04500.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G04500.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 5'ss of exon 7
GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagttattttttgggaaaataattcatagggttggattggttactggtgatttttacattaaatttttttttgctttcacaatcaatgtttggc
|||||||| |||||||||||||| |||||||||||||| || || || ||  |||||||||| ||||||||||| |||||||||||||||||||||||||   |  ||         ||   |  |  ||  |  ||    | | || || ||    |||  |  | |     ||     | ||         
GATTTCAAGATTCAGAACATTGTTGGCTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGTgtaagttgagtccttgc-------atgcctttttaggacgcctttcacatttgttatgttgttcttatgtcctgtgccttttgtgttaacag--------

upper sequence: GLYMA03G04500.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 5'ss of exon 6
GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagtt------attttttgggaaaataattcatagggttggattggttactggtgatttttacattaaatttttttttgctttcacaatcaatgtttggc
|| ||||| |||||||||||||| || ||||||||||| || || || ||  |||||||||| ||||||||||| |||||||||||||||||||||||||   |      || ||||   |  ||| ||| |    |   ||  ||||   |  ||| | |  |    |   ||||  ||| ||               
GACTTCAAGATTCAGAACATTGTTGGTTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGTgtaagttgaatccttgcatgtttttttaggatatttctt----tcacatatgttat--gctattctcatgtcttgtgccttttgtcttccag--------------

upper sequence: GLYMA03G04500.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os10g29660.2 (Oryza sativa), 5'ss of exon 4
GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagttattt--tttgggaaaataattcataggg------ttggattg-----gttactggtgatttttacattaaatttttttttgctttcacaatcaatgtttggc-------------------------------------------
|||||||| || ||||||||||| || || ||||||||||| || || || || |||||||| ||||| ||||| ||||| || ||||| ||||||||||  ||| ||  |||   | | |   ||| |  |      ||| |||      |  |||| ||    ||   | | |  | |   ||  |     | | || |||                                              
GATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGTgtaagttgattacttacttttttacattgtctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcag

upper sequence: GLYMA03G04500.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G161418_T05 (Zea mays), 5'ss of exon 7
GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttag--------ttatttt-ttgggaaaataattcatagggttggattggttactggtgatttttacattaaatttttttttgctttcacaatcaatgtttggc
||||| || |||||||| ||||| |||||||||||||||||||| || ||  |||| ||||| ||||||||||| |||||||| |||||||||||| ||           ||||||| |    | | |||||| |         |||  | |   |  ||     || | ||||||  ||  ||| | |             
GATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGTgtatgtccaaggatggtttattttatcaccacagtaattcttttaccctttttgtctgc--attcttggataatgacatttttcatttgttttatag------------

upper sequence: GLYMA03G04500.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G149238_T04 (Zea mays), 5'ss of exon 6
GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagt----tagttattt--tttgggaaaataattcatagggttggattggttactggtgatttttacatt--aaatttttttttgctttcacaatcaatgtttggc
|| || || |||||||| ||||| |||||||||||||| ||||| || ||  |||| ||||| ||||| ||||| |||||||| |||||||||||| ||    |  ||  ||  ||||| |  | ||||  |         ||  ||        | ||   |||  | ||||||  ||  ||| |||             
GACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGTgtatgtccaatgattgcttattttggcatcacaattttttttacctttttttttgtctcccttcttggaatttgacatttttcatttgttttacag------------

upper sequence: GLYMA03G04500.1 (Glycine max), 5'ss of exon 7
lower sequence: AT3G13445.1 (Arabidopsis thaliana), 5'ss of exon 7
GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagttattttttgggaaaataattcatagggttggattggttactggtgatttttacattaaatt------tttttttgctttcaca-atcaatgtttggc---
|||||||| |||||||| ||||| || |||||||||||||| ||||| ||| | || || |||||||| || || || | ||||||||||||||| ||| |     | ||     | | | ||  |||    |||  |  |  | | |||    || ||    |        ||    || || || ||    || |||    
GATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGTgtgagtga-----tcttaacttatacatttagtagtcaaggaccgacttttagagataaaaacgttgtgctgatggccattacctctctctcatattggcgtgtggttag

upper sequence: GLYMA03G04500.1 (Glycine max), 5'ss of exon 7
lower sequence: AT1G55520.1 (Arabidopsis thaliana), 5'ss of exon 7
GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagtt-attttttgggaaaataattcatagggttggattggttactggtgatttttacattaaatttttttttgctttcacaatcaatgtttggc
||||| || || ||||||||||| ||||| ||||||||||| ||||||||  |||| || ||||||||||| || ||| |||||||||||||||||||| |  | |    ||| ||  |||    |||    |    ||| |  |  |   | | |   |  ||   |     || |||  ||  |||   |  
GATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGTgtaagtgatctcaagcattgtgatcata---tatacttgtaacatgggtgttaatcggtctgatgattcatacct-----ctctcatcattgatgccag--

upper sequence: GLYMA03G04500.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 5'ss of exon 7
GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagtta-gttattttttgggaaaataattcatagggttggattggttactggtgatttttacattaaatttttttttgctttcacaatcaatgtttggc--
||||| || ||||||||||| || ||||| |||||||| || ||||||||| |||| || || ||||||||||| |||||||| || || || |||||| | |  ||| |||  | |  | | | ||    ||  |||  |   |    || |  ||  ||  |      |    || | ||  || ||| |    
GATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGCgtaagtgatgacattgttttcggagttcaattatttattt--atttttctgtaaaaatgtgaaccatacttgggaagtcatgttta-aactaaggttggaaca

upper sequence: GLYMA03G04500.1 (Glycine max), 5'ss of exon 7
lower sequence: PP1S246_34V6.1 (Physcomitrella patens), 5'ss of exon 6
GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagttattttttgggaaaataattcatagggttggattggttactggtgatttttacattaaatttttttttgctttcac--aatcaatgtttggc
|| |||||||||||||| ||||| || || ||||| || |||||||| || ||||| |||||| | |||||| ||||||||  ||| |||||||| ||  | |      |||   | |  |   | |    |   ||  |   |     |||    | | |   ||| |||||    ||   || | ||| ||  
GACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGTgtgagc-actccggacttgcttacacgaagtagaaaaatatcttattgtgttaaattttcagaaatgatggtttctttgcccaaacttgatgattgtgtga-

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|31461676|gb|CD403704.1|CD403704
EST:     TCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT                         TATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCNAAA
genomic: TCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagt ... ggtggtatagTATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCAAAA
EST: gi|27445915|gb|CA953038.1|CA953038
EST:     TCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT                         TATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCTAAA
genomic: TCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagt ... ggtggtatagTATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCAAAA
EST: gi|254322493|gb|GR837907.1|GR837907
EST:     TCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT                         TATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCAAAA
genomic: TCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagt ... ggtggtatagTATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCAAAA
EST: gi|193372010|gb|FK334625.1|FK334625
EST:     TGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT                         TATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCAAAA
genomic: TGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagt ... ggtggtatagTATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCAAAA
EST: gi|193447546|gb|FK415071.1|FK415071
EST:     GGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT                         TATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCAAAA
genomic: GGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagt ... ggtggtatagTATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCAAAA
EST: gi|208110383|gb|GD911811.1|GD911811
EST:     GGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT                         TATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCAAAA
genomic: GGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagt ... ggtggtatagTATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCAAAA
EST: gi|193395393|gb|FK357886.1|FK357886
EST:     CGGCTGGGGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT                         TATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCAAAA
genomic: CGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagt ... ggtggtatagTATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCAAAA
EST: gi|208049718|gb|GD847081.1|GD847081
EST:     GGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT                         TATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCAAAA
genomic: GGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagt ... ggtggtatagTATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCAAAA
EST: gi|31455890|gb|CD397918.1|CD397918
EST:     TCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT                         TATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCAAAA
genomic: TCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagt ... ggtggtatagTATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCAAAA
EST: gi|208233100|gb|GE032853.1|GE032853
EST:     ACGGCTGGGGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT                         TATGAACCAGAGCTGTTTCCAGG
genomic: ACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagt ... ggtggtatagTATGAACCAGAGCTGTTTCCAGG
EST: gi|208120323|gb|GD915568.1|GD915568
EST:     GGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT                         TATGAACCAGAGCTGTTTCCAGGGCTAATCTACCGTATGAAGCAACCTAAA
genomic: GGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagt ... ggtggtatagTATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCAAAA
EST: gi|208025200|gb|GD823864.1|GD823864
EST:     GGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT                         TATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCAAAA
genomic: GGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagt ... ggtggtatagTATGAACCAGAGCTGTTTCCAGGACTAATCTACCGTATGAAGCAACCAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagttattttttgggaaaataattcatagggttggattggttactggtgatttttacattaaatttttttttgctttcacaatcaatgtttggc

- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggttgg