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

TTATTCTCTTCCTTATTGTCCACCAAATAAAATAGTGGATAGTGCTGAAAATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgttttatatgaaattttaattcttgtgttgttaattatgttatgctaatcaacttatttgctctgacatatatgcag

Basic information

species Glycine max
transcript GLYMA17G34020.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G34020.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os09g38530.1 (Oryza sativa), 5'ss of exon 2
TTATTCTCTTCCTTATTGTCCACCAAATAAAATAGTGGATAGTGCTGAAAATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgttttatatgaa----attttaattcttgtgttgttaattatgttatgctaatcaacttatttgctctgacatatatgcag------------
||| || |||||||  ||    ||| | |  || || || |||||||||||||| || || || |||||||||||||||||||| || ||||  ||||||||  ||      | |     ||||| |   || |||  || |   |  |||||   | ||  | | |   |   |||   |   |            
TTACTCCCTTCCTTTCTGCAAGCCAGAAACTATCGTTGACAGTGCTGAAAATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTGgttagtaccgggtaactcatattttgaagtttatgtccttgaa-gtaatatgcc--ttaatctctgtttgccatcattctttttgtttgagctacag

upper sequence: GLYMA17G34020.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G458845_T01 (Zea mays), 5'ss of exon 2
TTATTCTCTTCCTTATTGTCCACCAAATAAAATAGTGGATAGTGCTGAAAATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgttttatatgaa----------attttaattcttgtgttgttaattatgttatgctaatcaact--tatttgctctgacatatatgcag----------
||| |||||||||| |||    ||||| |  ||||| || ||||| || |||||||||||||| || ||||||||||||||||| || |||| |||||||||  ||  || || |           || || |   ||||  | |  | | | |||    | | | ||  ||| | || ||   | | |              
TTACTCTCTTCCTTTTTGCAAGCCAAACATGATAGTTGACAGTGCAGAGAATCTTGGAGAAGTTCTGCGTGGTGATCGCATTGAGAACTCTCCTTATGTGgtcagtactagattactgctagtcacatattcacctttgtaatttgtaatgtattaaatcactgagctgttatctactttgttgtttctcgtttgtgctatag

upper sequence: GLYMA17G34020.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G180575_T01 (Zea mays), 5'ss of exon 2
TTATTCTCTTCCTTATTGTCCACCAAATAAAATAGTGGATAGTGCTGAAAATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgttttatatgaaatttt-----aattcttgtgttgttaattatgttatgctaatcaacttatttgctctgacatatatgcag-----------------
||| ||||||||||  |||  |||||| |  ||||| || ||||| || |||||||||||||| || ||||||||||||||||| || |||| |||||||||  ||  || || |    ||     |  |   |  |||| | || |  | | | ||   ||||| | |   ||   | | |                     
TTACTCTCTTCCTTTCTGTAAACCAAACACGATAGTTGACAGTGCAGAGAATCTTGGAGAAGTTCTGCGTGGTGATCGCATTGAGAACTCTCCTTATGTGgtcagtactagattactgcttgtcacatattcagcattgtaatttgtaatgtaccaaatcacttagtcgtcatgcactttgtcgttttacgtttgtgttgtag

upper sequence: GLYMA17G34020.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G046005_T02 (Zea mays), 5'ss of exon 2
TTATTCTCTTCCTTATTGTCCACCAAATAAAATAGTGGATAGTGCTGAAAATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgttttatatgaaatttt-----aattcttgtgttgttaattatgttatgctaatcaacttatttgctctgacatatatgcag-------------------
||| ||||||||||  |||  |||||| |  ||||| || ||||| || |||||||||||||| || ||||||||||||||||| || |||| |||||||||  ||  || || |    ||     |  |   |  |||| | || |  | | | ||   ||| | | |   || ||  | ||| |                   
TTACTCTCTTCCTTTCTGTAAACCAAACACGATAGTTGACAGTGCAGAGAATCTTGGAGAAGTTCTGCGTGGTGATCGCATTGAGAACTCTCCTTATGTGgtcagtactagattactgcttgtcacatattcagcattgtaatttgtaatgtaccaaatcactgagtcgtcatg-cactt-tgccgttttacgtttgtgttgtag

upper sequence: GLYMA17G34020.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G006117_T02 (Zea mays), 5'ss of exon 2
TTATTCTCTTCCTTATTGTCCACCAAATAAAATAGTGGATAGTGCTGAAAATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgttttatatgaaattt-------taatt---cttgtgttgttaattatgttatgctaatcaacttatttgctctgacatatatgcag-------
|||||| ||||| |  ||    ||| |||  ||||| || ||||| ||||||||||| || || |||||||| ||||||||||| || |||| |||||||||  |||   |||  ||  |       |||||    || |||  |    |||||  ||  |   |  || |    ||||     |||   |       
TTATTCCCTTCCGTTCTGCAAGCCAGATACCATAGTCGACAGTGCCGAAAATCTTGGGGAGGTACTTCGTGGCGATCGCATTGAGAACTCTCCTTATGTGgttagttccgtatataacataacagattaattgagattttgtcctcgggtatgt-gtgtgacatattttttccattctgcttgttatttggagtatag

upper sequence: GLYMA17G34020.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G146951_T01 (Zea mays), 5'ss of exon 2
TTATTCTCTTCCTTATTGTCCACCAAATAAAATAGTGGATAGTGCTGAAAATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgtt-ttatatgaaattttaattcttgtgtt--gttaattatgttatgctaatcaacttatttgctctg-acatatatgcag-----
 |||||||| || |  ||    ||  |||  ||||| || ||||| |||||||| || ||||| |||||||| |||||||||||||| ||||  |||  ||| |||| ||  |       ||  ||  | || |  ||   | |     ||   |  |  ||   || |  | | ||||||         
CTATTCTCTCCCATTCTGCAAGCCGGATACCATAGTTGACAGTGCAGAAAATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctttcactgtgcattggtttatctgatcagtgtttgacaccttgggcactagtttgactgttgagcatatatatttttttcag

upper sequence: GLYMA17G34020.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G039811_T01 (Zea mays), 5'ss of exon 2
TTATTCTCTTCCTTATTGTCCACCAAATAAAATAGTGGATAGTGCTGAAAATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgt-------atgttttatatgaaattttaatt---cttgtgttgttaattatgttatgctaatcaacttatttgct-ctgacatatatgcag-------
||| || ||||| |  ||    ||| ||   ||||| || ||||| |||||||| || || || |||||||| ||||||||||| || |||| |||||||||       || | | | || | |  ||||||    ||  ||  |    || ||  ||      || || |||  | ||||    |||   |       
TTACTCCCTTCCATTCTGCAAGCCAGATGCCATAGTTGACAGTGCCGAAAATCTCGGGGAGGTTCTTCGTGGCGATCGCATTGAGAACTCTCCTTATGTGgttagtaccatatataacataacagattaattgaggtttcgtcctcgggtaagt-gtgtggcgtaatttttttctttctgattgttatttggggtatag

upper sequence: GLYMA17G34020.1 (Glycine max), 5'ss of exon 2
lower sequence: AT5G10840.1 (Arabidopsis thaliana), 5'ss of exon 2
TTATTCTCTTCCTTATTGTCCACCAAATAAAATAGTGGATAGTGCTGAAAATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgttttatatgaaattttaattcttgt----------gttgttaattatgttatgctaatcaacttattt--gctctgacatatatgcag---------
||| || ||||||| |||||  || |  || || ||||| ||| |||| |||||||||||||||||||| ||||| || ||||| ||| | |  ||   |||  || |  |||  |||||| | | ||||          | ||| ||  || |||||    | |  | | |    | ||  |     || |          
TTACTCCCTTCCTTTTTGTCGCCCTAGCAAGATTGTGGACAGTACTGAGAATCTTGGAGAAGTGCTTCGGGGTGACCGGATTGAGAATGCCCCATACTCGgttagtctcgtattcaatttttaattttgtaattcatcaggctgtcaaaaatattatgtctgtgatttaactctaacccttgcggggctgaaacaattgcag

upper sequence: GLYMA17G34020.1 (Glycine max), 5'ss of exon 2
lower sequence: AT5G25100.2 (Arabidopsis thaliana), 5'ss of exon 3
TTATTCTCTTCCTTATTGTCCACCAAATAAAATAGTGGATAGTGCTGAAAATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgttttatatgaaattttaattcttgtgttgttaattatgttatgctaatcaacttatttgctctgacatatatgcag
||| |||||||||| |||||  || || || || ||||| ||| |||| |||||||| ||||| ||||||||||| || || |||||| ||| ||||  ||| ||| |    |   ||    |||  ||| ||  |  |||  | |        ||||| |    | ||  ||| ||| ||
TTACTCTCTTCCTTTTTGTCGTCCTAAGAAGATTGTGGACAGTACTGAGAATCTTGGTGAAGTTCTTCGTGGTGACCGAATCGAAAATGCTCCTTATTCGgtttgtctctgttttgatac--atttatgtatttctctttacttga---ctgctaacttgtggagtttggaata-atgtag

upper sequence: GLYMA17G34020.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv04s0008g06640.t01 (Vitis vinifera), 5'ss of exon 2
TTATTCTCTTCCTTATTGTCCACCAAATAAAATAGTGGATAGTGCTGAAAATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgtttta-tatgaaatttt------aattcttgtgttg-ttaattatgttatgctaatcaacttatttgctctgacatatatgcag---
 |||||||| |||||||| |  |||   ||||| ||||| | ||| || ||||| || |||||||||||||||||||| |||||||| || | |||||||||  ||||||  ||     |||      || |   | | || ||  ||||||||   ||||  |||  |||          || ||  |   
CTATTCTCTGCCTTATTGCCGCCCAGGAAAAATTGTGGACAATGCAGAGAATCTCGGGGAAGTGCTTCGTGGTGATCGTATTGAAAACTCCCCTTATGTGgtcagttttaacatcttgcttttttgacaagttgagggctgcttgtttatgttaa--taattgactcttttagctgagtggatttgttgcag

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|213620512|gb|DB959212.1|DB959212
EST:     ATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTG                         TTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTT
genomic: ATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgtttta ... atatatgcagTTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTT
EST: gi|213598705|gb|DB964271.1|DB964271
EST:     ATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTG                         TTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTT
genomic: ATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgtttta ... atatatgcagTTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTT
EST: gi|12773257|gb|BG238184.1|BG238184
EST:     ATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTG                         TTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTT
genomic: ATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgtttta ... atatatgcagTTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTT
EST: gi|213599111|gb|DB962218.1|DB962218
EST:     ATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTG                         TTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTT
genomic: ATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgtttta ... atatatgcagTTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTT
EST: gi|209718610|gb|BW674736.1|BW674736
EST:     ATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTG                         TTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTT
genomic: ATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgtttta ... atatatgcagTTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATTCTCTTCCTTATTGTCCACCAAATAAAATAGTGGATAGTGCTGAAAATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgttttatatgaaattttaattcttgtgttgttaattatgttatgctaatcaacttatttgctctgacatatatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT