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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCTGAACTTGATGCAAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacctgctccctgttcttatgtcttctgacgttctctgctcctatgtcttatgttttcctacctaaacactttattttctgatgcag

Basic information

species Zea mays
transcript AC235535.1_FGT001
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 14
lower sequence: 13113.m00246 (Oryza sativa), 5'ss of exon 14
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCTGAACTTGATGCAAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacctgctccctgttcttatgtcttctgacgttctctgctcctatgtcttatgttttcctacctaaacactttattttctgatgcag
||||||||||| ||||||||||||||||| ||||||||||| |||||||||||||||||||||||||||||||| || ||||||||||| |||||||| ||||||||||     || |   |    |  | |      ||| | ||  |   |||| || ||  ||   |                      
ATTGACCGTATCATAGCTAAAGGAGAGGAAACAACAGCTGAGCTTGATGCAAAAATGAAAAAGTTCACAGAGGATGCTATTAAATTTAAAATGGATGACAgtatgtacccttctcccgcagtctctttctttctatcactcaggtctaa---ctta-gtctttttatgcag---------------------

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 14
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCTGAACTTGATGCAAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacctgctccctgttcttatgtct-tctgacgttctctgctcctatgtcttatgttttcctacctaaacactttattttctgatgcag--------
|||||||| || || ||||| ||||| ||  |||||||  ||||||||||||||||||| ||||||||||| || || ||||| || || |||||||| |||||| |||  ||| || |   | | ||| ||| |   |||||    |  |  ||| | | |  || | || |  |  ||    || ||  ||        
ATTGACCGCATCATCGCTAAGGGAGAAGAAGCAACAGCACAACTTGATGCAAAAATGAAGAAGTTCACAGAAGATGCTATTAAGTTCAAAATGGATGACAgtatg-accctctctctctctctctctctctctcaatatctctcacacacttccttctctatgtctgcatatattcagtacaaactcataaagtttggtct

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 14
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCTGAACTTGATGCAAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacctg---ctccctgttcttatgtc--------ttctgacgttctctgctcctatgtcttatgttttcctacctaaacactttat--tttctgatgcag----------------
|||||  | ||||| ||||||||||||||| |||| || || |||||||| |||||||| || || || || || ||||| ||||||||||||||||| |||||||||||    || ||||||||    |         |  || | | ||||  |   | || ||||| |||| |   |    | ||||   || || || | |                
ATTGATAGAATTATTGCTAAAGGAGAGGAGGCAACTGCCGAGCTTGATGCCAAAATGAAGAAATTTACTGAAGATGCCATCAAATTTAAGATGGATGACAgtatgtacctatgactacctgttctagctttaaaaacaatattggcatgctct--ttacaagttttatgctttcttctgtttgtagtttagagttactaatactgatactttcttttgtag

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 14
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCTGAACTTGATGCAAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacctgctccctgt---tcttatgtcttctgacgttctctgctcctatg-tctta------tgttttcctacctaaacactt-tattttctgatgcag
|||||| | ||||| ||||||||||||||  |||||||||| |||||||| || |||||||| || || || || || || ||||||||||||||||| |||||||| |   |   | |   |  |   | | || | |||   |      ||| | |||      | ||||  |   ||||    | ||| | |  | |   
ATTGACAGAATTATTGCTAAAGGAGAGGAAGCAACAGCTGAGCTTGATGCTAAGATGAAAAAATTTACTGAAGATGCTATCAAATTTAAGATGGATGACAgtatgtaacctttgaatataatttctggctttgctaaagttggtttgattgatgatgttaaaaatctattttgttgtttaaatttctgtatatccacaag---

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA07G38050.2 (Glycine max), 5'ss of exon 14
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCTGAACTTGATGCAAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacctgctccctgt---tcttatgtcttctgacgttctctgctcctatgtcttatgttttcctacctaaacactttattttctg-atgcag-----
|||||| | ||||| ||||||||||| ||  |||||||||| |||||||| || |||||||| || || || || || || ||||||||||||||||| |||||||| |   |   | |   |  |   | | || |  ||   |      ||||| | |      |||  |      || | || ||| || |       
ATTGACAGAATTATTGCTAAAGGAGAAGAAGCAACAGCTGAGCTTGATGCTAAGATGAAAAAATTTACTGAAGATGCTATCAAATTTAAGATGGATGACAgtatgtaacctttaaatataaattctggctttgctaaatttggtttgattgatgtcgt-tagaaatctattttgttgtttaaattcctgtatacccataag

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA15G10370.1 (Glycine max), 5'ss of exon 14
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCTGAACTTGATGCAAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacctgc--tccctgttcttatgtc--ttctgacgttctctgctcctatgtcttatgttttcctacctaaacactttattttctgatgcag-----------------
|||||  | ||||| ||||||||||||||| |||| ||||| || ||||| || ||||| || || || || || ||||| ||||||||||||||||| ||||||| |||    | |  | | | |   |  |  || | |  |||   |   | |  |   || | ||  ||  |   | || || || || | |                 
ATTGATAGAATTATTGCTAAAGGAGAGGAGGCAACTGCTGAGCTAGATGCCAAGATGAAGAAATTTACTGAAGATGCCATCAAATTTAAGATGGATGACAgtatgtgcctataattctagctttaaaaacaatattggcatgatctttacaagttttatgctttcttctgtctgtagtttatagttactaatactggtgctttctttttgtag

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 14
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 14
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCTGAACTTGATGCAAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacctgctccctgttcttatgtcttctgacgttctctgctcctatgtcttatgttttcctacctaaacactttattttctgatgcag
|||||  | || || || |||||||| ||| ||||||||||||||||||| || ||||| || |||||||| || || ||  | ||||| |||||||| |||| |    | | |     |  ||| ||  ||       | ||    ||| | | |||||||  ||         |||||||  ||  |   
ATTGATAGAATCATTGCCAAAGGAGAAGAGGCAACAGCTGAACTTGATGCTAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAgtaagggtgt-cacttacctactatttcccctattaggttgtgtgaatat-tgtaatgttttgataatctgttgttttatttgttgtag---

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 14
lower sequence: AT3G06400.3 (Arabidopsis thaliana), 5'ss of exon 14
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCTGAACTTGATGCAAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacctgctccctgttcttatgtcttctgacgttctctgctcctatgtcttatgttttcctacctaaacactttattttctgatgcag
       | || || || |||||||| ||| ||||||||||||||||||| || ||||| || |||||||| || || ||  | ||||| |||||||| |||| |    | | |     |  ||| ||  ||       | ||    ||| | | |||||||  ||         |||||||  ||  |   
------AGAATCATTGCCAAAGGAGAAGAGGCAACAGCTGAACTTGATGCTAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAGTAAGGgtgt-cacttacctactatttcccctattaggttgtgtgaatat-tgtaatgttttgataatctgttgttttatttgttgtag---

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 14
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 14
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCTGAACTTGATGCAAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgt--acctgctccct---gttcttatgtcttctgacgttctctgctcctatgtcttatgttttcc-----tacctaaacactt-tattttctgatgcag
|| ||| | || || ||||||||||| ||| |||||||||| |||||||| || ||||| || || ||||| || ||||| |||||||| ||||||||||||||||  | |  ||  |    | ||| |    || |    || ||| ||  |     |||||           ||  | |||| || |  |   |  | |||
ATAGACAGGATCATTGCTAAAGGAGAAGAGGCAACAGCTGAGCTTGATGCTAAGATGAAGAAATTTACAGAAGATGCCATCAAATTTAAAATGGATGATAgtatgtggatccactatccagggctctcactcattatttacttatctacttttgaaagttatggggctaaaatataatttaacatttatcctgctttgttcag

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 14
lower sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 14
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCTGAACTTGATGCAAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacctgctccctgttcttatgtcttctgacgttctctgctcctatgtcttatgttttcctacctaaacactttattttctgatgcag
||||| || || || || |||||||| ||  | || |||||||||||||| || ||||| || || || ||||||||||| |||||||||||||| || |||| || |  |  |   ||| || |||  ||     || |||     |  || | |                                    
ATTGATCGCATCATTGCAAAAGGAGAAGAAGCCACTGCTGAACTTGATGCCAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACAgtaagttctagtgc---gtttttgtgttctcc----ttatctagcgtttcgtttaacag---------------------------------

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 14
lower sequence: EFJ32950 (Selaginella moellendorffii), 5'ss of exon 13
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCTGAACTTGATGCAAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacctgctccctgttcttatgtcttctgacgttctctgctcctatgtcttatgttttcctacctaaacactttattttctgatgcag
|| || ||||| || || || ||||| |   |||| |||||||| |||||||| ||||| |||||||| ||||| || ||| | ||||||||||||||| ||| || |   ||   |  ||             | | |  |    |||||| || | |||| |                            
ATAGATCGTATAATTGCGAAGGGAGAAGCTGCAACTGCTGAACTGGATGCAAAGATGAAGAAGTTCACGGAGGATGCGATTCAGTTTAAGATGGATGATCgtaagtgcactcttattaatc-------------catcccatcacactatgttttgtattttacag--------------------------

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|32929959|gb|CF034771.1|CF034771
EST:     AAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATA                         ATGCCGAACTGTATGATTTTGATGATGAGAAG
genomic: AAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCCGAACTGTATGATTTTGATGATGAGAAG
EST: gi|211502860|gb|FK981747.1|FK981747
EST:     AATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATA                         ATGCCGAACTGTATGATTTTGATGATGAGAAG
genomic: AATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCCGAACTGTATGATTTTGATGATGAGAAG
EST: gi|33094019|gb|CF054013.1|CF054013
EST:     AAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATA                         ATGCCGAACTGTATGATTTTGATGATGAGAAG
genomic: AAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCCGAACTGTATGATTTTGATGATGAGAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 395

ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCTGAACTTGATGCAAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCCGAACTGTATGATTTTGATGATGAGAAG


Block sizes: 49 (upstream exon), 32 (downstream exon)
Score: 213

ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCTGAACTTGATGCAAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCCGAACTGTATGATTTTGATGATGAGAAG


Block sizes: 49 (upstream exon), 32 (downstream exon)
Score: 224

ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCTGAACTTGATGCAAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCCGAACTGTATGATTTTGATGATGAGAAG


Block sizes: 49 (upstream exon), 32 (downstream exon)
Score: 213

ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCTGAACTTGATGCAAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCCGAACTGTATGATTTTGATGATGAGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCTGAACTTGATGCAAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacctgctccctgttcttatgtcttctgacgttctctgctcctatgtcttatgttttcctacctaaacactttattttctgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA