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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTGAGTATGTGCCTGAAACTGTTCATCGTGTTGTGAAGCATTACAACAAGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattctgttatgtacctttttggatactttgttcttttgacttatgttgtgtagcaggctatattcagacaaactagccagtagcataccgagatgactttgaatttagtttgaaatttgttgacag

Basic information

species Oryza sativa
transcript LOC_Os01g14860.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14860.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G835235_T04 (Zea mays), 5'ss of exon 5
TCTTGAGTATGTGCCTGAAACTGTTCATCGTGTTGTGAAGCATTACAACAAGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattctgttatgtacctttttggatactttgttcttttgacttatgttgtgtagcaggctatattcagacaaactagccagtagcataccgagatgactttgaatttagt-ttgaaatttgttgacag-----------------------------------------------
 ||||||||||| || || || |||||||| |||||||| ||| ||||||||||| |||| || ||||||||||| ||||||||||| |||||||||||||||||||| |||    |  | | |||| || |   ||  ||  |||||  || | |    |  |          |     ||   ||  | | | |      |||||  | | | |||        |||  |                                               
CCTTGAGTATGTTCCGGAGACAGTTCATCGAGTTGTGAAACATCACAACAAGATGCACCAACGCATGCCACTTATTTATGTGAAGCTTTATATGTACCAGgtaatattttgtccctt--cctcttggttattgcattagttgtacttaacttattttttggattcagaatgtttattgctgcagctaaaaaagctattgtcttttgacctaaatattggctgcctctgatggatgcgctagttcttttttcgtattgattttgtattggtttttggcag

upper sequence: LOC_Os01g14860.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G129482_T01 (Zea mays), 5'ss of exon 1
TCTTGAGTATGTGCCTGAAACTGTTCATCGTGTTGTGAAGCATTACAACAAGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattctgttatgtacctttttggat-actttgttctt--ttgacttatgttgtgtagcaggctatatt--------cagacaaactagccagtagcataccgagatgactttgaatttagtttgaaatttgttgacag--------------------------------------
                                                    ||| |||| |  ||||||||||| ||||||||||| |||||||||||||||||||| |||    | |  ||    ||  ||||  |  |  || |||||| || |    |     || ||        |||  |||  ||| | | |  |   ||  | | | |    |   | |||    ||  | |||                                      
----------------------------------------------------ATGCACCAACACATGCCACTTATTTATGTGAAGCTTTATATGTACCAGgtaatattttgtcccttcctcttggctattgctttagttgtacttaacttatttttttggactcagaatgtttattgctgcagctaaaaaagcta-ttgtcttttgacctaaatattggctgcctctgatggatgc-gccagttcttttttcgtattgattttgtattggtttttggcag

upper sequence: LOC_Os01g14860.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G024151_T01 (Zea mays), 5'ss of exon 5
TCTTGAGTATGTGCCTGAAACTGTTCATCGTGTTGTGAAGCATTACAACAAGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattctgttatgtacctttttg--gatactttgtt-----cttttgacttatgttgtgtagcaggct--atattcagacaaactagccagtagcataccgagatgactttgaatttagtttgaaatttgttgacag------------------------------------
 |||||||||||||| || || |||||||| |||||||||||| |||||||||||||||| || ||||||||||| |||||||||||||||||||||||||||||  | |||  ||| ||||||||  | |  |||  |     |||    |||||||| ||   |  | |  || || | || ||| | |   |  |||  ||     |  |||  |         ||| || |                                         
CCTTGAGTATGTGCCGGAGACAGTTCATCGAGTTGTGAAGCATCACAACAAGATGAACCAACGCATGCCACTTATTTATGTGAAGCTGTATATGTACCAGgtaatggtttgtcctgttcctttttgctgttgttttaattataccttaaagcttatgttttgggccctgtttgatgttgaaactaacaaacatatttcatttcgcctaaatattgtctgctccaatgaatgtgctagttctttttcaatatttgatattatattggattttggcag

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|58602640|gb|CK013168.1|CK013168
EST:     GATGAACCAGCGTAGTGGCACTTATCTATGTGAAGCTGTATATGTACCAG                         ATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
genomic: GATGAACCAGCGTA-TGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattct ... ttgttgacagATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
EST: gi|58686155|gb|CK074842.1|CK074842
EST:     AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAG                         ATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
genomic: AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattct ... ttgttgacagATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
EST: gi|2317492|gb|C22546.1|C22546
EST:     AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAG                         ATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
genomic: AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattct ... ttgttgacagATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
EST: gi|58664832|gb|CK053518.1|CK053518
EST:     AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAG                         ATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
genomic: AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattct ... ttgttgacagATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
EST: gi|58665294|gb|CK053980.1|CK053980
EST:     AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAG                         ATTTGTAGGGCATTAGCTTACATCC
genomic: AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattct ... ttgttgacagATTTGTAGGGCATTAGCTTACATCC
EST: gi|58673993|gb|CK062679.1|CK062679
EST:     AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAG                         ATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
genomic: AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattct ... ttgttgacagATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
EST: gi|58676495|gb|CK065182.1|CK065182
EST:     AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAG                         ATTTGTAGGGCATTAGCTTACATCCATAAT
genomic: AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattct ... ttgttgacagATTTGTAGGGCATTAGCTTACATCCATAAT
EST: gi|58665103|gb|CK053789.1|CK053789
EST:     AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAG                         ATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTT
genomic: AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattct ... ttgttgacagATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTT
EST: gi|29687086|gb|CB683361.1|CB683361
EST:     AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAG                         ATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
genomic: AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattct ... ttgttgacagATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
EST: gi|218486932|gb|FG950343.1|FG950343
EST:     AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAG                         ATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCNCAGA
genomic: AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattct ... ttgttgacagATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
EST: gi|38469291|gb|CF953422.1|CF953422
EST:     AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAG                         ATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
genomic: AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattct ... ttgttgacagATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
EST: gi|29677190|gb|CB673465.1|CB673465
EST:     AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAG                         ATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
genomic: AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattct ... ttgttgacagATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
EST: gi|58652484|gb|CK041164.1|CK041164
EST:     AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAG                         ATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
genomic: AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattct ... ttgttgacagATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
EST: gi|58679239|gb|CK067926.1|CK067926
EST:     AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAG                         ATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
genomic: AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattct ... ttgttgacagATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
EST: gi|58671331|gb|CK060017.1|CK060017
EST:     AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAG                         ATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
genomic: AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattct ... ttgttgacagATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
EST: gi|218496430|gb|FG946684.1|FG946684
EST:     AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGT-CCAG                         ATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
genomic: AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattct ... ttgttgacagATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
EST: gi|58675968|gb|CK064655.1|CK064655
EST:     AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAG                         ATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
genomic: AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattct ... ttgttgacagATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
EST: gi|58590979|gb|CF989287.1|CF989287
EST:     AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAG                         ATATGTAGGGCATTAGCTTACATCCATAATAGCATCGGA
genomic: AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattct ... ttgttgacagATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGA
EST: gi|58679895|gb|CK068582.1|CK068582
EST:     AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAG                         ATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA
genomic: AGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattct ... ttgttgacagATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTGAGTATGTGCCTGAAACTGTTCATCGTGTTGTGAAGCATTACAACAAGATGAACCAGCGTATGCCACTTATCTATGTGAAGCTGTATATGTACCAGgtaatattctgttatgtacctttttggatactttgttcttttgacttatgttgtgtagcaggctatattcagacaaactagccagtagcataccgagatgactttgaatttagtttgaaatttgttgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG