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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAAGCTTTCCTGCATCACTCTTGGATCTCCCAACTGTTGTGGAGTCATACAAGACATATGATGATTCAGTGCTAATTAAAACAGCTGATATTGGTCAGgtaaagcataggttttgtgtataagatctgttttattaactgtaggcttttaagactctcctgttgagattataacag

Basic information

species Oryza sativa
transcript LOC_Os05g28010.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g28010.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G147614_T02 (Zea mays), 5'ss of exon 3
TGAAAGCTTTCCTGCATCACTCTTGGATCTCCCAACTGTTGTGGAGTCATACAAGACATATGATGATTCAGTGCTAATTAAAACAGCTGATATTGGTCAGgtaaa-gcataggttttgtgtataagatctgttt---tattaactgtaggcttttaagactctcctgttgagat----tataacag--------------
||| |||||||||||||| ||||||||||| ||  |||| |||||||||||||| |||||||||||||| || ||||||||||| |||||| ||||||||||||| |   | ||||  |||||   | ||||||   ||||||   | |  | || | |   |||  |  | |     |  |||||              
TGAGAGCTTTCCTGCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGATTCTGTACTAATTAAAACTGCTGATGTTGGTCAGgtaaaagtgcatgtttaatgtatgtcacctgtttatttattaaacttcgtatcttcaaatcgtccactgaaaacaaactgaaacagatgattatggtaag

upper sequence: LOC_Os05g28010.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G029038_T01 (Zea mays), 5'ss of exon 2
TGAAAGCTTTCCTGCATCACTCTTGGATCTCCCAACTGTTGTGGAGTCATACAAGACATATGATGATTCAGTGCTAATTAAAACAGCTGATATTGGTCAGgtaaa-gcataggttttgtgtataagatctgttt---tattaactgtaggcttttaagactctcctgttgagattataacag-----
||| |||||||||||||| ||||||||||| ||  |||| |||||||||||||| |||||||||||||| || ||||||||||| |||||| ||||||||||||| |   | ||||  |||||   | ||||||   |||||| | | |  | || | |   |||  | || |  | |  |      
TGAGAGCTTTCCTGCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGATTCTGTACTAATTAAAACTGCTGATGTTGGTCAGgtaaaagtgcatgtttaatgtatgtcacctgtttatttattaaatttcgtatcttcaaatcgtccactggaaaacaaactaaaacag

upper sequence: LOC_Os05g28010.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G147614_T01 (Zea mays), 5'ss of exon 3
TGAAAGCTTTCCTGCATCACTCTTGGATCTCCCAACTGTTGTGGAGTCATACAAGACATATGATGATTCAGTGCTAATTAAAACAGCTGATATTGGTCAGgtaaa-gcataggttttgtgtataagatctgttt---tattaactgtaggcttttaagactctcctgttgagat----tataacag
||| |||||||||||||| ||||||||||| ||  |||| |||||||||||||| |||||||||||||| || ||||||||||| |||||| ||||||||||||| |   | ||||  |||||   | ||||||   ||||||   | |  | || | |   |||  |  | |     |  |||||
TGAGAGCTTTCCTGCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGATTCTGTACTAATTAAAACTGCTGATGTTGGTCAGgtaaaagtgcatgtttaatgtatgtcacctgtttatttattaaacttcgtatcttcaaatcgtccactgaaaacaaactgaaacag

upper sequence: LOC_Os05g28010.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G454830_T01 (Zea mays), 5'ss of exon 3
TGAAAGCTTTCCTGCATCACTCTTGGATCTCCCAACTGTTGTGGAGTCATACAAGACATATGATGATTCAGTGCTAATTAAAACAGCTGATATTGGTCAGgtaaa-gcataggttttgtgtataagatctgttt---tattaactgtaggcttttaagactctcctgttgagattataacag-----
||| ||||||||| |||| ||||||||||| ||  |||| |||||||||||||| |||||||||||||  || ||||||||||| |||||| ||||||||||||| |   | ||||  |||||   | || |||   |||||| | | |  | || | |   |||  |  | |  | |  |      
TGAGAGCTTTCCTTCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGATTATGTACTAATTAAAACTGCTGATGTTGGTCAGgtaaaagtgcatgtttaatgtatgtcacctatttatttattaaatttcgtatcttcaaatcgtccactgaaaaacaaactaaaacag

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|58612587|gb|CK040299.1|CK040299
EST:     ACAAGACATATGATGATTCAGTGCTACTTAAAACAGCTGATATTGGTCAG                         ATGATTATGGTACGAGAAGCAGAAGATCCTGCTCCAGACGGAGTTGAATAC
genomic: ACAAGACATATGATGATTCAGTGCTAATTAAAACAGCTGATATTGGTCAGgtaaagcata ... attataacagATGATTATGGTAAGAGAAGAAGAAGATCCTGCTCCAGAAGGAGTTGAATAC
EST: gi|88732456|gb|CI755633.1|CI755633
EST:     ACAAGACATATGATGATTCAGTGCTAATTAAAACAGCTGATATTGGTCAG                         ATGATCATGGTAAGAGAAGA
genomic: ACAAGACATATGATGATTCAGTGCTAATTAAAACAGCTGATATTGGTCAGgtaaagcata ... attataacagATGATTATGGTAAGAGAAGA
EST: gi|88223765|gb|CI223614.1|CI223614
EST:     GCTGATATTGGTCAG                         ATGATTATGGTAAGAGAAGAAGAAGATCCTGCTCCAGAAGGAGTTGAATAC
genomic: GCTGATATTGGTCAGgtaaagcata ... attataacagATGATTATGGTAAGAGAAGAAGAAGATCCTGCTCCAGAAGGAGTTGAATAC
EST: gi|88977292|gb|CI025029.1|CI025029
EST:     ACAAGACATATGATGATTCAGTGCTAATTAAAACAGCTGATATTGGTCAG                         ATGATTATGGTAAGAGAAGAAGAAGATCCTGCTCCAGAAGGAGTTGAATAC
genomic: ACAAGACATATGATGATTCAGTGCTAATTAAAACAGCTGATATTGGTCAGgtaaagcata ... attataacagATGATTATGGTAAGAGAAGAAGAAGATCCTGCTCCAGAAGGAGTTGAATAC

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 1 RNA-Seqlibrary.


Block sizes: 42 (upstream exon), 70 (downstream exon)
Score: 18

TGAAAGCTTTCCTGCATCACTCTTGGATCTCCCAACTGTTGTGGAGTCATACAAGACATATGATGATTCAGTGCTAATTAAAACAGCTGATATTGGTCAGgtaaagcata ... attataacagATGATTATGGTAAGAGAAGAAGAAGATCCTGCTCCAGAAGGAGTTGAATACAAGCATGGTCTTACTCCTCCAATGAGGGACGCACGCAGGCGGCGTTTCC




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAAGCTTTCCTGCATCACTCTTGGATCTCCCAACTGTTGTGGAGTCATACAAGACATATGATGATTCAGTGCTAATTAAAACAGCTGATATTGGTCAGgtaaagcataggttttgtgtataagatctgttttattaactgtaggcttttaagactctcctgttgagattataacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT