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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGCAAAACCTTCCGCGCCGCCGCCATCTCGGACCACCGTAGCACGCCGCCTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcaccatctctcccgcttcctcccctccacttcgagggctggtttgatctcgcgagatctgatctgacgtttgcttcgttcttggtttttgcgcggcgcag

Basic information

species Oryza sativa
transcript LOC_Os01g54870.1
intron # 1
splice site 5'
intron type U2

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|163920059|gb|EG712013.1|EG712013
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88426781|gb|CI584144.1|CI584144
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88692748|gb|CI736323.1|CI736323
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|58603976|gb|CK014504.1|CK014504
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88591210|gb|CI708131.1|CI708131
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|218487192|gb|FG947791.1|FG947791
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|33660274|gb|CF291241.1|CF291241
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88398227|gb|CI588115.1|CI588115
EST:     TCACCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGTGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: TCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATG-GGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88423882|gb|CI609913.1|CI609913
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|38480189|gb|CF964278.1|CF964278
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|2311521|gb|C27676.1|C27676
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88579846|gb|CI691836.1|CI691836
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88403881|gb|CI611536.1|CI611536
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88734587|gb|CI758095.1|CI758095
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|58591145|gb|CF989453.1|CF989453
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCGTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88356780|gb|CI619266.1|CI619266
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88572140|gb|CI663711.1|CI663711
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88308773|gb|CI653660.1|CI653660
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88422346|gb|CI689157.1|CI689157
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88743392|gb|CI766900.1|CI766900
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|33817115|gb|CF334396.1|CF334396
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|287211|gb|D16015.1|D16015
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88720686|gb|CI743985.1|CI743985
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88591569|gb|CI709609.1|CI709609
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|55411639|gb|CV724015.1|CV724015
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGTTTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88737708|gb|CI761216.1|CI761216
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|44675111|gb|CR288545.1|CR288545
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88343377|gb|CI621745.1|CI621745
EST:     CTCCCCGCCGAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88333775|gb|CI643807.1|CI643807
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88328846|gb|CI646921.1|CI646921
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGA
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCA-GGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGA
EST: gi|218487665|gb|FG948992.1|FG948992
EST:     CTCCCCGCCCAGCGACCTCGGCGACTCCGGCGAAGATGGGCGCCTTCATG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACG
EST: gi|88426140|gb|CI574023.1|CI574023
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88422928|gb|CI615228.1|CI615228
EST:     CT-CCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TT-CACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCGGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88725288|gb|CI748547.1|CI748547
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|88334861|gb|CI648636.1|CI648636
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|218488907|gb|FG956921.1|FG956921
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
EST: gi|4714280|gb|AU058247.1|AU058247
EST:     CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGG                         TTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG
genomic: CTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAG

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: 73 (upstream exon), 64 (downstream exon)
Score: 174

CCGCAAAACCTTCCGCGCCGCCGCCATCTCGGACCACCGTAGCACGCCGCCTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcacca ... cgcggcgcagTTCCACCAGTACCAGGTGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCTACCAACGAGGTCCGCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGCAAAACCTTCCGCGCCGCCGCCATCTCGGACCACCGTAGCACGCCGCCTCCCCGCCCAGCGACCTCGGCAACTCCGGCGAAGATGGGCGCCTTCAGGgttagcaccatctctcccgcttcctcccctccacttcgagggctggtttgatctcgcgagatctgatctgacgtttgcttcgttcttggtttttgcgcggcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG