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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactaccactgtttactagagtatttggccataccattctcgtgccttcgattataggttcttgaccaactactctgattgccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACAAGAAGCGTGTCAACGAGTACGGCTTCGGTGGGGAAGACGAGCCACAAGC

Basic information

species Oryza sativa
transcript LOC_Os04g36050.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G016894_T01 (Zea mays), 3'ss of exon 10
-------------------------------gtaactaccactgtttactagagtatttggccataccattctcgtgcc-ttcgattataggttcttgaccaactactctgattgccatgt----gcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACAAGAAGCGTGTCAACGAGTACGGCTTCGGTGGGGAAGACGAGCCACAAGC
                                ||||| |   |     |  |   |     |    |  |   | | || |||   | ||| | | | ||| ||| ||||   || |||||    ||||||||||||||||||||||||||||| ||||| |||  ||| || || |||||||||||||| |||||||  |||||||| || || ||||| ||   |||
gtaagatgatctatcacttctttttagtcagataactgctggttaaatcagggaaaccattctgctctttggacataccattcttgtttagatccctaaccgactgctct--ctgacatgtctcggcagATGTTATCTTCTTGATATACCTCTATCAGAGGTGGAAGTATCCGGTCGACAAGAAGCGTGTTAACGAGTTTGGCTTCGGGGGCGAGGACGAACCGGCAGC

upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G437119_T02 (Zea mays), 3'ss of exon 11
----------------------gtaacta--ccactgtttactagagtatttgg-ccataccattctcgtgccttcgattataggttcttgaccaact-act-ctgattgccatgt---gcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACAAGAAGCGTGTCAACGAGTACGGCTTCGGTGGGGAAGACGAGCCACAAGC
                       ||   |    |||| |   || || |      |||| |  ||||  |    |       ||| |  |  | || | ||| ||   || | |||   |||||||||||||||||||||||| |||||||||| |||   || || || ||||||||||||||||||||||  |||||||| || || || || ||   |||
gtaagatgatctatcacttcttttagtcaaataactgctagttacagcagggaaaccattctgttcttttaatctt--ccgcaggcttctatctaattgactgctctctgacgtgtttggcagATGTTATCTTCTTGATATACGTCTACCAGAGGTGGAAATATCCGGTCGACAAGAAGCGTGTCAACGAGTTTGGCTTCGGAGGCGAGGAGGAACCCGCAGC

upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G08500.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaactaccactgt---ttactagagtatttggccataccattctcgt---gccttcgatt----ataggttcttgaccaactactctgattgccatg--tgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACAAGAAGCGTGTCAACGAGTACGGCTTCGGTGGGGAAGACGAGCCACAAGC
|| | ||| | |     || |  |||| | | | || |    ||| |    |  || || |    | |  |   |||  | |||   |   ||   |   ||||||||| || ||||| |||||| | |||||||||||||| || || || ||||| |  |||||||||||||  || || || || || || ||| |    | 
gtgaatacaaatccatcttccctgagtttattgacacatgtctctaggatagttttggaattcacaaaaatcgatgatgatctaaatttggtgttgttgttgcagATGTGATATTCTTAATATACTTGTACCAGAGATGGGTTTATCCTGTGGACAAAACACGTGTCAACGAGTTTGGTTTTGGAGGTGAGGATGAGTCTGTGGA

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|33794444|gb|CF323106.1|CF323106
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|163928407|gb|EG711331.1|EG711331
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|38478536|gb|CF962669.1|CF962669
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|9788969|gb|BE530979.1|BE530979
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|218503668|gb|FG954354.1|FG954354
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|218504968|gb|FG957275.1|FG957275
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|86480776|gb|CI123409.1|CI123409
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|33793207|gb|CF322484.1|CF322484
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|38475772|gb|CF959905.1|CF959905
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCT
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCT
EST: gi|218488433|gb|FG948916.1|FG948916
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|218488312|gb|FG953545.1|FG953545
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|218488425|gb|FG948908.1|FG948908
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|87008351|gb|CI301109.1|CI301109
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|38476812|gb|CF960945.1|CF960945
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGGATATACCTCTACCAGAGATGGGTGTACCCAGTTGAC
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTT-GATATACCTCTACCAGAGATGGGTGTACCCAGTTGAC
EST: gi|29623967|gb|CB628978.1|CB628978
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|88401126|gb|CI685111.1|CI685111
EST:     AGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: AGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|29626353|gb|CB631364.1|CB631364
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|88844851|gb|CI022205.1|CI022205
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|29623966|gb|CB628977.1|CB628977
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|58688332|gb|CK077019.1|CK077019
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|218481009|gb|FG969194.1|FG969194
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|58598976|gb|CK009504.1|CK009504
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTGTCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
EST: gi|66923041|gb|CX109889.1|CX109889
EST:     ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATG                         ATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA
genomic: ATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACA

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: 72 (upstream exon), 50 (downstream exon)
Score: 12

AGGCAAATGACCTACAAGTTCCTCAACACCATAATTGATGACCTTTTCGCATTTGTGATCAAAATGCCGATGCTGCATCGTCTCTCAGTTTTCAGAGATGgtaactacca ... ccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACAAGAAGCGTGTCAACGAGTACGGCTTCGGTGGGGAAGACGAGCCACAAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcgtgccttcgattataggttcttgaccaactactctgattgccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACAAGAAGCGTGTCAACGAGTACGGCTTCGGTGGGGAAGACGAGCCACAAGC
              attata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactaccactgtttactagagtatttggccataccattctcgtgccttcgattataggttcttgaccaactactctgattgccatgtgcagATGTTATCTTCTTGATATACCTCTACCAGAGATGGGTGTACCCAGTTGACAAGAAGCGTGTCAACGAGTACGGCTTCGGTGGGGAAGACGAGCCACAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA