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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccacatctttatttgttattgttttttatacttgccagtcgtgcatgtcctcctaaatatgtttgctttgttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCATACTACTATATGCAGCATAAAGAGGATCTCTTAGCAAGGTTTCTACATTG

Basic information

species Oryza sativa
transcript LOC_Os11g39650.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g39650.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G011364_T01 (Zea mays), 3'ss of exon 9
gtatgccacatctttatttgtta---ttgttttttatacttgccagtcgt-gcatgtcctcc--taaatatgtttg-ctttgttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCATACTACTATATGCAGCATAAAGAGGATCTCTTAGCAAGGTTTCTACATTG
||| |   |||||||| ||  ||   |||||||||   |   ||| || | ||| | ||| |  |||| |||  || || ||| ||| |||| | ||| |||||| ||||| |||| ||| ||||||||||||||||||  ||||||| || |||||| ||||| ||  | || |||| ||| |  | |||
gtacgttgcatctttaattcatagatttgtttttttccccatccattccttgcaagccctacactaaaaatggatggctgtgtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGTACTACTGTACGCAGCACAAAGAAGACATTTTGGCAATGTTGCAGCGTTG
















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|88222407|gb|CI222363.1|CI222363
EST:     CTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|88281049|gb|CI402247.1|CI402247
EST:     TTGGATCACCTAAGAGTCGTG                         GTATGANTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: TTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|86506017|gb|CI148650.1|CI148650
EST:     CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|86498028|gb|CI140661.1|CI140661
EST:     CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|29675265|gb|CB671540.1|CB671540
EST:     CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|87033190|gb|CI187814.1|CI187814
EST:     GGATCACCT-AGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: GGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|86503658|gb|CI146291.1|CI146291
EST:     ACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: ACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|88469475|gb|CI406746.1|CI406746
EST:     GATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: GATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|29665512|gb|CB661787.1|CB661787
EST:     CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|87011566|gb|CI279475.1|CI279475
EST:     CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|86495429|gb|CI138062.1|CI138062
EST:     CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|29671178|gb|CB667453.1|CB667453
EST:     CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|87028003|gb|CI276359.1|CI276359
EST:     CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|89185519|gb|CI051847.1|CI051847
EST:     CTTCGATTCTATTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCCATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|86498891|gb|CI141524.1|CI141524
EST:     CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|218487277|gb|FG955018.1|FG955018
EST:     CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|218488104|gb|FG955050.1|FG955050
EST:     CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|86498140|gb|CI140773.1|CI140773
EST:     CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|86495472|gb|CI138105.1|CI138105
EST:     CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGGCCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|86493402|gb|CI136035.1|CI136035
EST:     CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|87011559|gb|CI279468.1|CI279468
EST:     CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|86492827|gb|CI135460.1|CI135460
EST:     CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|86498441|gb|CI141074.1|CI141074
EST:     CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|86494509|gb|CI137142.1|CI137142
EST:     CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
EST: gi|88222357|gb|CI222313.1|CI222313
EST:     CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG                         GTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT
genomic: CTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCAT

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: 21 (upstream exon), 69 (downstream exon)
Score: 2

GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTGgtatgccaca ... gttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCATACTACTATATGCAGCATAAAGAGGATCTCTTAGCAAGGTTTCTACATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatacttgccagtcgtgcatgtcctcctaaatatgtttgctttgttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCATACTACTATATGCAGCATAAAGAGGATCTCTTAGCAAGGTTTCTACATTG
                          tcctaaa  putative branch site (score: 2)
                                         ctttgttct  putative PPT
                             taaatatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccacatctttatttgttattgttttttatacttgccagtcgtgcatgtcctcctaaatatgtttgctttgttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCATACTACTATATGCAGCATAAAGAGGATCTCTTAGCAAGGTTTCTACATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG