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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcttcagccaatcacccatacacgcaattcatgctaacttctgggcaagcatcacttgaatactgatctatttttctatcatcaatttacgagggagtttttccaacatatcctttttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCATGCTAGCAAAGAACATTGTGGAGCCAGCTCAAGCAATGCAACAGGCAACT

Basic information

species Oryza sativa
transcript LOC_Os07g07250.1
intron # 6
splice site 3'
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|86602731|gb|CI357095.1|CI357095
EST:     AACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: AACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|15847551|gb|BI795827.1|BI795827
EST:     TTGATGTCAGTGTCTGGAACTCTTATCATGACGACC-ATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: TTGAT-TCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|88993344|gb|CI257772.1|CI257772
EST:     ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|86874331|gb|CI335943.1|CI335943
EST:     ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|86490911|gb|CI133544.1|CI133544
EST:     ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|89181646|gb|CI113152.1|CI113152
EST:     ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|86832718|gb|CI345133.1|CI345133
EST:     ATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|4716113|gb|AU057229.1|AU057229
EST:     ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|58689367|gb|CK078054.1|CK078054
EST:     ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|4716114|gb|AU057230.1|AU057230
EST:     TCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: TCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|86603620|gb|CI112380.1|CI112380
EST:     ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|88830265|gb|CI076521.1|CI076521
EST:     ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|86603371|gb|CI112131.1|CI112131
EST:     ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|88833635|gb|CI077116.1|CI077116
EST:     ATTGATTCAGTGTCTGGAACTCTGATCATGACGACCAATCATGTTAAGAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|86430950|gb|CI083373.1|CI083373
EST:     ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|44675035|gb|CR288469.1|CR288469
EST:     ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|29616633|gb|CB621645.1|CB621645
EST:     ATTGATTCATTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|86523788|gb|CI163994.1|CI163994
EST:     TTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCA
genomic: TTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAAC-ATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCA
EST: gi|89195956|gb|CI395374.1|CI395374
EST:     GACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: GACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|86535508|gb|CI175714.1|CI175714
EST:     ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|87024602|gb|CI259317.1|CI259317
EST:     ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|86842608|gb|CI341761.1|CI341761
EST:     GAACTCTTATCATGACGACCAATCATTTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: GAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|88831685|gb|CI369367.1|CI369367
EST:     CTCTTATCATGACGACCAATCATGTTAACAT                         CCACGACCAGTTTATCGAAAGCTTGAAG-ATCTTAACATGCGGACTTCCAT
genomic: CTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|86414045|gb|CI068252.1|CI068252
EST:     ATTGATTCAGTGCCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|88268705|gb|CI378640.1|CI378640
EST:     AGTGATTCAGTGTCTGGAACTCTTATCATGACGGCCAATCATG-TAACAT                         CCACGAGCGGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|29660023|gb|CB656298.1|CB656298
EST:     ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|86430626|gb|CI083049.1|CI083049
EST:     ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|88263159|gb|CI366933.1|CI366933
EST:     ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
EST: gi|58676883|gb|CK065570.1|CK065570
EST:     ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACAT                         CCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT
genomic: ATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCAT

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: 71 (upstream exon), 73 (downstream exon)
Score: 30

GGGAGTTGTGGATAATGAACTTAGTTAGAAATTCAAAGCTCGATGCCAAGATTGATTCAGTGTCTGGAACTCTTATCATGACGACCAATCATGTTAACATgtaagtttct ... ttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCATGCTAGCAAAGAACATTGTGGAGCCAGCTCAAGCAATGCAACAGGCAACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctatcatcaatttacgagggagtttttccaacatatcctttttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCATGCTAGCAAAGAACATTGTGGAGCCAGCTCAAGCAATGCAACAGGCAACT
                                     tatcctttttcatt  CT-rich tract
         atcaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttcttcagccaatcacccatacacgcaattcatgctaacttctgggcaagcatcacttgaatactgatctatttttctatcatcaatttacgagggagtttttccaacatatcctttttcattgcagCCACGAGCAGTTTATCGAAAGCTTGAAGAATCTTAACATGCGGACTTCCATGCTAGCAAAGAACATTGTGGAGCCAGCTCAAGCAATGCAACAGGCAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA