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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccactcattaactttttcataccattacaatactgtttttgtggacctatgtttgatttgtattcacttttgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGATGCTGAACGACGCATCTCTCAGATTTTGGGCCATTAAAACGAATTGGAA

Basic information

species Oryza sativa
transcript LOC_Os08g22864.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g22864.2 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G327394_T01 (Zea mays), 3'ss of exon 25
gtaagccactcattaac-tttttcataccattacaatactgttttt-gtggacctatgtttgatttgtattca---cttttgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGATGCTGAACGACGCATCTCTCAGATTTTGGGCCATTAAAACGAATTGGAA
||||||  || |  ||| ||||||| |  |  |||  | ||||| | || || || | ||  || ||  ||||     ||  || |  |||||| |||| ||  |||||||||| || || || ||||| || ||   ||||||||||||||||||||| ||||||||||| || || | | |||  || 
gtaagc--ctgacaaacatttttcacataaccacatcattgtttatagttgaactgtattc-atctgggttcaaaatgttcattccgcagATACCTGAGTGTTCTAAAGGTCAATGTGCCGGGTAGAGAAATACCTGCGGATGCTGAACGACGCATCTCACAGATTTTGGGTCACTAGATCTAATCAGAC
















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|86853148|gb|CI324850.1|CI324850
EST:     TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA                         ATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
genomic: TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
EST: gi|29626379|gb|CB631390.1|CB631390
EST:     TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA                         ATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
genomic: TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
EST: gi|86437704|gb|CI119624.1|CI119624
EST:     TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA                         ATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
genomic: TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
EST: gi|29624113|gb|CB629124.1|CB629124
EST:     TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA                         ATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
genomic: TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
EST: gi|88269996|gb|CI381294.1|CI381294
EST:     TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA                         ATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
genomic: TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
EST: gi|88966526|gb|CI353078.1|CI353078
EST:     GCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA                         ATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
genomic: GCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
EST: gi|58586846|gb|CF985154.1|CF985154
EST:     TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA                         ATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
genomic: TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
EST: gi|88382101|gb|CI533305.1|CI533305
EST:     TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA                         ATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
genomic: TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
EST: gi|86603014|gb|CI357378.1|CI357378
EST:     TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA                         ATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
genomic: TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
EST: gi|86480164|gb|CI122797.1|CI122797
EST:     TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA                         ATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
genomic: TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
EST: gi|29626007|gb|CB631018.1|CB631018
EST:     TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA                         ATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
genomic: TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
EST: gi|86480174|gb|CI122807.1|CI122807
EST:     TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA                         ATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
genomic: TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
EST: gi|88505109|gb|CI432615.1|CI432615
EST:     TTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA                         ATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
genomic: TTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
EST: gi|88437181|gb|CI526330.1|CI526330
EST:     TTTCTGCAAAAGA                         ATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
genomic: TTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
EST: gi|88670678|gb|CI724794.1|CI724794
EST:     TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA                         ATACTTGAGCGT
genomic: TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGT
EST: gi|88286403|gb|CI524902.1|CI524902
EST:     ACATGAATATTTATTTTCTGCAAAAGA                         ATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
genomic: ACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
EST: gi|88671305|gb|CI724351.1|CI724351
EST:     TCTTTGCTTGGATTTATTGCAGAACATGAATATNTATTTCCTGCAAAAGA                         ATACTTGAGCG
genomic: TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCG
EST: gi|58692351|gb|CK081038.1|CK081038
EST:     TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA                         ATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
genomic: TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
EST: gi|86437028|gb|CI118750.1|CI118750
EST:     TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA                         ATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
genomic: TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
EST: gi|88253653|gb|CI352279.1|CI352279
EST:     TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA                         ATACTTGAGCCTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
genomic: TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
EST: gi|88996514|gb|CI260018.1|CI260018
EST:     TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA                         ATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA
genomic: TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGA

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), 50 (downstream exon)
Score: 4

TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGAgtaagccact ... tgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGATGCTGAACGACGCATCTCTCAGATTTTGGGCCATTAAAACGAATTGGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacaatactgtttttgtggacctatgtttgatttgtattcacttttgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGATGCTGAACGACGCATCTCTCAGATTTTGGGCCATTAAAACGAATTGGAA
                         gtttgat  putative branch site (score: 4)
                                     ttcacttttgtttc  putative PPT
                              atttgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccactcattaactttttcataccattacaatactgtttttgtggacctatgtttgatttgtattcacttttgtttcatagATACTTGAGCGTGTTAAAGGTCAACGTTCCTGGAAGAGAGATGCCAATGGATGCTGAACGACGCATCTCTCAGATTTTGGGCCATTAAAACGAATTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG