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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagaaaaatcaaaaggttcaaacgtttagatgaataacatctgatttccccctcttgttgtttcctgtgtcaatagaaacttctccttagcatattcagATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA

Basic information

species Oryza sativa
transcript LOC_Os08g39420.1
intron # 9
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g39420.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G126517_T01 (Zea mays), 3'ss of exon 10
--agagaaaaatcaaaaggttcaaacgtttagatgaataacatctgatttccccctcttgttgtttcctgtgtcaatagaaacttctccttagc-atattcagATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA
  | | |||  |  |  ||    ||     | ||     | |||   ||     ||||| | ||| |||   || | ||| | |||||||||   || || ||||||||| ||||| ||||||||||||||| ||||||| || |||||||| ||||||||| | ||||| ||||||| || || ||
ggaaacaaaggttcactgggcataattacaaaat--cccatatc-agttgtgtgctcttttagttcccttcatccaaagacagttctccttattgatgtttagATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTGCCCTTTCTAACCTTCAGCAGAGAGAAATAAGCA

upper sequence: LOC_Os08g39420.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA09G00500.2 (Glycine max), 3'ss of exon 11
agagaaaaatcaaaaggttcaaacgtttagatgaata-acatctgatttccccctcttgttgtt--tcctgtgtcaatagaaacttctccttagcatattcagATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA
  | | ||||   |   |        | | |||| |  | || | || |||   |    |  ||  ||  |||| ||    ||  |||    |  | ||| ||| ||||| ||||| ||||| |||||||||||||| |||||| ||||||| |||||| || |  || |    | | |  ||||  
taatataaattttagtctattgtaactaatatgatttcaaatgtaatgtccaaattaaatatttgatctagtgttaaagtgaa--tcttaacaata-atttagACATTGCTCTTGTGAAGAATAATGCTCTTGTTGGAGCTAAAGTTGCTGTAGCCCTTGCTCAA-TTAAGAGAAAATTGTCAAAG-
















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|88846577|gb|CI373345.1|CI373345
EST:     CTTGACAGAGTGAAAGTACTAACTGGACGATCTTCGCTAGAAGCCA                         ATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGG
genomic: CTTGACAGAGTGAAAGTACTAACTGGACGATCTTCGCTAGAAGCCAgtatcctaca ... gcatattcagATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGG
EST: gi|88224122|gb|CI223971.1|CI223971
EST:     CATGCTTGACAGAGTGAAAGTACTAACTGGACGATCTTCGCTAGAAGCCA                         ATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGG
genomic: CATGCTTGACAGAGTGAAAGTACTAACTGGACGATCTTCGCTAGAAGCCAgtatcctaca ... gcatattcagATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGG
EST: gi|88835296|gb|CI370599.1|CI370599
EST:     CATGCTTGACAGAGTGAAAGTACTAACTGGACGATCTTCGCTAGAAGCCA                         ATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGG
genomic: CATGCTTGACAGAGTGAAAGTACTAACTGGACGATCTTCGCTAGAAGCCAgtatcctaca ... gcatattcagATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGG
EST: gi|86853962|gb|CI329408.1|CI329408
EST:     CATGCTTGACAGAGTGAAAGTACTAACTGGACGATCTTCGCTAGAAGCCA                         ATATTGCGCTTGTAAAGAACAATGCTCTTTTTGGTGCTAAAATTGCTGTGG
genomic: CATGCTTGACAGAGTGAAAGTACTAACTGGACGATCTTCGCTAGAAGCCAgtatcctaca ... gcatattcagATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGG
EST: gi|15858529|gb|BI811341.1|BI811341
EST:     CATGCTTGACAGAGTGAAAGTACTAACTGGACGATCTTCGCTAGAAGCCA                         ATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGG
genomic: CATGCTTGACAGAGTGAAAGTACTAACTGGACGATCTTCGCTAGAAGCCAgtatcctaca ... gcatattcagATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGG
EST: gi|86879940|gb|CI340002.1|CI340002
EST:     CATGCTTGACAGAGTGAAAGTACTAACTGGACGATCTTCGCTAGAAGCC-                         A-ATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGG
genomic: CATGCTTGACAGAGTGAAAGTACTAACTGGACGATCTTCGCTAGAAGCCAgtatcctaca ... gcatattcagATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGG
EST: gi|89174503|gb|CI110701.1|CI110701
EST:     CATGCTTGACAGAGTGAAAGTACTAACTGGACGATCTTCGCTAGAAGCCA                         ATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGG
genomic: CATGCTTGACAGAGTGAAAGTACTAACTGGACGATCTTCGCTAGAAGCCAgtatcctaca ... gcatattcagATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGG
EST: gi|88846107|gb|CI372875.1|CI372875
EST:     TAACTGGACGATCTTCGCTAGAAGCCA                         ATATTGCGCTTGTAAAGAACAATGCTCATTGTTGGTGCTAAAATTGCTGTG
genomic: TAACTGGACGATCTTCGCTAGAAGCCAgtatcctaca ... gcatattcagATATTGCGCTTGTAAAGAACAATGCTC-TTGTTGGTGCTAAAATTGCTGTG

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: 75 (upstream exon), 50 (downstream exon)
Score: 8

CTATGTTGTTTCAGGGATAAAAATATAATAGGCAACGCGATCACTCCCTTCATGCTTGACAGAGTGAAAGTACTAACTGGACGATCTTCGCTAGAAGCCAgtatcctaca ... gcatattcagATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccccctcttgttgtttcctgtgtcaatagaaacttctccttagcatattcagATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA
                                      ctccttagc  putative branch site 
                           aatagaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agagaaaaatcaaaaggttcaaacgtttagatgaataacatctgatttccccctcttgttgtttcctgtgtcaatagaaacttctccttagcatattcagATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA

- agaaaaa
- - - - - - - - - - - - - - - - -aataaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatagaaa