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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgttacaccttggatgctcttataactattttgttctttgatctgtcttctttccatcccatttatggttaataatttgctaatagATGATATGGAGATCGCCCCTGATTTTTTTGACTACTTCGAGGCTGCAGCTAAATTACTTGATAACGATAA

Basic information

species Oryza sativa
transcript LOC_Os02g58590.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58590.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G426275_T04 (Zea mays), 3'ss of exon 10
gtgttacaccttggatgctcttataactattttgttctttgatctgtcttctttccatcccatttatggttaataatttgctaatagATGATATGGAGATCGCCCCTGATTTTTTTGACTACTTCGAGGCTGCAGCTAAATTACTTGATAACGATAA
|| | | | ||   ||| || | |  | |||   ||  |  |||  | |  |||||| |  || | |  | | ||||||  |||||||||| |||||||| ||||| |||||||| ||||||||||||||||||||||||||||||||||| || ||
gtctgatatctactatgttccttt--ccattc-attactacatccttttgttttccaacagatct-tcataattaatttcttaatagATGACATGGAGATTGCCCCGGATTTTTTCGACTACTTCGAGGCTGCAGCTAAATTACTTGATAATGACAA

upper sequence: LOC_Os02g58590.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv00s0972g00010.t01 (Vitis vinifera), 3'ss of exon 3
------gtgt-tacaccttggatgctcttataactattttgttctttgatctgtcttc----------------tttccatcccatttatggtta-ataatttgctaatagATGATATGGAGATCGCCCCTGATTTTTTTGACTACTTCGAGGCTGCAGCTAAATTACTTGATAACGATAA
       | | |   | ||  |   ||||  | || |||| | ||||  | | |                    | || || | |   |   ||   |  || |  |  |||||||||||| || ||||||||||| ||||||||||| |||||||| ||     | || || || |||||
gtgccaatatctgtgctttaaaatatctttcaccttttttctcctttatttttttactagagaatggggaataatgtctatgctaagaaaaattctgttgttggaaagcagATGATATGGAAATTGCCCCTGATTTCTTTGACTACTTTGAGGCTGCCGCAGCTCTCCTGGACAATGATAA

upper sequence: LOC_Os02g58590.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv00s0585g00030.t01 (Vitis vinifera), 3'ss of exon 10
------gtgt-tacaccttggatgctcttataactattttgttctttgatctgtcttc----------------tttccatcccatttatggtta-ataatttgctaatagATGATATGGAGATCGCCCCTGATTTTTTTGACTACTTCGAGGCTGCAGCTAAATTACTTGATAACGATAA
       | | |   | ||  |   ||||  | || |||| | ||||  | | ||                   | || || | |   |   ||   |  || |  |  |||||||||||| || ||||||||||| ||||||||||| |||||||| ||     | || || || |||||
gtgccaatatctgtgctttaaaatatctttcaccttttttctcctttattttttcactagagaatggggaataatgtctatgctaagaaaaattctgttgttggaaagcagATGATATGGAAATTGCCCCTGATTTCTTTGACTACTTTGAGGCTGCCGCAGCTCTCCTGGACAATGATAA

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|88720385|gb|CI743684.1|CI743684
EST:     TTTGCGCGAGTAATAATTCTGGAAG                         ATGATATGGAGATCGCCCCTGANNNNNNNGACTACTTCGAGGCTGCAGCTA
genomic: TTTGCGCGAGTAATAATTCTGGAAGgtgttacacc ... ttgctaatagATGATATGGAGATCGCCCCTGATTTTTTTGACTACTTCGAGGCTGCAGCTA
EST: gi|218480194|gb|FG949561.1|FG949561
EST:     CAAACACAACTTTGCGCGAGTTATAATTCTGGAAG                         ATGATATGGAGATCGCCCCTGANNNNNNNGACTACTTCGAGGCTGCAGCTA
genomic: CAAACACAACTTTGCGCGAGTAATAATTCTGGAAGgtgttacacc ... ttgctaatagATGATATGGAGATCGCCCCTGATTTTTTTGACTACTTCGAGGCTGCAGCTA
EST: gi|29626072|gb|CB631083.1|CB631083
EST:     GGATGAGCTATTCATCAAACACAACTTTGCGCGAGTTATAATTCTGGAAG                         ATGATATGGAGATCGCCCCTGANNNNNNNGACTACTTCGATGCTGCAGCTA
genomic: GGATGAGCTATTCATCAAACACAACTTTGCGCGAGTAATAATTCTGGAAGgtgttacacc ... ttgctaatagATGATATGGAGATCGCCCCTGATTTTTTTGACTACTTCGAGGCTGCAGCTA
EST: gi|33797216|gb|CF324472.1|CF324472
EST:     GGATGAGCTATTCATCAAACACAACTTTGCGCGAGTAATAATTCTGGAAG                         ATGATATGGAGATCGCCCCTGANNNNNNNGACTACTTCGAGGCTGCAGCTA
genomic: GGATGAGCTATTCATCAAACACAACTTTGCGCGAGTAATAATTCTGGAAGgtgttacacc ... ttgctaatagATGATATGGAGATCGCCCCTGATTTTTTTGACTACTTCGAGGCTGCAGCTA
EST: gi|29681006|gb|CB677281.1|CB677281
EST:     GGATGAGCTATTCATCAAACACAACTTTGCGCGAGTAATAATTCTGGAAG                         ATGATATGGAGATCGCCCCTGANNNNNNNGACTACTTCGAGGCTGCAGCTA
genomic: GGATGAGCTATTCATCAAACACAACTTTGCGCGAGTAATAATTCTGGAAGgtgttacacc ... ttgctaatagATGATATGGAGATCGCCCCTGATTTTTTTGACTACTTCGAGGCTGCAGCTA

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: 67 (upstream exon), 57 (downstream exon)
Score: 23

AACATTACAAATGGGCCTTGGATGAGCTATTCATCAAACACAACTTTGCGCGAGTAATAATTCTGGAAGgtgttacacc ... ttgctaatagATGATATGGAGATCGCCCCTGATTTTTTTGACTACTTCGAGGCTGCAGCTAAATTACTTGATAACGATAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttctttgatctgtcttctttccatcccatttatggttaataatttgctaatagATGATATGGAGATCGCCCCTGATTTTTTTGACTACTTCGAGGCTGCAGCTAAATTACTTGATAACGATAA
                                   ggttaat  putative branch site (score: 23)
                             atttatggttaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttacaccttggatgctcttataactattttgttctttgatctgtcttctttccatcccatttatggttaataatttgctaatagATGATATGGAGATCGCCCCTGATTTTTTTGACTACTTCGAGGCTGCAGCTAAATTACTTGATAACGATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT