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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatatctgtcaagatgttcagagggtagcaacatgtttaactattttccaagattcagacattgactgatagctttgttttggggttcagTTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATG

Basic information

species Oryza sativa
transcript LOC_Os03g11734.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g11734.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G163154_T04 (Zea mays), 3'ss of exon 9
gtaagaatat---ctgtcaagatgttcagagg---gtagcaacatgtttaactattttccaagattcagacattgactgatagctttgtt-ttggggttcagTTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATG
||||| |  |   ||| |  |    ||  |     |  ||  |||    ||  ||||  ||||||||||||| ||| | | |  | | || |   ||||||||||||||| || || ||||| || ||||| || ||||||||||| |||||||||||||| ||||| |||||||||| |||||| ||||||||||||
gtaaggacgtgccctggcctggctatcgaaacaacgccgctccatacgcaagcatttcacaagattcagacactgaattagacatcttttatctcggttcagTTTGTCGCCGGGACGCAGACCATCAATTCCCTGGCCTTCGTGTTTGATGGCATCAACTTTGGAGCGTCAGACTACAGATACTCTGCTTACTCCATG

upper sequence: LOC_Os03g11734.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G418400_T01 (Zea mays), 3'ss of exon 4
-----------------------------gtaagaatatctgtcaagatgttcagagg---gtagcaacatgtttaactattttccaagattcagacattgact--gatagctttgttttggggttcagTTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATG
                             ||        ||| |  |    ||  |     |  ||  ||| |  ||  ||||  ||||||||||||| ||| |  || | |||| | |   | ||||||||||| ||||||| ||||| || ||||| || |||||| |||| |||||||||||||| ||||| |||||||||| |||||| ||||||||||||
gtcattcacagaggcatcccactaaggatgtggcctagcctggcctggctatcgaaacaacgccgctccatatgcaagcatttcacaagattcagacactgaattagacaacttt-tatcttgattcagTTTGTCACTGGCACGCAGACCATCAATTCCCTGGCCTTCATGTTTGATGGCATCAACTTTGGAGCGTCAGACTACAGATACTCTGCTTACTCCATG
















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|56550155|gb|CX056259.1|CX056259
EST:     TTTTCACAAAGGACATCGACGTGATCGATGTCATTCACAAAGGCATTCCT                         TTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGC
genomic: TTTTCACAAAGGACATCGACGTGATCGATGTCATTCACAAAGGCATTCCTgtaagaatat ... tggggttcagTTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGC
EST: gi|218504647|gb|FG960764.1|FG960764
EST:     TTTTCACAAAGGACATCGACGTGATCGATGTCATTCACAAAGGCATTCCT                         TTTGTCGCTGGCACACAGACGATAAA
genomic: TTTTCACAAAGGACATCGACGTGATCGATGTCATTCACAAAGGCATTCCTgtaagaatat ... tggggttcagTTTGTCGCTGGCACACAGACGATAAA
EST: gi|89185192|gb|CI050926.1|CI050926
EST:     TCGACGTGATCGATGTCATTCACAAAGGCATTCCT                         TTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGC
genomic: TCGACGTGATCGATGTCATTCACAAAGGCATTCCTgtaagaatat ... tggggttcagTTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGC
EST: gi|86498292|gb|CI140925.1|CI140925
EST:     CACAAAGGCATTCCT                         TTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGC
genomic: CACAAAGGCATTCCTgtaagaatat ... tggggttcagTTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGC
EST: gi|86497553|gb|CI140186.1|CI140186
EST:     TTTTCACAAAGGACATCGACGTGATCGATGTCATTCACAAAGGCATTCCT                         TTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGC
genomic: TTTTCACAAAGGACATCGACGTGATCGATGTCATTCACAAAGGCATTCCTgtaagaatat ... tggggttcagTTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGC
EST: gi|86495252|gb|CI137885.1|CI137885
EST:     TTTTCACAAAGGACATCGACGTGATCGATGTCATTCACAAAGGCATTCCT                         TTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGC
genomic: TTTTCACAAAGGACATCGACGTGATCGATGTCATTCACAAAGGCATTCCTgtaagaatat ... tggggttcagTTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGC
EST: gi|89194404|gb|CI116841.1|CI116841
EST:     TCACAAAGGCATTCCT                         GTTGTCGCTGGCACACAGGACGATAAATTCACTAGCCTTCGTGTTCGATGG
genomic: TCACAAAGGCATTCCTgtaagaatat ... tggggttcagTTTGTCGCTGGCACACA-GACGATAAATTCACTAGCCTTCGTGTTCGATGG

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: 73 (upstream exon), 63 (downstream exon)
Score: 14

CATGGGTCTCACTGTTGTGCTTGGGGTTGGCATGAAGTTTGGGGCTGGAATTTTCACAAAGGACATCGACGTGATCGATGTCATTCACAAAGGCATTCCTgtaagaatat ... tggggttcagTTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaactattttccaagattcagacattgactgatagctttgttttggggttcagTTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATG
                            gactgat  putative branch site (score: 14)
                                     ctttgtttt  putative PPT
                                      tttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaatatctgtcaagatgttcagagggtagcaacatgtttaactattttccaagattcagacattgactgatagctttgttttggggttcagTTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT