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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttctaatcatgcatagcctatttatgcacatgttctgttgtacatccctgttcatagaaaaaagatcaggtctgctaagtttttgtaattatcttcagGTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAGGACTTCCTTGAAAGTGGTTTAGTACAGCTTGATAAAAGCATTGAAGAAA

Basic information

species Oryza sativa
transcript LOC_Os12g03190.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03190.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G151977_T01 (Zea mays), 3'ss of exon 9
ttttctaatcatgcatagcctatttatgcacatgttctgttgt--acatccctgttcatagaaaaaagatcaggtctgct-aagtttttgtaattatct-----tcagGTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAGGACTTCCTTGAAAGTGGTTTAGTACAGCTTGATAAAAGCATTGAAGAAA
  ||  |||   |       |  |||| || ||| |  | | |  | ||          ||  |     |||| |   || ||| ||||||| || |||     |||||||||||||||||| || |||||||| |||||||||||| |||||||||||||||||||||||||||||||||| || ||||| || ||||| |||||||
--tttcaattccg-----ttttcttataca-atgctacggtattgatattttgccctgcagtcagtgattcagttacactgaagattttgtatttctctacgcctcagGTTGAGAGTTTATATCCTAGTGAATTAGGACCTGATGCAGTGTCCACAAAGGACTTCCTTGAAAGTGGTTTAGTGCAACTTGACAAGAGCATGGAAGAAA
















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|89182020|gb|CI113526.1|CI113526
EST:     TGATCTTAGCTAGGCTTCTGGGGCAACGGATCAGCATGGAGAATATTAAT                         GTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAG
genomic: TGATCTTAGCTAGGCTTCTGGGGCAACGGATCAGCATGGAGAATATTAATgtatgcatat ... ttatcttcagGTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAG
EST: gi|86490550|gb|CI133183.1|CI133183
EST:     TGATCTTAGCTAGGCTTCTGGGGCAACGGATCAGCATGGAGAATATTAAT                         GTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAG
genomic: TGATCTTAGCTAGGCTTCTGGGGCAACGGATCAGCATGGAGAATATTAATgtatgcatat ... ttatcttcagGTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAG
EST: gi|7273923|gb|AU083467.1|AU083467
EST:     TGATCTTAGCTAGGCTTCTGGGGCAACGGATCAGCATGGAGAATATTAAT                         GTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAG
genomic: TGATCTTAGCTAGGCTTCTGGGGCAACGGATCAGCATGGAGAATATTAATgtatgcatat ... ttatcttcagGTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAG
EST: gi|86435122|gb|CI106355.1|CI106355
EST:     TCAGCATGGAGAATATTAAT                         GTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAG
genomic: TCAGCATGGAGAATATTAATgtatgcatat ... ttatcttcagGTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAG
EST: gi|86499082|gb|CI141715.1|CI141715
EST:     TGATCTTAGCTAGGCTTCTGGGGCAACGGATCAGCATGGAGAATATTAAT                         GTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAG
genomic: TGATCTTAGCTAGGCTTCTGGGGCAACGGATCAGCATGGAGAATATTAATgtatgcatat ... ttatcttcagGTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAG
EST: gi|88990011|gb|CI018861.1|CI018861
EST:     GGATCAGCATGGAGAATATTAAT                         GTTGAGGGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAG
genomic: GGATCAGCATGGAGAATATTAATgtatgcatat ... ttatcttcagGTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAG
EST: gi|86539123|gb|CI179329.1|CI179329
EST:     TGATCTTAGCTAGGCTTCTGGGGCAACGGATCAGCATGGAGAATATTAAT                         GTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAG
genomic: TGATCTTAGCTAGGCTTCTGGGGCAACGGATCAGCATGGAGAATATTAATgtatgcatat ... ttatcttcagGTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAG
EST: gi|86413783|gb|CI067990.1|CI067990
EST:     AGCATGGAGAATATTAAT                         GTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAG
genomic: AGCATGGAGAATATTAATgtatgcatat ... ttatcttcagGTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAG

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: 70 (upstream exon), 64 (downstream exon)
Score: 12

GCATTGATCTTAGCTAGGCTTCTGGGGCAACGGATCAGCATGGAGAATATTAATgtatgcatat ... ttatcttcagGTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAGGACTTCCTTGAAAGTGGTTTAGTACAGCTTGATAAAAGCATTGAAGAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccctgttcatagaaaaaagatcaggtctgctaagtttttgtaattatcttcagGTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAGGACTTCCTTGAAAGTGGTTTAGTACAGCTTGATAAAAGCATTGAAGAAA
                                             ttatcttc  CT-rich tract
                                taagtttttgtaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttctaatcatgcatagcctatttatgcacatgttctgttgtacatccctgttcatagaaaaaagatcaggtctgctaagtttttgtaattatcttcagGTTGAGAGTTTATACCCCAGTGAATTTGGACCTGATGCAATGTCCACAAAGGACTTCCTTGAAAGTGGTTTAGTACAGCTTGATAAAAGCATTGAAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - tcatgca
- - - - - - - - - - - -ttatgca
- - - - - - - - - - - - - - - - - - ctgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtttttg