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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataccaagcccagacgttattttatacaagcaacaagtttttttttctcattgtttcctctggtcgtggttatattactgactgcatgctatgtttacagGCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAG

Basic information

species Oryza sativa
transcript LOC_Os01g07100.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07100.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G048804_T02 (Zea mays), 3'ss of exon 9
-ataccaagcccagacgttattttatacaagcaacaagttttt---ttttctcattgtttcctctggtcgtggttatattactgactgcatgctatgtttacagGCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAG
 ||  || |      |    |||  |||  |  | | ||  |    | |  |  ||||||||     ||  | || | | ||      |      ||||||||| || || |||||||||||||||||||| || ||||| || |||||||| ||||||||||||||||  ||  |||| ||| |||||
catttcatgttgtttcaacttttgttacttggtatatgtcatggaatatattttttgtttccagcactctagcttttgtaacatgtgacgc----tgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG
















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|86503745|gb|CI146378.1|CI146378
EST:     GAAATCCCCAAAACAGATTTAATTCAGTTCATCAAGTATCTCTTACCGAC                         GCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAA
genomic: GAAATCCCCAAAACAGATTTAATTCAGTTCATCAAGTATCTCTTACCGACgtaagtcttt ... atgtttacagGCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAA
EST: gi|88903452|gb|CI088990.1|CI088990
EST:     TTAATTCAGTTCATCAAGTATCTCTTACCGAC                         GCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAA
genomic: TTAATTCAGTTCATCAAGTATCTCTTACCGACgtaagtcttt ... atgtttacagGCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAA
EST: gi|86419758|gb|CI054559.1|CI054559
EST:     GAAATCCCCAAAACAGATTTAATTCAGTTCATCAAGTATCTCTTACCGAC                         GCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAA
genomic: GAAATCCCCAAAACAGATTTAATTCAGTTCATCAAGTATCTCTTACCGACgtaagtcttt ... atgtttacagGCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAA
EST: gi|58679649|gb|CK068336.1|CK068336
EST:     TCTCTTACCGAC                         GCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAA
genomic: TCTCTTACCGACgtaagtcttt ... atgtttacagGCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAA
EST: gi|87020089|gb|CI277821.1|CI277821
EST:     GAAATCCCCAAAACAGATTTAATTCAGTTCATCAAGTATCTCTTACCGAC                         GCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAA
genomic: GAAATCCCCAAAACAGATTTAATTCAGTTCATCAAGTATCTCTTACCGACgtaagtcttt ... atgtttacagGCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAA
EST: gi|218478384|gb|FG957616.1|FG957616
EST:     GAAATCCCCAAAACAGATTTAATTCAGTTCATCAAGTATCTCTTACCGAC                         GCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAA
genomic: GAAATCCCCAAAACAGATTTAATTCAGTTCATCAAGTATCTCTTACCGACgtaagtcttt ... atgtttacagGCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAA
EST: gi|88828968|gb|CI073838.1|CI073838
EST:     CAGATTTAATTCAGTTCATCAAGTATCTCTTACCGAC                         GCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAA
genomic: CAGATTTAATTCAGTTCATCAAGTATCTCTTACCGACgtaagtcttt ... atgtttacagGCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAA
EST: gi|88228931|gb|CI226782.1|CI226782
EST:     CAAAACAGATTTAATTCAGTTCATCAAGTATCTCTTACCGAC                         GCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAA
genomic: CAAAACAGATTTAATTCAGTTCATCAAGTATCTCTTACCGACgtaagtcttt ... atgtttacagGCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAA
EST: gi|86499373|gb|CI142006.1|CI142006
EST:     GAAATCCCCAAAACAGATTTAATTCAGTTCATCAAGTATCTCTTACCGAC                         GCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAA
genomic: GAAATCCCCAAAACAGATTTAATTCAGTTCATCAAGTATCTCTTACCGACgtaagtcttt ... atgtttacagGCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAA

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: 68 (upstream exon), 70 (downstream exon)
Score: 19

CAAATTTGCTCATGGACGAGCTGAAGGATCAACTAAAATCTGCTGACTTGGAAATCCCCAAAACAGATTTAATTCAGTTCATCAAGTATCTCTTACCGACgtaagtcttt ... atgtttacagGCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcattgtttcctctggtcgtggttatattactgactgcatgctatgtttacagGCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAG
                              tactgac  putative branch site (score: 19)
                        ttatattact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataccaagcccagacgttattttatacaagcaacaagtttttttttctcattgtttcctctggtcgtggttatattactgactgcatgctatgtttacagGCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - caagccc
- - - - - - - - - - - - - - - caacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatgc