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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAGgttggctacttggctacttgttttactttgctctctgaggtttgtttttctttcagtactgtcattgactattctttctctattccgcag

Basic information

species Oryza sativa
transcript LOC_Os10g41590.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g41590.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G341271_T05 (Zea mays), 5'ss of exon 4
CTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAGgttggctacttggctacttgttttactttgctctctgaggtttgtttttcttt--cagtactgtcatt------gactattctttctctattccgcag
|||||||||||||| || |||||||| || || ||||||||||||||  |   ||||||||| ||||| ||||||||| | ||||||||||| | ||      | ||| || || ||||  | | |||||   ||   ||   ||||  ||   ||      || | ||   ||  | |||| |||
CTGATTGATGATTTGGTTCTGCTTGGAGTACGGGCTGGTGGGGATTTGGATAATTTGCAAGCACTTGACCATGAAGAGTTATCAGAAGgttg-cgacaa----atttggttaacgttgccttttaaggttcaattcatttcagcagtgatgcttttttagctgattgtttactcattgttccacag
















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|88424216|gb|CI581771.1|CI581771
EST:     TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAG                         AATCTCTTGAGTCA
genomic: TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAGgttggctact ... tattccgcagAATCTCTTGAGTCA
EST: gi|88728249|gb|CI751759.1|CI751759
EST:     TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAG                         AATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCTCTTCAGA
genomic: TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAGgttggctact ... tattccgcagAATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCTCTTCAGA
EST: gi|88296461|gb|CI669237.1|CI669237
EST:     TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGTGATGTCAGAAG                         AATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCTCTTCAGACTCTTGA
genomic: TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAGgttggctact ... tattccgcagAATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCTCTTCAGACTCTTGA
EST: gi|88454307|gb|CI569879.1|CI569879
EST:     TGGGGATTTAAACGGTTTGCA-GCGCTTGATCATGAACAGATGTCAGAC-                         AATCTCTTGAGTCATGTC-TTCTGAGGAGATATTTCTCTTCAGACTCTTGA
genomic: TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAGgttggctact ... tattccgcagAATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCTCTTCAGACTCTTGA
EST: gi|88317188|gb|CI626831.1|CI626831
EST:     TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCACAAG                         AATCTCTTGACTCATGTCCTTCTGAGGAGA
genomic: TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAGgttggctact ... tattccgcagAATCTCTTGAGTCATGTCCTTCTGAGGAGA
EST: gi|88309663|gb|CI656404.1|CI656404
EST:     TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGTGATGTCAGAAG                         AATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCTCTTCAGACTCTTGA
genomic: TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAGgttggctact ... tattccgcagAATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCTCTTCAGACTCTTGA
EST: gi|88407459|gb|CI586300.1|CI586300
EST:     TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAG                         AATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCTCTTCAGACTCTTGA
genomic: TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAGgttggctact ... tattccgcagAATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCTCTTCAGACTCTTGA
EST: gi|88403667|gb|CI575551.1|CI575551
EST:     TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAG                         AATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCCCTTCAGACTCTTGA
genomic: TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAGgttggctact ... tattccgcagAATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCTCTTCAGACTCTTGA
EST: gi|88400700|gb|CI596121.1|CI596121
EST:     TGGGGATTTAAAGGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAG                         AATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCTCTTCAGACTCTTGA
genomic: TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAGgttggctact ... tattccgcagAATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCTCTTCAGACTCTTGA
EST: gi|88316061|gb|CI618937.1|CI618937
EST:     TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAG                         AATCTCTTGAGTCATGTCCTTCTGAGGAG
genomic: TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAGgttggctact ... tattccgcagAATCTCTTGAGTCATGTCCTTCTGAGGAG
EST: gi|88431474|gb|CI579591.1|CI579591
EST:     TGGGGATTTAAACGGTTTGCAAGCGCTTGATCTTGAAGAGATGTCAGAAG                         AATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCTCTTCAGACTCTTGA
genomic: TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAGgttggctact ... tattccgcagAATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCTCTTCAGACTCTTGA
EST: gi|88729990|gb|CI753605.1|CI753605
EST:     TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAG                         AATCTCTTGAGTCATGTCCCTTCTGAGGAGATATTT
genomic: TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAGgttggctact ... tattccgcagAATCTCTTGAGTCATGTCC-TTCTGAGGAGATATTT
EST: gi|58669159|gb|CK057845.1|CK057845
EST:     TGGGGATTTAAACGGTTTGCACGCGCTTGATCATGAAGAGATGTCAGAAG                         AATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCTCTTCAGACTCTTTA
genomic: TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAGgttggctact ... tattccgcagAATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCTCTTCAGACTCTTGA
EST: gi|88394940|gb|CI607667.1|CI607667
EST:     TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAG                         AATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCTCTTCAGACTCTTGA
genomic: TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAGgttggctact ... tattccgcagAATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCTCTTCAGACTCTTGA
EST: gi|88336123|gb|CI647317.1|CI647317
EST:     TGGGGATTTAAACGGTTCGCAAGCGCTTGATCATGAAGTGATGTCAGAAG                         AATCTCTTGAGTCATGTCCTTCTGAGGAGATAT
genomic: TGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAGgttggctact ... tattccgcagAATCTCTTGAGTCATGTCCTTCTGAGGAGATAT

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: 37 (upstream exon), 66 (downstream exon)
Score: 11

CTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAGgttggctact ... tattccgcagAATCTCTTGAGTCATGTCCTTCTGAGGAGATATTTCTCTTCAGACTCTTGAATTCCAGGAATTTCAGAAATAATGATGACAGTAGCCTGTCAAAATTAGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAGgttggctacttggctacttgttttactttgctctctgaggtttgtttttctttcagtactgtcattgactattctttctctattccgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG