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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATGgtatggtactgttgtgtattccaatttgaatttaaatatctcaaacgctttcaattgaccatctgttcttccttcag

Basic information

species Oryza sativa
transcript LOC_Os04g51610.1
intron # 29
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 29
lower sequence: GRMZM2G140328_T03 (Zea mays), 5'ss of exon 29
GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATGgtatggtactgttgtgtattccaatttgaatttaaatatctcaaacgctttcaattgaccatctgttcttccttcag
||| || ||||| |||||| ||||||||||||||||||| || |||||||| || ||| | || | | || ||| | | | | || | | ||| | ||||||| |||||
GGAGCCATTGATTACAAATATCATGTGGAGAAACTTAATTATCATGgtatgctatatttgc-tgttgtattctgtgtttct-tgttatagat-tttcctactgaacgcttgttctttgttcag
















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|86514508|gb|CI157141.1|CI157141
EST:     GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG                         GCTCTGTTTCAAGTTATAGTCCTCCTTACTCTCAACTTTAGGGGCACAAAC
genomic: GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATGgtatggtact ... cttccttcagGCTCTGTTTCAAGTTATAGTCCTCCTTACTCTCAACTTTAGGGGCACAAGC
EST: gi|25806928|gb|CA762889.1|CA762889
EST:     CCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG                         GCTCTGTTTCAAGTTATAGTCCTCCTTACTCTCAACTTTAGGGGCACAAGC
genomic: CCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATGgtatggtact ... cttccttcagGCTCTGTTTCAAGTTATAGTCCTCCTTACTCTCAACTTTAGGGGCACAAGC
EST: gi|29685708|gb|CB681983.1|CB681983
EST:     GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG                         GCTCTGTTTCAAGTTATAGTCCTCCTTACTCTCAACTTTAGGGGCACAAGC
genomic: GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATGgtatggtact ... cttccttcagGCTCTGTTTCAAGTTATAGTCCTCCTTACTCTCAACTTTAGGGGCACAAGC
EST: gi|87027607|gb|CI272372.1|CI272372
EST:     GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG                         GCTCTGTTTCAAGTTATAGTCCTCCTTACTCTCAACTTTAGGGGCACAAGC
genomic: GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATGgtatggtact ... cttccttcagGCTCTGTTTCAAGTTATAGTCCTCCTTACTCTCAACTTTAGGGGCACAAGC
EST: gi|86518067|gb|CI158273.1|CI158273
EST:     CTTAATCATAATG                         GCTCTGTTTCAAGTTATAGTCCTCCTTACTCTCAACTTTAGGGGCACAAGC
genomic: CTTAATCATAATGgtatggtact ... cttccttcagGCTCTGTTTCAAGTTATAGTCCTCCTTACTCTCAACTTTAGGGGCACAAGC
EST: gi|58594188|gb|CF992496.1|CF992496
EST:     GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG                         GCTCTGTTTCAAGTTATAGTCCTCCTTACTCT
genomic: GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATGgtatggtact ... cttccttcagGCTCTGTTTCAAGTTATAGTCCTCCTTACTCT
EST: gi|29679578|gb|CB675853.1|CB675853
EST:     GAAGGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG                         GCTCTGTTTCAAGTTATAGTCCTCCTTACTCTCAACTTTAGGGGCACAAGC
genomic: GAAGGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATGgtatggtact ... cttccttcagGCTCTGTTTCAAGTTATAGTCCTCCTTACTCTCAACTTTAGGGGCACAAGC
EST: gi|29667908|gb|CB664183.1|CB664183
EST:     GAAGGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG                         GCTCTGTTTCAAGTTATAGTCCTCCTTACTCTCAACTTTAGGGGCACAAGC
genomic: GAAGGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATGgtatggtact ... cttccttcagGCTCTGTTTCAAGTTATAGTCCTCCTTACTCTCAACTTTAGGGGCACAAGC
EST: gi|218500877|gb|FG965670.1|FG965670
EST:     GGAACCCTTGAATAACAAATGTCATGTGGAGAAACTTAATCATAATG                         GCTCTGTTTCAAGTTATAGTCCTCCTTACTCTTAACTTTAGGGGCACAAGC
genomic: GGAACCCTTGA-TAACAAATGTCATGTGGAGAAACTTAATCATAATGgtatggtact ... cttccttcagGCTCTGTTTCAAGTTATAGTCCTCCTTACTCTCAACTTTAGGGGCACAAGC
EST: gi|29688806|gb|CB685081.1|CB685081
EST:     AACAAATGTCATGCGTAGAAACTTAATCATAATG                         GCTCTGTTTCAAGTTATAGTCCTCCTTACTCTCAACTTTAGGGGCACAAGC
genomic: AACAAATGTCATGTGGAGAAACTTAATCATAATGgtatggtact ... cttccttcagGCTCTGTTTCAAGTTATAGTCCTCCTTACTCTCAACTTTAGGGGCACAAGC

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: 72 (upstream exon), 74 (downstream exon)
Score: 29

GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATGgtatggtact ... cttccttcagGCTCTGTTTCAAGTTATAGTCCTCCTTACTCTCAACTTTAGGGGCACAAGCCTTTTGCAGCTAAAAAACGACAACCAGGCACATGCAGACAAAGTCAAAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATGgtatggtactgttgtgtattccaatttgaatttaaatatctcaaacgctttcaattgaccatctgttcttccttcag

- - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - GGAGAA