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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCAGTGTAGCGTCCTTCTTTGTCAGCCGAGTTGACACACTTATTGACAAAATGCTCGAGAAGATCGGAACACCTGAGGCACTTGCCCTCAGAGGAAAGgtacgcacaatcaaaattacatgcctcctaagtcctagcattaggaatttccaaactagcagttctaatctgcattttggtcactctgtattacag

Basic information

species Oryza sativa
transcript LOC_Os01g70170.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g70170.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G134256_T01 (Zea mays), 5'ss of exon 4
GACCAGTGTAGCGTCCTTCTTTGTCAGCCGAGTTGACACACTTATTGACAAAATGCTCGAGAAGATCGGAACACCTGAGGCACTTGCCCTCAGAGGAAAGgtacgcacaatcaaaattacatgcctcctaagtcctagcattaggaatttccaaactagcagttctaatctgcattttggtcactctgtattacag---
 || || || || |||||||||||||||||||| ||||| ||||||||||||||||| || ||||| |||||||||||||| |||||| | ||||||||||||  || ||  | |||||  |||||| | |         |||| || ||  |||||  |        | |||| | ||  ||  || ||| |      
TACTAGCGTTGCATCCTTCTTTGTCAGCCGAGTGGACACCCTTATTGACAAAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaactataattaactgcctcttga-------tgttagaaacttttaaactgtccacaaagttatgcaatatgaccatactctatcatgtcag

upper sequence: LOC_Os01g70170.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv01s0150g00190.t01 (Vitis vinifera), 5'ss of exon 5
GACCAGTGTAGCGTCCTTCTTTGTCAGCCGAGTTGACACACTTATTGACAAAATGCTCGAGAAGATCGGAACACCTGAGGCACTTGCCCTCAGAGGAAAGgtacgcacaatcaaaattacatgcctcctaagtcctagcattaggaatttccaaactagcagttctaatctgcattttggtcactctgtattacag
 || ||||| || |||||||||||||| || || ||||| || ||||||||  |||| ||||| || ||||| || ||||| ||||  ||| |||||||||||   | ||   || |||||  |    |  ||| |    ||  |  |||  ||   ||  |  ||||| | |||   |     | | | ||  ||
TACAAGTGTTGCCTCCTTCTTTGTCAGTCGGGTAGACACCCTCATTGACAAGTTGCTTGAGAAAATTGGAACTCCAGAGGCCCTTGATCTCCGAGGAAAGgta---ataaattaatttacaatcaaatt--gtcatccttttgagggtttaaaactcag--gacctaatat-catgg-gacttttatatgttctag
















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|86435044|gb|CI106277.1|CI106277
EST:     CACCTGAGGCACTTGCCCTCAGAGGAAAG                         GCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAGAAATTC
genomic: CACCTGAGGCACTTGCCCTCAGAGGAAAGgtacgcacaa ... tgtattacagGCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAGAAATTC
EST: gi|27554160|gb|CA998060.1|CA998060
EST:     AAATGCTCGAGAAGATCGGAACACCTGAGGCACTTGCCCTCAGAGGAAAG                         GCTGCTGTAGCACAGGCAAAGCTAGCCAACCA
genomic: AAATGCTCGAGAAGATCGGAACACCTGAGGCACTTGCCCTCAGAGGAAAGgtacgcacaa ... tgtattacagGCTGCTGTAGCACAGGCAAAGCTAGCCAACCA
EST: gi|29688089|gb|CB684364.1|CB684364
EST:     AAATGCTCGAGAAGATCGGAACACCTGAGGCACTTGCCCTCAGAGGAAAG                         GCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAGAAATTC
genomic: AAATGCTCGAGAAGATCGGAACACCTGAGGCACTTGCCCTCAGAGGAAAGgtacgcacaa ... tgtattacagGCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAGAAATTC
EST: gi|88228697|gb|CI228177.1|CI228177
EST:     ATCGGAACACCTGAGGCACTTGCCCTCAGAGGAAAG                         GCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAGAAATTC
genomic: ATCGGAACACCTGAGGCACTTGCCCTCAGAGGAAAGgtacgcacaa ... tgtattacagGCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAGAAATTC
EST: gi|86258385|gb|CI064738.1|CI064738
EST:     GGCACTTGCCCTCAGAGGAAAG                         GCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAG-AATTC
genomic: GGCACTTGCCCTCAGAGGAAAGgtacgcacaa ... tgtattacagGCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAGAAATTC
EST: gi|88249166|gb|CI249015.1|CI249015
EST:     ACACCTGAGGCACTTGCCCTCAGAGGAAAG                         GCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAGAAATTC
genomic: ACACCTGAGGCACTTGCCCTCAGAGGAAAGgtacgcacaa ... tgtattacagGCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAGAAATTC
EST: gi|88223848|gb|CI223697.1|CI223697
EST:     GGCACTTGCCCTCAGAGGAAAG                         GCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAGAAATTC
genomic: GGCACTTGCCCTCAGAGGAAAGgtacgcacaa ... tgtattacagGCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAGAAATTC
EST: gi|33693591|gb|CF321830.1|CF321830
EST:     AAATGCTCGAGAAGATCGGAACACCTGAGGCACTTGCCCTCAGAGGAAAG                         GCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAGAAATTC
genomic: AAATGCTCGAGAAGATCGGAACACCTGAGGCACTTGCCCTCAGAGGAAAGgtacgcacaa ... tgtattacagGCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAGAAATTC
EST: gi|55410654|gb|CV723030.1|CV723030
EST:     GGCACTTGCCCTCAGAGGAAAG                         GCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAGAAATTC
genomic: GGCACTTGCCCTCAGAGGAAAGgtacgcacaa ... tgtattacagGCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAGAAATTC
EST: gi|88745334|gb|CI768694.1|CI768694
EST:     AAATGCTCGACAAGATCGGAACACCTGAGGCACTTGCCCTCAGAGGAAAG                         GCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAGAAATTC
genomic: AAATGCTCGAGAAGATCGGAACACCTGAGGCACTTGCCCTCAGAGGAAAGgtacgcacaa ... tgtattacagGCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAGAAATTC

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: 75 (upstream exon), 72 (downstream exon)
Score: 67

GACCAGTGTAGCGTCCTTCTTTGTCAGCCGAGTTGACACACTTATTGACAAAATGCTCGAGAAGATCGGAACACCTGAGGCACTTGCCCTCAGAGGAAAGgtacgcacaa ... tgtattacagGCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAGAAATTCTCTGGCCCGAGGTGGGAGGCTTTGGTCAAGAAAGGTGCCAAGAAGCAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCAGTGTAGCGTCCTTCTTTGTCAGCCGAGTTGACACACTTATTGACAAAATGCTCGAGAAGATCGGAACACCTGAGGCACTTGCCCTCAGAGGAAAGgtacgcacaatcaaaattacatgcctcctaagtcctagcattaggaatttccaaactagcagttctaatctgcattttggtcactctgtattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA