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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCCGAAGCAGCTGAACGCGCCGCTGGAGGAGGTGGATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagcaaccaccaaaaaaaaagtgcgtggattgttcagtgtttggtccaccgacgcattgctgaattgtggcaatctgtttggtgcag

Basic information

species Oryza sativa
transcript LOC_Os03g52840.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G135283_T01 (Zea mays), 5'ss of exon 3
TGGCCGAAGCAGCTGAACGCGCCGCTGGAGGAGGTGGATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccag-----caaccaccaaaaaaaaagtgcgtggattgttcagt-------gtttggtccaccgacgcattgctgaattgtggca--atctgtttggtgcag-------------------------------------------
||| | |||||| |||||||||||||||| ||||| || |||||||| || ||||||||||||||||||||||||||||||||||||||  |        ||  || |       |  | |||    | ||||||         ||   |   |   |  ||| || ||| |   |  || |||||  | |                                             
TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCTGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtccctgtttcttcagtcatcttttccta--tacgtactcttttcagtcatttccacttctccagtcattgttttgttggattatattattatttgtttttttccaagaccctactgagttctgtccgtgtcaatgcgtctggtggcag

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA14G36280.2 (Glycine max), 5'ss of exon 3
TGGCCGAAGCAGCTGAACGCGCCGCTGGAGGAGGTGGATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaa---ccagcaaccaccaaaaaaaaagtgcgtggatt---gttcagtgtttggtccaccgacgcattgctgaattgt-------ggcaatctgtttggtgcag---------
|||   |||||||| ||||  || || ||||   | |||||||||||||||||||| ||||| | ||| ||||| || ||||||||||| |   | ||   |   | | |      ||| | | ||    || |    |  |    ||||     |||   |||||       || | | |||||| | | |         
TGGATAAAGCAGCTCAACGATCCTCTCGAGGCCATCGATCCCGAGATCGCCGACATAATCGAACTCGAAAAGGCGCGTCAATGGAAGgtgaatccgagtttcattctacagtgctttgctttgctttgaattaataaataagctttccgattttatgcatgattgttgtttacggaagtttgtttg-tacggaatttgtag
















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|58592438|gb|CF990746.1|CF990746
EST:     ATCGCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG                         GGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
genomic: ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagca ... tttggtgcagGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
EST: gi|88424270|gb|CI581825.1|CI581825
EST:     ATCCCGAGATCGCCAACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG                         GGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
genomic: ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagca ... tttggtgcagGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
EST: gi|88428580|gb|CI565048.1|CI565048
EST:     ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG                         GGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
genomic: ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagca ... tttggtgcagGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
EST: gi|88760569|gb|CI770125.1|CI770125
EST:     ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG                         GGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
genomic: ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagca ... tttggtgcagGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
EST: gi|29634685|gb|CB639694.1|CB639694
EST:     ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG                         GGTCTGGAGCTCATCCC
genomic: ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagca ... tttggtgcagGGTCTGGAGCTCATCCC
EST: gi|88734102|gb|CI757610.1|CI757610
EST:     ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG                         GGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
genomic: ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagca ... tttggtgcagGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
EST: gi|88397959|gb|CI583277.1|CI583277
EST:     ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG                         GGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
genomic: ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagca ... tttggtgcagGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
EST: gi|88424301|gb|CI581856.1|CI581856
EST:     ATCCCGAGATCGCCAACATCATCGAGCACGACAAGGCCCGCCAATGGAAG                         GGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
genomic: ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagca ... tttggtgcagGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
EST: gi|88398541|gb|CI595942.1|CI595942
EST:     ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG                         GGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
genomic: ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagca ... tttggtgcagGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
EST: gi|88826721|gb|CI777286.1|CI777286
EST:     ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG                         GGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
genomic: ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagca ... tttggtgcagGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
EST: gi|88344989|gb|CI625835.1|CI625835
EST:     ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG                         GGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
genomic: ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagca ... tttggtgcagGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
EST: gi|58605751|gb|CK033784.1|CK033784
EST:     ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG                         GGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAC
genomic: ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagca ... tttggtgcagGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
EST: gi|88745591|gb|CI768951.1|CI768951
EST:     ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG                         GGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
genomic: ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagca ... tttggtgcagGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
EST: gi|87023586|gb|CI286337.1|CI286337
EST:     ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG                         GGTCTGGAGCTCATCCCGTCGGAGAACTTCAACTCGGTGTCAGTGATGCAG
genomic: ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagca ... tttggtgcagGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
EST: gi|88733450|gb|CI756627.1|CI756627
EST:     ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG                         GGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
genomic: ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagca ... tttggtgcagGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
EST: gi|86901078|gb|CI306267.1|CI306267
EST:     ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG                         GGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
genomic: ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagca ... tttggtgcagGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
EST: gi|58691682|gb|CK080369.1|CK080369
EST:     ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG                         GGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
genomic: ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagca ... tttggtgcagGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
EST: gi|58605862|gb|CK033895.1|CK033895
EST:     ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG                         GGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG
genomic: ATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagca ... tttggtgcagGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAG

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), 75 (downstream exon)
Score: 106

TGGCCGAAGCAGCTGAACGCGCCGCTGGAGGAGGTGGATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagca ... tttggtgcagGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCCGAAGCAGCTGAACGCGCCGCTGGAGGAGGTGGATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAGgtaaccagcaaccaccaaaaaaaaagtgcgtggattgttcagtgtttggtccaccgacgcattgctgaattgtggcaatctgtttggtgcag

- - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG