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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgcctccatgttgattcagttgtccatggacatttgcatcttttgtttcctgtaactgaatgaaatgttgacggtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAAGGTGGAGGCGGTCCAGGGTACACAGTAATGTAGACGATAGCAAAATACT

Basic information

species Oryza sativa
transcript LOC_Os10g37210.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g37210.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G032222_T02 (Zea mays), 3'ss of exon 17
--gtatttgcctccatgttgattcagttgtccatggacatttgcatcttttgtttcctgt----------aactgaatgaaatgttgacggtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAAGGTGGAGGCGGTCCAGGGTACACAGTAATGTAGACGATAGCAAAATACT
    |  | | |     ||| |     | ||    || | |  |   ||| |  ||   |          | || | | |  |||| || |||||| |||||||| |||||||||||||||||||| |||||||| ||||| ||||||||||||||||| ||||| || ||||||||||||||||       |  ||   
tttgagcttcttaggacttgctcttcctttctggagaaactccctcttttagcctctgctgggccatccaagctaatttacttgttcactgtatcttcagGCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAAGGTGGAGGTGGTCCTGGTTACACAGTAATGTAGAATGCTCAATGATGAA

upper sequence: LOC_Os10g37210.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA15G03360.1 (Glycine max), 3'ss of exon 17
----------gtatttgcctccatgttgattca-gttgtccatggacatttgcatcttttgtttcctgt--aactgaatgaaatgttgacggtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAAGGTGGAGGCGGTCCAGGGTACACAGTAATGTAGACGATAGCAAAATACT-
          | | |  | | | | || | | |   | | | |  ||   |  |   ||||||||||       | |||  |   |||    | | | ||||||||||| |||||||||||||||||||| || || ||||| || || ||||| || || || ||||| ||| |||| |||||| | || | |   | |  
ccattaggatgcaatgtcttgcttctttaataatactatacctacactagtaaagtctttgtttcctacccggtttaattcacacttgttcat-tattcagGCTTGTGATATCAAAGATCCAAAGCAAAATATTGAGTGGACAGTGCCTGAAGGGGGTGGAGGCCCAGGATACTCAGTCATGTAGTC-ATGGTATTGTTCAC

upper sequence: LOC_Os10g37210.1 (Oryza sativa), 3'ss of exon 17
lower sequence: AT2G43400.1 (Arabidopsis thaliana), 3'ss of exon 17
----------gtatttgcctccatgttgattcagttgtc-catggacatttgcatcttttgtttcctgtaactgaa--tgaaat--gttgacggtatctgc----------agGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAAGGTGGAGGCGGTCCAGGGTACACAGTAATGTAGACGATAGCAAAATACT
           |  | | ||  |||    ||  |||     |||   |||    || || | ||  | |    |||  | ||||  |||  |  | | |            |||| ||||||||||||||||||||||| ||||| || ||||| || || |||||||| || || || |  ||  |  | |||||| |  ||  |    || 
gtacgcatcacttgtcgacttgatgcactttgtgttaaagtatgtctattcatgtcattcgattgattttggagaagcttaaattggttttctttttttttttaatctaaaagGCATGTGACATCAAAGATCCAAAGCAGAACATAGAGTGGACAGTGCCTGAAGGTGGTGGAGGCCCTGCCTATTCCCTCATGTAGTCCTTAAGATTCAACA

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|88245808|gb|CI245657.1|CI245657
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
EST: gi|29615151|gb|CB620164.1|CB620164
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
EST: gi|88280721|gb|CI401919.1|CI401919
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
EST: gi|88273475|gb|CI393881.1|CI393881
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
EST: gi|88259171|gb|CI363464.1|CI363464
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
EST: gi|29657656|gb|CB653931.1|CB653931
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAAGCAAAACATGGAATGGACCGTTCCAGAA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
EST: gi|29675569|gb|CB671844.1|CB671844
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
EST: gi|29662394|gb|CB658669.1|CB658669
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTTTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
EST: gi|86889572|gb|CI318763.1|CI318763
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
EST: gi|29637767|gb|CB642776.1|CB642776
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAAGCAAAACATGGAATGGACCGTTCCAGAA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
EST: gi|86859459|gb|CI278866.1|CI278866
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCNCAGA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTC-CAGA
EST: gi|88279088|gb|CI400088.1|CI400088
EST:     AGGTGACCAGAAGCTTCACATAAATGCTCAAAAT-GTTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAACCAAAACATCGAATGGACCGTTCCAGAA
genomic: AGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGT-CTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
EST: gi|88278566|gb|CI399566.1|CI399566
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAGATTGTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
EST: gi|88280463|gb|CI401661.1|CI401661
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCCAAGCCAAACATCGAATG-ACCGTNTCCAGA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGT-TCCAGA
EST: gi|29669361|gb|CB665636.1|CB665636
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
EST: gi|88489550|gb|CI426822.1|CI426822
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
EST: gi|29667105|gb|CB663380.1|CB663380
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
EST: gi|29676401|gb|CB672676.1|CB672676
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
EST: gi|29659147|gb|CB655422.1|CB655422
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
EST: gi|29681493|gb|CB677768.1|CB677768
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
EST: gi|88291777|gb|CI539948.1|CI539948
EST:     AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTTTCTTCATTGCAAG                         GCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA
genomic: AAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAA

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: 63 (upstream exon), 69 (downstream exon)
Score: 25

GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAGgtatttgcct ... gtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAAGGTGGAGGCGGTCCAGGGTACACAGTAATGTAGACGATAGCAAAATACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacatttgcatcttttgtttcctgtaactgaatgaaatgttgacggtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAAGGTGGAGGCGGTCCAGGGTACACAGTAATGTAGACGATAGCAAAATACT
                                     tgttgac  putative branch site (score: 25)
            ttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgcctccatgttgattcagttgtccatggacatttgcatcttttgtttcctgtaactgaatgaaatgttgacggtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAAGGTGGAGGCGGTCCAGGGTACACAGTAATGTAGACGATAGCAAAATACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG