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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcattactgaatcttgttaagtttatcctttgcactctgagcttctctctatagaaattgtctgacttggtacatttgctgatgcag

Basic information

species Oryza sativa
transcript LOC_Os06g39640.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GRMZM2G079080_T02 (Zea mays), 5'ss of exon 20
GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcattactgaatcttgttaagtttatcctttgcactctgagcttct--ctctatagaaattgtctgacttggtacatttgctgatgcag
||||| |||||||| ||||||||||| ||||| |||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||  ||| | ||      || || |||| ||| ||||||| ||| |||    || | |   |||| ||| |  | | |  | | |||||||||
GGAACGAGTAGGCCTGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtaatgcacttcttttatatgctatgtttgtcccttgcactttgaactttgaactttttgagaattttcttagattg-atgtatactgatgcag

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 20
lower sequence: AC189879.3_FGT003 (Zea mays), 5'ss of exon 19
GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcattactgaatct-tgttaagtttatcctttgcactctgagcttctctctatagaaattgtctgacttggtacat---ttgctgatgcag
|||||||||||||| ||||||||||| ||||| |||||||||||||||||||| |||||||||||||| ||| |||||||||||||||||||||||||  ||| | ||   | | | |||  ||| ||||||||||  | |  || | | |  |||| ||   |  |||| || |    ||  ||||||||
GGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACACgtaacgcacttctttgtatattttatatttgtcctttgcacatttaaattttttttg-agaattttcttagcttgttatacatgttattgatgcag

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA17G12850.1 (Glycine max), 5'ss of exon 20
GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcattactgaatcttgttaagtttatcctttgcactctgagcttctctctatagaaattgtctgacttggtacatttgctgatgcag
|| |||||||| |||||||| || || || || ||||| ||||||||||||||||| || || || ||  |  |||| |||||| | |||||||||||    |   ||   ||   | |   |||   ||    |||     ||||    || |||||   || | ||  |    |||  |      
GGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACACgtaaaaaacctct--ctcacatcat-cttaaatttgttgctccattattcttgtgat-gaaataacctca-ttattttgattgtag------

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA06G23920.1 (Glycine max), 5'ss of exon 20
GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcattactgaatcttgttaagtttatcctttgcactctgagcttctctctatagaaattgtctgacttggtacatttgctgatgcag
|| |||||||| ||||| ||||| |||||||| ||||| |||||||||||||||||||| || || ||| |  | || |||||  | |||||||||||    ||| ||  ||         |  ||  |||   ||||   ||  | |  | |  |  |  |   | |   |  || | ||  |   
GGTACAAGTAGACCAGCACACTATCACGTCCTCTGGGACGAGAACAATTTCACTGCAGATGAGATTCAGTCTCTAACCAACAATTTGTGCTACACgtaaacgatttctctattcctcatcttgaattttttattctct---ctatttttaagatgacataaccttcctaacattttggttgcag---

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 20
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 5'ss of exon 18
GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacg------gca-----ttactgaatcttgttaagtttatcctttgcactc--tgagcttctctctatag---------------aaattgtctgacttggtacatttgctgatgcag------------
                           ||  | |||||||||||||||||||| ||||| | ||| ||  | ||||| ||||| ||||||||||| || |      |||     |   ||  | ||| ||||  | |  ||    |    |||  ||   | |  |                |||||||     |    || ||| | ||   |             
---------------------------GTTTTATGGGATGAGAACAATTTCACAGCAGATGGAATTCAATCCTTGACGAACAATCTTTGCTACACATATGCAAGGTGCACACGATCGGTGTCTGTTGgtaagcctgtttttccttcctaatgaagtttcatatgcatctgcattcaagaattaaattgttcccttgaaaactttttcggaaaaaaatgtcaaagatt

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|86492970|gb|CI135603.1|CI135603
EST:     GCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC                         TTATGCACGGTGCACACGCTCTGTTTCTGTTG
genomic: GCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcatt ... gctgatgcagTTATGCACGGTGCACACGCTCTGTTTCTGTTG
EST: gi|163920974|gb|EG710111.1|EG710111
EST:     AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC                         TTATGCACGGTGCACACGCTCTGTTTCTGTTG
genomic: AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcatt ... gctgatgcagTTATGCACGGTGCACACGCTCTGTTTCTGTTG
EST: gi|86435965|gb|CI107198.1|CI107198
EST:     AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC                         TTATGCACGGTGCACACGCTCTGTTTCTGTTG
genomic: AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcatt ... gctgatgcagTTATGCACGGTGCACACGCTCTGTTTCTGTTG
EST: gi|87016539|gb|CI273749.1|CI273749
EST:     AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC                         TTATGCACGGTGCACACGCTCTGTTTCTGTTG
genomic: AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcatt ... gctgatgcagTTATGCACGGTGCACACGCTCTGTTTCTGTTG
EST: gi|29636941|gb|CB641950.1|CB641950
EST:     AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC                         TTATGCACGGTGCACACGCTCTGTTTCTGTTG
genomic: AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcatt ... gctgatgcagTTATGCACGGTGCACACGCTCTGTTTCTGTTG
EST: gi|88225229|gb|CI225145.1|CI225145
EST:     AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC                         TTATGCACGGTGCACACGCTCTGTTTCTGTTG
genomic: AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcatt ... gctgatgcagTTATGCACGGTGCACACGCTCTGTTTCTGTTG
EST: gi|86594915|gb|CI258169.1|CI258169
EST:     AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC                         TTATGCACGGTGCACACGCTCTGTTTCTGTTG
genomic: AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcatt ... gctgatgcagTTATGCACGGTGCACACGCTCTGTTTCTGTTG
EST: gi|29674861|gb|CB671136.1|CB671136
EST:     AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC                         TTATGCACGGTGCACACGCTCTGTTTCTGTTG
genomic: AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcatt ... gctgatgcagTTATGCACGGTGCACACGCTCTGTTTCTGTTG
EST: gi|88906357|gb|CI375429.1|CI375429
EST:     AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTG-TACAC                         TTATGCACGGTGCACACGCTCTGTTTCTGTTG
genomic: AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcatt ... gctgatgcagTTATGCACGGTGCACACGCTCTGTTTCTGTTG
EST: gi|8404400|gb|AU091754.1|AU091754
EST:     AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC                         TTATGCACGGTGCACACGCTCTGTTTCTGTTG
genomic: AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcatt ... gctgatgcagTTATGCACGGTGCACACGCTCTGTTTCTGTTG
EST: gi|86431420|gb|CI085031.1|CI085031
EST:     AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC                         TTATGCACGGTGCACACGCTCTGTTTCTGTTG
genomic: AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcatt ... gctgatgcagTTATGCACGGTGCACACGCTCTGTTTCTGTTG
EST: gi|86477748|gb|CI120381.1|CI120381
EST:     AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC                         TTATGCACGGTGCACACGCTCTGTTTCTGTTG
genomic: AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcatt ... gctgatgcagTTATGCACGGTGCACACGCTCTGTTTCTGTTG
EST: gi|29636972|gb|CB641981.1|CB641981
EST:     AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGGTACAC                         TTATGCACGGTGCACACGCTCTGTTTCTGTTG
genomic: AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcatt ... gctgatgcagTTATGCACGGTGCACACGCTCTGTTTCTGTTG
EST: gi|27576993|gb|CA999687.1|CA999687
EST:     AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC                         TTATGCACGGTGCACACGCTCTGTTTCTGTTG
genomic: AATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcatt ... gctgatgcagTTATGCACGGTGCACACGCTCTGTTTCTGTTG

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: 48 (upstream exon), 32 (downstream exon)
Score: 10

GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcatt ... gctgatgcagTTATGCACGGTGCACACGCTCTGTTTCTGTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcattactgaatcttgttaagtttatcctttgcactctgagcttctctctatagaaattgtctgacttggtacatttgctgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG