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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggtaccgttggggatgatagatgggattatgtgctatttgatacgttgaagcacgaggctgctcatatatctggtatgttatatctgattgtgtatctcctcctatactgcag

Basic information

species Oryza sativa
transcript LOC_Os01g15110.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15110.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G015509_T01 (Zea mays), 5'ss of exon 4
AGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggtaccgttggggatgatagatgggattatgtgctatttgatacgttgaagcacgaggctgctcatatatctggtatgttatatctgattgtgtatctcctcctatactgcag
|||||||||||||||||||| |||||||||||||||||||||||||| ||||| ||||||||||||||||| ||||| || | |||||||  |||||||||||||||  |||        |||   |||  ||| | |||  ||||||  |||  |||||  |  |  |  | ||| |  |   || ||||| ||| | | ||| ||  | |  | |||
AGGGATCAGGGAATACAAGAGATTCAGCACCAAATTACTGAAGTAAACGAAATTTTCAAAGATCTTGCTGTGCTAGTTCATGGTCAAGGAGCAATGATTGgtatgtg--acc--------tgacgtatgaaatt-tctgcagtttgatgggtttgagcacttgatt--ttgt-tatttcatcaatt-tatctaattatatttcttcttgtttggttcag

upper sequence: LOC_Os01g15110.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G017329_T01 (Zea mays), 5'ss of exon 5
AGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggtaccgttggggatgatagatgggattatgtgctatttgatacgttgaagcacgaggctgctcatatatctggtatgttatatctgattgtgtatctcctcctatactgcag
|||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||| ||||| |||||||| |||||||||  |||||| ||| |||||  || ||  | |  || |     |   | ||  ||||  ||||      || | |  |  |  ||   |   |   ||  ||  |||||   |  |               
AGGGATCAGGGAATACAAGAGATTCAGCACCAAATCACTGAAGTAAATGAAATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtgg--cctttctgaaaaattggatctacattttgaaatttcctacgcca---catg-gattatttttacggcacatg-attggatgggattggaaaatttta------------

upper sequence: LOC_Os01g15110.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G120115_T01 (Zea mays), 5'ss of exon 5
AGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggtaccgttggggatgatagatgggattatgtgctatttgatacgttgaagcacgaggctgctcatatatctggtatgttatatctgattgtgtatctcctcctatactgcag
|||||||||||||||||||| ||||| |||||||| ||||||||||||||||||||||||||||||||||| |||||||| |||||||||  |||||| ||||||||       | |       | || ||||    | |  ||  | ||||| |||||  |  ||||  |  |  |           |||| ||||||| ||||||  | |    |||
AGGGATCAGGGAATACAAGAGATTCAACACCAAATCACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgaccttccttg------caaattggat---atacatttcaacacgttcaagcataaatctgcctacttcccc----------atctaattgtgtttctccttttgtgaaccag

upper sequence: LOC_Os01g15110.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA01G01960.1 (Glycine max), 5'ss of exon 5
AGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgta-tgtggtaccgttggggatgatagatgggattatgtgctatttgatacgttgaagcacgagg-ctgctcatatatctggtatgttatatctgattgtgtatctcctcctatactgcag
|| || || || || |||||||| |||   || |||  |||||||||||| || ||||||||||||||||| || ||||| || ||||||  |||||||||||   | ||              |       ||||    |  | |  |||  |        | | ||   | | | | |   || ||| |  |   |||  |  | |   | |   |   
AGAGAGCAAGGCATTCAAGAAATCCAGTCGCAGATTGGTGAAGTAAATGAGATTTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCAATGATTGgtaacttagtttttcccctcccagttttgctaattacacacattcttgtactatatttttaaatgtctagacttttttttttaattttaaactttgatgtaaaatttccattttgtag---

upper sequence: LOC_Os01g15110.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA16G08200.1 (Glycine max), 5'ss of exon 5
AGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggtaccgttggggatgatagatgg-gattatgtgctatttgatacgttgaagcacgaggctgctcatatat-ctggtatgttatatctgattgtgtatctcctcctatactgcag
||||| || || || |||||||| || || ||||||  |||||| ||||| |||||||||||||||||||| || ||||| || ||||||   ||||||||||  |  | || ||     |  |   |   |||||  |||   ||  ||  ||   | | ||   |  |  | | | |  ||      ||||| ||     |     |   ||  || ||
AGGGAGCAAGGCATTCAAGAAATACAACAGCAAATTGGTGAAGTTAATGAGATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttattccatttccttttgttcttcctgattacttgcatctt--tattttactgaatgaatttatttttctgtacctgttcacgctatctaatgcc--actaaatttcattttgtag

upper sequence: LOC_Os01g15110.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA16G13410.1 (Glycine max), 5'ss of exon 5
AGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggtaccgttggggatgatagatgg-gattatgtgctatttgatacgttgaagcacgaggctgctcatat-atctggtat-gttatatctgattgtgtatctcctcctatactgcag
||||| || || || |||||||| ||||| ||||||  |||||| ||||| |||||||||||||||||||| || ||||| || ||||||   ||||||||||  |  | || ||     |  |   |   | |||  ||    ||  ||  ||   | ||    ||||||| || | || ||     || || | ||| ||||                  
AGGGAGCAAGGCATTCAAGAAATACAGCAGCAAATTGGTGAAGTTAATGAGATCTTCAAAGATCTTGCTGTACTTGTCCATGAGCAAGGAGCCATGATTGgtaatttattccattcccttttgttcttcctggttacttgtatctt--tattttactgtac----ctgctcacattacctagtgccactaaatttcattttgtag-----------------

upper sequence: LOC_Os01g15110.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA09G33950.1 (Glycine max), 5'ss of exon 5
AGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgta-tgtggtaccgttgggg-atgatagatgggattatgtgctatttgatacgttgaagcacgaggctgctcatatatctggtatgttatatctgattgtgtatctcctcctatactgcag
|| ||||| || || ||||||||||||   ||||||  |||||||||||| || ||||||||||||||||| || ||||| || ||||||  |||||||||||   | ||    |      ||| |       ||||    |  | |  | | |      |            || |  || | | || ||| ||||     || |  | | ||  || ||
AGAGATCAAGGTATTCAAGAAATTCAGTCGCAAATTGGTGAAGTAAATGAGATTTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCAATGATTGgtaacttagtgttttcccttcatgcttttgctaattacacacattctagttc-taactctatttttaaatgtctagacttgtttttttttatttgatgtaaaatat--ttccattttgtag

upper sequence: LOC_Os01g15110.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G46860.1 (Arabidopsis thaliana), 5'ss of exon 5
AGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggtaccgttggggatgatagatgggattatgtgctatttgatacgttgaagcacgaggctgctcatatatctggtatgttatatctgattgtgtatctcctcctatactgcag
|| || || |||||||||||||| || || ||||||  ||| || || || || |||||||||||||| ||||| ||  |||||||||||   ||||| ||||      ||  |     |   |  ||  ||  |  |||  ||  |   | || ||   |||    | | | | |||    ||                                   
AGAGAGCAAGGAATACAAGAAATCCATCAGCAAATTGGTGAGGTTAACGAGATATTCAAAGATCTTGCGGTTCTGGTTAACGATCAAGGAGTCATGATAGgta---aagacaatctattaaacttaattaga--acatgcccttgaa---gctgcagttagagaactcacttttttctttcttgcag--------------------------------

upper sequence: LOC_Os01g15110.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv16s0039g01850.t01 (Vitis vinifera), 5'ss of exon 5
AGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggtaccgttggggatgatagatgggattatgtgctatttgatacgttgaagcacgaggctgctcatatatctggtatgttatatctgattgtgtatctcctcctatactgcag
|| || || ||||| |||||||||||||| || |||  ||| || |||||||| ||||||||||| ||||| || |||||||  ||||||   |||||||||| ||   ||                    ||| | |  | |  | ||| ||    |  ||  || ||  ||    ||   || |  |   || ||   | |   || | |  |||||
AGAGAGCAAGGAATCCAAGAAATTCAGCAACAGATTGGTGAGGTGAATGAAATTTTCAAAGATCTGGCTGTACTGGTCCACGGACAAGGAACTATGATTGgtaagtcacac--------------------attgt-tcttgtccgttacatttcctcttgaaacttcttgtaatgttgacttgatcaaatagagtgctgaacatatctt-tcttgcag

upper sequence: LOC_Os01g15110.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv02s0012g01850.t01 (Vitis vinifera), 5'ss of exon 5
AGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggtaccgttggggatgatagatgggattatgtgctatttgatacgttgaagcacgaggctgctcatatatctggtatgttatatctgattgtgtatctcctcctatactgcag
||||| ||||||||||||||||| ||||||||||||   || || ||||| || ||||||||||||||||| || ||||| || ||||||   ||||||||||  |  |     ||    |  |   | |  ||    ||||||   |    |||  || |  ||||    |   |    | | |  | || |                          
AGGGAGCAGGGAATACAAGAAATCCAGCACCAAATTGGCGAGGTGAATGAGATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcat----ctgactctcttgtctagagtt---cgctattcccttt-ctgattcaggctgctgactctcatttcaatttctcttttcag--------------------------

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|300216044|gb|HO088670.1|HO088670
EST:     AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTG                         ATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
genomic: AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggta ... tatactgcagATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
EST: gi|38477394|gb|CF961527.1|CF961527
EST:     AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTG                         ATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
genomic: AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggta ... tatactgcagATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
EST: gi|88502344|gb|CI429850.1|CI429850
EST:     AATCTTCAAAGATCTTGGTGTTCTAGTCCACGATCAAGGACAAATGATTG                         ATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
genomic: AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggta ... tatactgcagATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
EST: gi|29666448|gb|CB662723.1|CB662723
EST:     AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTG                         ATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
genomic: AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggta ... tatactgcagATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
EST: gi|58613206|gb|CK040918.1|CK040918
EST:     TAGTCCACGATCAAGGACAAATGATTG                         ATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
genomic: TAGTCCACGATCAAGGACAAATGATTGgtatgtggta ... tatactgcagATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
EST: gi|58680591|gb|CK069278.1|CK069278
EST:     AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTG                         ATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
genomic: AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggta ... tatactgcagATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
EST: gi|88504172|gb|CI431678.1|CI431678
EST:     ATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTG                         ATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
genomic: ATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggta ... tatactgcagATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
EST: gi|86593942|gb|CI260171.1|CI260171
EST:     AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTG                         ATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
genomic: AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggta ... tatactgcagATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
EST: gi|88218005|gb|CI217854.1|CI217854
EST:     AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTG                         ATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
genomic: AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggta ... tatactgcagATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
EST: gi|29662791|gb|CB659066.1|CB659066
EST:     AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTG                         ATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
genomic: AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggta ... tatactgcagATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
EST: gi|88216094|gb|CI215943.1|CI215943
EST:     AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTG                         ATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
genomic: AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggta ... tatactgcagATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
EST: gi|88200203|gb|CI200053.1|CI200053
EST:     CAAGGACAAATGATTG                         ATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCCA
genomic: CAAGGACAAATGATTGgtatgtggta ... tatactgcagATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
EST: gi|29662790|gb|CB659065.1|CB659065
EST:     AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTG                         ATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
genomic: AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggta ... tatactgcagATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA
EST: gi|218500481|gb|FG960261.1|FG960261
EST:     AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTG                         ATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCCA
genomic: AATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggta ... tatactgcagATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAA

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), 75 (downstream exon)
Score: 85

AGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggta ... tatactgcagATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAAAAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggtaccgttggggatgatagatgggattatgtgctatttgatacgttgaagcacgaggctgctcatatatctggtatgttatatctgattgtgtatctcctcctatactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT