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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaattggcttctccctaacggatacattttgtggtctttctcctaagtactccctccgtcccaaaaaaaaggcaacctagaaggggatgtgacccctcctagtataacgaatctgaaaggagggagtacgatgccttttttggtttttgttccagtcatctgaacgctcatggtattgcatgtacttgcag

Basic information

species Oryza sativa
transcript LOC_Os10g41710.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g41710.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G090872_T02 (Zea mays), 5'ss of exon 5
GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaattggcttctccctaacggatacattttgtggtctttctcctaagtactccctccgtcccaaaaaaaaggcaacctagaaggggatgtgacccctcctagtataacgaatctgaaaggagggagtacgatgccttttttggtttttgttccagtcatctgaacgctcatggtattgcatgtacttgcag
                 |  | ||| |    | |  | | |    |   | ||| | | | ||  |||   |  | | | |  | |    ||  | |  | | |       | ||  |||  |  || |   |  |    |||| | | |    ||        |||  |||   ||   ||  | | || ||| |  | |   | | |       |||  | |   
----------------AATGTACTTTTACTTTTACCGTAGTACAATGCTCATAATGTAGA-ATACTGTAACCAGTTTGC-ACTTGCAGGTTCTCTTCTCAGACATCAATG-CTTATGAGgtaac-tggcttattttctcttaacaattttttttggccttgccgcgagccctacatt---ttccgattcaatcaacctagctgacttagctcattgtgttgtag---

upper sequence: LOC_Os10g41710.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G050961_T05 (Zea mays), 5'ss of exon 5
-------------GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaattggcttctccctaacggatacattttgtggtctttctcctaagtactccctccgtcccaaaaaaaaggcaacctagaaggggatgtgacccctcctagtataacgaatctgaaaggagggagtacgatgccttttttggtttttgttccagtcatctgaacgctcatggtattgcatgtacttgcag
             ||||||||||| ||||| |||||||||||||||| ||  ||   |||||  ||||   |   |||| ||| ||| |      ||   |||| | |      |   |  ||||||||     ||  |  | | |  |  | ||                                                                                     
TTTGCACTTGCAGGTTCTCTTCTCAGACATCAATGCTTATGAGgtaactggcttattttctct-taacaatt---ttttttggccttgcc-----gtgagccctacattttccgattcaatcaacctagc---tgacttagctcattgtgttgtag------------------------------------------------------------------------------------

upper sequence: LOC_Os10g41710.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G050961_T04 (Zea mays), 5'ss of exon 4
GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaattggcttctccctaacggatacattttgtggtctttctcctaagtactccctccgtcccaaaaaaaaggcaacctagaaggggatgtgacccctcctagtataacgaatctgaaaggagggagtacgatgccttttttggtttttgttccagtcatctgaacgctcatggtattgcatgtacttgcag
                 |  | ||| |    | |  | | |    |   | ||| | | | ||  |||   |  | | | |  | |    ||  | |  | | |       | ||  |||  |  || |   |  |    |||| | | |    ||      | |  ||     |    |||  | | || ||| |  | |   | | |       |||  | |   
----------------AATGTACTTTTACTTTTACCGTAGTACAATGCTCATAATGTAGA-ATACTGTAACCAGTTTGC-ACTTGCAGGTTCTCTTCTCAGACATCAATG-CTTATGAGgtaac-tggcttattttctcttaacaattttttttggcct---tgccgtgagccctacattttccgattcaatcaacctagctgacttagctcattgtgttgtag---

upper sequence: LOC_Os10g41710.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G050961_T01 (Zea mays), 5'ss of exon 5
GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaattggcttctccctaacggatacattttgtggtctttctcctaagtactccctccgtcccaaaaaaaaggcaacctagaaggggatgtgacccctcctagtataacgaatctgaaaggagggagtacgatgccttttttggtttttgttccagtcatctgaacgctcatggtattgcatgtacttgcag
||||||||||| ||||| |||||||||||||||| ||  ||   |||||  ||||   |   |||| ||| ||| |      ||   |||| | |      |   |  ||||||||     ||  |  | | |  |  | ||                                                                                     
GTTCTCTTCTCAGACATCAATGCTTATGAGgtaactggcttattttctct-taacaatt---ttttttggccttgcc-----gtgagccctacattttccgattcaatcaacctagc---tgacttagctcattgtgttgtag------------------------------------------------------------------------------------

upper sequence: LOC_Os10g41710.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G090872_T03 (Zea mays), 5'ss of exon 5
GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaattggcttctccctaacggatacattttgtggtctttctcctaagtactccctccgtcccaaaaaaaaggcaacctagaaggggatgtgacccctcctagtataacgaatctgaaaggagggagtacgatgccttttttggtttttgttccagtcatctgaacgctcatggtattgcatgtacttgcag
||||||||||| ||||| |||||||||||||||| ||  ||   |||||  ||||   |   |||| ||| ||| |  | |      |||| | |      |   |  ||||||||     ||  |  | | |  |  | ||                                                                                     
GTTCTCTTCTCAGACATCAATGCTTATGAGgtaactggcttattttctct-taacaatt---ttttttggccttgccgcgag-----ccctacattttccgattcaatcaacctagc---tgacttagctcattgtgttgtag------------------------------------------------------------------------------------

upper sequence: LOC_Os10g41710.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G090872_T04 (Zea mays), 5'ss of exon 6
-------------GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaattggcttctccctaacggatacattttgtggtctttctcctaagtactccctccgtcccaaaaaaaaggcaacctagaaggggatgtgacccctcctagtataacgaatctgaaaggagggagtacgatgccttttttggtttttgttccagtcatctgaacgctcatggtattgcatgtacttgcag
             ||||||||||| ||||| |||||||||||||||| ||  ||   |||||  ||||   |   |||| ||| ||| |  | |      |||| | |      |   |  ||||||||     ||  |  | | |  |  | ||                                                                                     
TTTGCACTTGCAGGTTCTCTTCTCAGACATCAATGCTTATGAGgtaactggcttattttctct-taacaatt---ttttttggccttgccgcgag-----ccctacattttccgattcaatcaacctagc---tgacttagctcattgtgttgtag------------------------------------------------------------------------------------

upper sequence: LOC_Os10g41710.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv15s0021g00830.t01 (Vitis vinifera), 5'ss of exon 6
GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaattggcttctccctaacggatacattttgtggtctttctcctaagtactccctccgtcccaaaaaaaaggcaacct-agaaggggatgtgacccctcctagtataacgaatctgaaaggagggagtacgatgccttttttggtttttgttccagtcatctgaacgctcatggtattgcatgtacttgcag
||||| ||||| ||||||||||||||||||||||||  | || ||   |  ||     ||  |||  |  | |  | | |||         |   ||      ||||| | | | | ||  ||| ||  ||  |||                                                                                            
GTTCTTTTCTCAGACATAAATGCTTATGAGgtaaat--actgact---ctgtagaaattaagtttattcatatagcacttaatatgatttactagcctttttcaaaggtacctttacaaatggaagtt-cctatcc--------------------------------------------------------------------------------------------

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|86506181|gb|CI148814.1|CI148814
EST:     GTTCTCTTCTCTGACATAAATGCTTATGAG                         GTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTGATCTG
genomic: GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaat ... gtacttgcagGTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTGATCTG
EST: gi|89171890|gb|CI040400.1|CI040400
EST:     GTTCTCTTCTCTGACATAAATGCTTATGAG                         GTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTGATCTG
genomic: GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaat ... gtacttgcagGTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTGATCTG
EST: gi|13165574|gb|AU174371.1|AU174371
EST:     GTTCTCTTCTCTGACATAAATGCTTATGAG                         GTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTGATCTG
genomic: GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaat ... gtacttgcagGTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTGATCTG
EST: gi|86415751|gb|CI029762.1|CI029762
EST:     GTTCTCTTCTCTGACATAAATGCTTATGAG                         GTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTGATCTG
genomic: GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaat ... gtacttgcagGTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTGATCTG
EST: gi|86531799|gb|CI172005.1|CI172005
EST:     GTTCTCTTCTCTGACATAAATGCTTATGAG                         GTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTGATCTG
genomic: GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaat ... gtacttgcagGTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTGATCTG
EST: gi|86846350|gb|CI280735.1|CI280735
EST:     GTTCTCTTCTCTGACATAAATGCTTATGAG                         GTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTNGATCT
genomic: GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaat ... gtacttgcagGTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCT-GATCT
EST: gi|89168879|gb|CI020960.1|CI020960
EST:     GTTCTCTTCTCTGACATAAATGCTTATGAG                         GTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTGATCTG
genomic: GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaat ... gtacttgcagGTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTGATCTG
EST: gi|86415935|gb|CI029946.1|CI029946
EST:     GTTCTCTTCTCTGACATAAATGCTTATGAG                         GTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTGATCTG
genomic: GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaat ... gtacttgcagGTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTGATCTG
EST: gi|15009090|gb|AU223478.1|AU223478
EST:     GTTCTCTTCTCTGACATAAATGCTTATGAG                         GTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTGATCTG
genomic: GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaat ... gtacttgcagGTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTGATCTG
EST: gi|86532547|gb|CI172753.1|CI172753
EST:     GTTCTCTTCTCTGACATAAATGCTTATGAG                         GTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTGATCTG
genomic: GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaat ... gtacttgcagGTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTGATCTG

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: 30 (upstream exon), 75 (downstream exon)
Score: 118

GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaat ... gtacttgcagGTGGACCTGGGTACCGATGAGAAGCACTGCTTCTGCCGTGAGTCTGATCTGTTAGCCGTTGTTGAATGAGTTTTTACTCCAAAATCGGAGTGTCCAATTC




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