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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacgaagcttgctactcccagctccttcataatgtgttattttattagtgtcaaaatttaatgaagtgatgctttcctgtcctgttctatcatattttgccgtgtctcatatcctgtgaactgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAA

Basic information

species Oryza sativa
transcript LOC_Os06g45120.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 9
gtacacgaagcttgctactcccagctccttcataatgtgttattttattagtgtcaaaatttaatgaagtgatgctttcctgtcctgttctatcatattttgccgtgtctcatatcctgtgaactgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAA
                                                ||   |||    |||   |||||   | | | ||  ||  | | | |||   |  | ||  | ||  | | ||   | ||| |||||||| |||||||| || || |||||||||||||| || |||||||| |||||||| || ||||||||||| ||||| |||||||||||||| ||||| |
-----------------------------------------------gtaaactcagttgttacc-aagtgtctcctccatgatctaat-tgtgatagcct-tcatgcttaatgacttctg--ttttttacagCGTGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATTCCTGGTGCTTTTGGTTGTGGTAAAACAGTCATTAGTCAGGCTCTTTCTA

upper sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 9
gtacacgaagcttgctactcccagctccttcataatgtgttattttattagtgtcaaaatttaatgaagtgatgctttcctgtcctgttctatcatattttgccgtgtctcatatcctgtgaactgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAA
                                                ||   |||   | | || |||||   | | | |   ||  | | | |||  ||  | ||  | ||  | | ||  || ||| |||||||| |||||||| || || |||||||||||||| || |||||||| || |||||||| ||||||||||| |||||||||||||||||||| ||||| |
-----------------------------------------------gtaaactcagt-tgttatcaagtgtctcatccataatctaat-tgtgatagctt-tcatgcgtaatgacttctg--ctttttacagCGTGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATACCTGGAGCTTTTGGTTGTGGTAAAACTGTCATTAGTCAGGCTCTTTCTA

upper sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 9
gtacacgaagcttgctactcccagctccttcataatgtgttattttattagtgtcaaaatttaatgaagtgatgctttcctgtcctgttctatcatattttgccgtgtctcatatcctgtgaactgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAA
                                      || |||  | | |  | ||   ||  |  |||| || |     ||| | |     ||| | |||| |  |    | |  |     ||||| ||||||||| |||||||| || || || || |||||||| ||||| ||||| |||||||| || ||||| ||||| |||||||| || |||||||||||||| |
--------------------------------------gtgatt--actcg-attaattcttcttacagtggtgata----gtcatttgaatacatgtgttgctgattgctttcttttc----ctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA

upper sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 9
gtacacgaagcttgctactcccagctccttcataatgtgttattttattagtgtcaaaatttaatgaagtgatgctttcctgtcctgtt-ctatcatat-tttgccgtgtctcatatcctgtgaactgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAA
                                            | |||||  |  ||| | |||| | |     | | ||   || |  ||    ||   |||  |||| |       | |    |  | ||||||||| |||||||| || || || || ||||| || ||||||||||| || ||||| |||||||||||||||||||| ||||| ||||| || ||||| |
-------------------------------------------gtaattagcatacaaactaaatgtattatcagtattctcatctatggctgctgtaagcttgaagtgtgttcctgatttttgtttcatctcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTCGGTGGAACTTGTGCCATACCTGGGGCATTTGGTTGTGGAAAAACAGTCATCAGTCAAGCTCTTTCTA

upper sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 9
gtacacgaagcttgctactcccagctccttcataatgtgttattttattagtgtcaaaatttaatgaagtgatgctttcctgtcctgttctatcatattttgccgtgtctcatatcctgtgaactgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAA
                                        || |  ||   ||||||  ||||        || | |  ||  | | ||  |     | || | |   ||    || | || ||  | | |||||||| || ||||| || ||||||||||| || || || |||||||| |||||||| |||||||| ||||| ||||| ||||| ||||| || ||||| |
---------------------------------------gtaatgcatcc-tgtcaaggtttagc----ccatacatgactaccattttgaaatgggtatttctgatactt---tcttttgtac--tctacagCGTGTTCTCGATGCTCTCTTTCCCTCAGTCCTGGGTGGGACTTGTGCAATTCCTGGGGCATTTGGCTGTGGGAAAACAGTCATCAGTCAAGCTCTTTCCA

upper sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 9
gtacacgaagcttgctactcccagctccttcataatgtgttattttattagtgtcaaaatttaatgaagtgatgctttc-ctgtcctgttctatcatattttgccgtgtctcatatcctgtgaactgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAA
                            ||   ||||| ||||  | ||    |   ||||||||  |  ||||  |   || || || | | |  ||| |||        | | | |      |  ||| |||||| | || ||||| |||||||| || || || ||||| || ||||| |||||||| || || |||||||| ||||| || ||||||||||| || ||||
--------------------------atttttcaatgt-ttatcatcttctgttttgaatttaattcatggatgagtcagctatcatgctgt-ttgtatgttgatccactccgttttc------ccctttacagCGTATTCTGGATGCTCTATTTCCATCTGTCCTCGGAGGTACCTGTGCAATTCCTGGTGCGTTCGGTTGTGGGAAAACAGTTATTAGTCAGGCTCTGTCAA

upper sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 9
gtacacgaagcttgctactcccagctccttcataatgtgttattttattagtgtcaaaatttaatgaagtgatgctttcctgtcctgttctatcatattttgccgtgtctcatatcctgtgaactgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAA
                            |||| |||   | | |  | ||   | | |  ||| | |  ||    | | ||||     |||    ||||||  | |   | || |  |||   |  ||| |||||| |||| ||||| ||||| || || ||||||||||| ||||| || |||||||| |||||||| |||||||| |||||||||||||| || || || |
-------------------------ggtttca-aattcatgactgaagtatatttatatgttacttacatg----tgtgctgtgaatatctcaagtattttctctttgttgat-tgttgtc--ccctttgcagCGTATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATTCCTGGTGCATTTGGATGTGGAAAGACTGTCATTAGTCAAGCGCTCTCTA

upper sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 9
gtacacgaagcttgctactcccagctccttcataatgtgttattttattagtgtcaaaatttaatgaagtgatgctt-tcctgtcctgttc-tatcatattttgccgtgtctcatatcctgtgaactgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAA
                                   ||||||        |    |  | | |  |   ||| |  || |  ||  |||      | | |||     |  |||  | |    ||  |  ||| |||||  |||| ||||| || ||||| || || |||||||| || || || |||||||| |||||||||||||| || || ||||| ||||| |||||||| |
-----------------------------------tgtgttgggaatccatgaaccgattatgttttcgtgctttttatattgcactgccaacgttaaattcctttgcttctattttgaattgccccttttgcagCGAATACTGGATGCTCTGTTTCCGTCTGTCCTTGGAGGTACCTGCGCCATTCCTGGTGCATTTGGTTGTGGGAAGACCGTCATCAGTCAAGCACTTTCTA

upper sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 8
gtacacgaagcttgctactcccagctccttcataatgtgttattttattagtgtcaaaatttaatgaagtgatgctttcctgtcctgttctatcatattttgccgtgtctcatatcctgtgaactgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAA
                                                                                |||    || |||  | |   ||     || |    |||     |  || |||||  |  | ||||| || ||||| || || || || ||||| ||||||||||| ||||||||||| |||||||| || || ||||||||||| ||||| |
-----------------------------------------------------------------------------gtatgtgaaattttat--tgtcgagctagagctgaa---ctggcctttccttacagCGCATTTTGGATGCTCTGTTTCCTTCCGTGCTAGGGGGAACCTGTGCTATTCCGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGA

upper sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 9
gtacacgaagcttgctactcccagctccttcataatgtgttattttattagtgtcaaaatttaatgaagtgatgctttcctgtcctgttctatcatattttgccgtgtctcatatcctgtgaactgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAA
                                                                                |||    || |||  | |   ||     || |    |||     |   |||||||  |  | ||||| || ||||| || || || || ||||| ||||||||||| ||||||||||| |||||||| || || ||||||||||| ||||| |
-----------------------------------------------------------------------------gtatgtgaaattttat--tgtcgagctagagctgaa---ctggccctttccttcagCGCATTTTGGATGCGCTGTTTCCTTCCGTGCTGGGGGGAACGTGTGCTATTCCGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGA

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|58601223|gb|CK011751.1|CK011751
EST:     GCCTGTTTCATCAAAGCTTGCTGCTGACACGCCTCTTGCTAACAGGACAG                         CGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATT
genomic: GCCTGTTTCATCAAAGCTTGCTGCTGACACGCCTCTT-CTAACAGGACAGgtacacgaag ... ctgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATT
EST: gi|427964|gb|D24110.1|D24110
EST:     GGCCTGTTTCATCAAAGCTTGCTGCTGACACGCCTCTTCTAACAGGACAG                         CGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATT
genomic: GGCCTGTTTCATCAAAGCTTGCTGCTGACACGCCTCTTCTAACAGGACAGgtacacgaag ... ctgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATT
EST: gi|29656411|gb|CB652686.1|CB652686
EST:     GCCTGTTTCATCAAAGCTTGCTGCTGACACGCCTCTTTCTA-CAGGACAG                         CGTGTACTTGATGCACT
genomic: GCCTGTTTCATCAAAGCTTGCTGCTGACACGCCTCTT-CTAACAGGACAGgtacacgaag ... ctgttttcagCGTGTACTTGATGCACT
EST: gi|29620942|gb|CB625953.1|CB625953
EST:     GGCCTGTTTCATCAAAGCTTGCTGCTGACACGCCTCTTCTAACAGGACAG                         CGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATT
genomic: GGCCTGTTTCATCAAAGCTTGCTGCTGACACGCCTCTTCTAACAGGACAGgtacacgaag ... ctgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATT

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), 66 (downstream exon)
Score: 109

ACATGGCCTGTCCGGTCACCAAGGCCTGTTTCATCAAAGCTTGCTGCTGACACGCCTCTTCTAACAGGACAGgtacacgaag ... ctgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgtcctgttctatcatattttgccgtgtctcatatcctgtgaactgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAA
                                             ctgttttc  CT-rich tract
         ttctatcatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacgaagcttgctactcccagctccttcataatgtgttattttattagtgtcaaaatttaatgaagtgatgctttcctgtcctgttctatcatattttgccgtgtctcatatcctgtgaactgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA