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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaataacagtacttttagtttttcatgttgctgaatctttgttttaatcgaataaaaatctaactttctgtcatttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCATGAGGTCACTAAAACGAAATGAAGCTACTTCCTCTTCCCTCTTCGGCCA

Basic information

species Oryza sativa
transcript LOC_Os02g14110.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g14110.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G146677_T01 (Zea mays), 3'ss of exon 9
gtacaataac-agtacttttagtttttcatgttgctgaatctttgt----tttaatcgaataaaaatctaactttctgtcatttc---tttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCATGAGGTCACTAAAACGAAATGAAGCTACTTCCTCTTCCCTCTTCGGCCA--
||| |  ||  | |  ||||  |||| |||   | ||| || |||     |||| | |||| |  |||||||||  |  | |  |   |||||||||||||||||| || ||||||||||| |  ||  | || ||||| ||||||||||| || ||| | || |||       ||||   || |||| || |   
gtatagcaattactgatttt--ttttacatcacgatgattcattgaacagtttattagaatga--atctaacttcatcccttgcccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCATGAGGTTACCAAACCAAATTGAGTTAGGGTCCTA--CCTTCTTTGGTCGAT
















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|88982906|gb|CI250510.1|CI250510
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|86492150|gb|CI134783.1|CI134783
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|86859475|gb|CI278876.1|CI278876
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|88968614|gb|CI098836.1|CI098836
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|33808186|gb|CF329982.1|CF329982
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATG-CAGAATAAG                         CATGGGCTGGTGTAACAACAGGAAATGTGGCG
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGG-CTGGTGTAACAACAGGAAATGTGGCG
EST: gi|87010181|gb|CI279278.1|CI279278
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|88224138|gb|CI223987.1|CI223987
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|86492839|gb|CI135472.1|CI135472
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|86592386|gb|CI251040.1|CI251040
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|88245936|gb|CI245785.1|CI245785
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|29689346|gb|CB685621.1|CB685621
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|86484720|gb|CI127353.1|CI127353
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|29683411|gb|CB679686.1|CB679686
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|88833489|gb|CI076970.1|CI076970
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|89186050|gb|CI047919.1|CI047919
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|88249439|gb|CI249288.1|CI249288
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|89179870|gb|CI044149.1|CI044149
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|86494910|gb|CI137543.1|CI137543
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|86494684|gb|CI137317.1|CI137317
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|86483891|gb|CI126524.1|CI126524
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|86496294|gb|CI138927.1|CI138927
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
EST: gi|86494861|gb|CI137494.1|CI137494
EST:     CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG                         CATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA
genomic: CGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCA

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), 74 (downstream exon)
Score: 63

ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAGGTGGATCGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAGgtacaataac ... tttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCATGAGGTCACTAAAACGAAATGAAGCTACTTCCTCTTCCCTCTTCGGCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgaatctttgttttaatcgaataaaaatctaactttctgtcatttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCATGAGGTCACTAAAACGAAATGAAGCTACTTCCTCTTCCCTCTTCGGCCA
                             atctaac  putative branch site (score: 63)
                                   ctttctgtcatttctt  CT-rich tract
         tttgttttaatcgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaataacagtacttttagtttttcatgttgctgaatctttgttttaatcgaataaaaatctaactttctgtcatttctttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCATGAGGTCACTAAAACGAAATGAAGCTACTTCCTCTTCCCTCTTCGGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC