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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtattcacttagtctaccttgctttctgctctagtgctttttattgccattctgttatttatggtgttgattagaacctcttctggtgctttatagGTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAGAGAGTGGTTCAAGAGAAGATGCCTGAAGGCGTGAATGACAATGGCCTTA

Basic information

species Oryza sativa
transcript LOC_Os03g59590.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g59590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G004459_T01 (Zea mays), 3'ss of exon 4
gtttgtattcacttagtctaccttgctttctgctc--tagtg----------ctttttattgccat--tctgttatttatggtgttgattagaacctcttctggtgctttatagGTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAGAGAGTGGTTCAAGAGAAGATGCCTGAAGGCGTGAATGACAATGGCCTTA
|||||| ||||   || ||||| |||||||        |||           ||  ||| |   ||  ||| || ||| | ||| ||  |        |  || ||||||| |||||  |||||| |||||||| |||||||||||||||||| |||| || |||||||| ||||| |||||||||||||||||||| ||||| |  |||||||
gtttgtgttcatgaaggctaccatgctttccatctagcagtatacaacataactacttaataatatactctattgtttctagtgatg--tgaggttcttcttgctgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAGAGAGTTGTTCAGGAGAAGATGCCTGAAGGCGTAAATGAAAGCGGCCTTA

upper sequence: LOC_Os03g59590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G071071_T01 (Zea mays), 3'ss of exon 4
gtttgtattcacttagtctaccttgctttctgctctagtg-------------ctttttattgccat--tctgttatttatggtgttgattaga--acctcttctggtgctttatagGTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAGAGAGTGGTTCAAGAGAAGATGCCTGAAGGCGTGAATGACAATGGCCTTA
|| ||| ||||   || ||||| ||||||||  |||||               ||  ||| ||  ||   || || ||| | || ||| | |||  |  | |  |  ||||||  |||||   || || | ||||||||||||||||||||||||| |||| || |||||||| ||||| |||||||||||||||||||| ||||| | ||||||||
gtctgtgttcatgaaggctaccctgctttcta-tctagcaacatacagcataactacttaatgatatacccttttgtttttagttttgctgagattatttttattactgctttgcagGTCCGGTGTTTTAGTGCTCCTCTCCAGCCTACTGAAATTTCAGGAGTTAAGAGAGTTGTTCAGGAGAAGATGCCTGAAGGCGTAAATGAAACTGGCCTTA

upper sequence: LOC_Os03g59590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S255_41V6.2 (Physcomitrella patens), 3'ss of exon 5
-----gtttgtattcacttagtctaccttgctttctgctctagtgctttttattgccattctgttatttatggtgttgattagaacctcttctggtgctttatagGTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAGAGAGTGGTTCAAGAGAAGATGCCTGAAGGCGTGAATGACAATGGCCTTA
     |     |   || |  |  ||  ||   | |     |   |  || || || ||     |  | ||| | ||  ||| |  |   ||      ||   ||||||| ||||||||||| ||||| |||||| | ||||| | ||| ||||||| ||||||    |||||| |  | || || |||||||| |||||  | |
taagggacatcaaagacctgatagactgtgacgtttttatgaaaacacttaatcgcaat--gagttctcatg-ttttacttaca--caagtcaaccttttgtcagGTCAAGTGCTTCAATGCGCCTCTACAGCCTCCCGAAATAGTAGGAGTGAAGAAAGTGGTCTCGGAGAAGTTAGCAGAGGGTGTGAATGAGAATGGGTTGA

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|117231571|gb|CT846921.1|CT846921
EST:     ACCATGACAGGGATGGAGCACTCAGTGATGTGGAGCTCAATGACTTTCAG                         GTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGC
genomic: ACCATGACAGGGATGGAGCACTCAGTGATGTGGAGCTCAATGACTTTCAGgtttgtattc ... tgctttatagGTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGC
EST: gi|29622950|gb|CB627961.1|CB627961
EST:     ACCATGACAGGGATGGAGCACTCAGTGATGTGGAGCTCAATGACTTTCAG                         GTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAG
genomic: ACCATGACAGGGATGGAGCACTCAGTGATGTGGAGCTCAATGACTTTCAGgtttgtattc ... tgctttatagGTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAG
EST: gi|29627475|gb|CB632486.1|CB632486
EST:     ACCATGACAGGGATGGAGCACTCAGTGATGTGGAGCTCAATGACTTTCAG                         GTCAAATGCTTCAATGCTCCTCTC
genomic: ACCATGACAGGGATGGAGCACTCAGTGATGTGGAGCTCAATGACTTTCAGgtttgtattc ... tgctttatagGTCAAATGCTTCAATGCTCCTCTC
EST: gi|88340745|gb|CI636905.1|CI636905
EST:     ACCATGACAGGGATGGAGCACTCAGTGATGTGGAGCTCAATGACTTTCAG                         GTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAG
genomic: ACCATGACAGGGATGGAGCACTCAGTGATGTGGAGCTCAATGACTTTCAGgtttgtattc ... tgctttatagGTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAG
EST: gi|88347698|gb|CI655051.1|CI655051
EST:     ACCATGACAGGGATGGAGCACTCAGTGATGTGGAGCTCAATGACTTTCAG                         GTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAG
genomic: ACCATGACAGGGATGGAGCACTCAGTGATGTGGAGCTCAATGACTTTCAGgtttgtattc ... tgctttatagGTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAG
EST: gi|58663189|gb|CK051875.1|CK051875
EST:     ACCATGACAGGGATGGAGCACTCAGTGATGTGGAGCTCAATGACTTTCAG                         GTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAG
genomic: ACCATGACAGGGATGGAGCACTCAGTGATGTGGAGCTCAATGACTTTCAGgtttgtattc ... tgctttatagGTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAG
EST: gi|58664780|gb|CK053466.1|CK053466
EST:     ACCATGACAGGGATGGAGCACTCAGTGATGTGGAGCTCAATGACTTTCAG                         GTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAG
genomic: ACCATGACAGGGATGGAGCACTCAGTGATGTGGAGCTCAATGACTTTCAGgtttgtattc ... tgctttatagGTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAG
EST: gi|88324742|gb|CI657610.1|CI657610
EST:     ACCATGACAGGGATGGAGCACTCAGTGATGTGGAGCTCAATGACTTTCAG                         GTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAG
genomic: ACCATGACAGGGATGGAGCACTCAGTGATGTGGAGCTCAATGACTTTCAGgtttgtattc ... tgctttatagGTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAG
EST: gi|58669513|gb|CK058199.1|CK058199
EST:     ACCATGACAGGGATGGAGCACTCAGTGATGTGGAGCTCAATGACTTTCAG                         GTCACATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAG
genomic: ACCATGACAGGGATGGAGCACTCAGTGATGTGGAGCTCAATGACTTTCAGgtttgtattc ... tgctttatagGTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAG

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), 64 (downstream exon)
Score: 38

TCTAAAGCCACGGTGTGTGAGGGCTTTGAAGCGGATTTTTATTCTATGTGACCATGACAGGGATGGAGCACTCAGTGATGTGGAGCTCAATGACTTTCAGgtttgtattc ... tgctttatagGTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAGAGAGTGGTTCAAGAGAAGATGCCTGAAGGCGTGAATGACAATGGCCTTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgccattctgttatttatggtgttgattagaacctcttctggtgctttatagGTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAGAGAGTGGTTCAAGAGAAGATGCCTGAAGGCGTGAATGACAATGGCCTTA
                       tgttgat  putative branch site (score: 38)
       attctgttatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtattcacttagtctaccttgctttctgctctagtgctttttattgccattctgttatttatggtgttgattagaacctcttctggtgctttatagGTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAGAGAGTGGTTCAAGAGAAGATGCCTGAAGGCGTGAATGACAATGGCCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG