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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacctcacaaccaaattcaactgatcctaacagctcgcttttcaatttacccgtactgaattttgtccttttttctgcattcagGAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAGCTAAACCAAAGGCTAAGACTGCATGAGTCAACATACACAGCTGCAATTT

Basic information

species Oryza sativa
transcript LOC_Os05g07870.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g07870.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G512279_T01 (Zea mays), 3'ss of exon 4
gtaacctcacaaccaa-attcaactgatcctaacagctcgcttttcaatttacccgta-ctgaattttgtccttttt-tctgcattcagGAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAGCTAAACCAAAGGCTAAGACTGCATGA-GTCAACATACACA-GCTGCAATTT
|||        |  || ||||  |         |   |   |   |   | | | ||  ||||||| |    ||||| | ||| | ||||||| || |||||||| |||||||| |||||||||||   |||||||||  | ||||||||||||| | |||||||| | ||||   |  | |  | ||   
gtacagaagtgattaatattcttcatgcaagtgccagttattgaacgtctcatcagtgtctgaattgtaagttttttctttgcctgcagGAACCGGTGTTGCTCTCGCTGGAGTGTTCCTGTACTCGTAGTTCAAAAAGTCAAAACCAAAGGCTACGGCTGCATGAAGACAACTCCCTGATGAGGTAAC--

upper sequence: LOC_Os05g07870.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G008642_T01 (Zea mays), 3'ss of exon 6
gtaacctcacaaccaa-attcaactgatcctaacagctcgcttttcaatttacccgta-ctgaatttt--gtccttttttctgcattcagGAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAGCTAAACCAAAGGCTAAGACTGCATGAGTCAACATACACAGCTGCAATTT
|||        |  || ||||  |         |   |  |||  ||  | | |  |  ||||||| |  ||  |||| | ||| | ||||||| || |||||||| |||||||| |||||||||||   |||||||||  | ||||||||||||| | ||||||||                       
gtacagcagtgattaatattcttcatgcaaatgccagttacttaccatctcatcaatgtctgaattgtaagtttttttctttgcctgcagGAACCGGTGTTGCTCTTGCTGGAGTGTTCCTGTACTCGCAGTTCAAAAAGTCAAAACCAAAGGCTACGGCTGCATGA-----------------------
















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|66924213|gb|CX111061.1|CX111061
EST:     CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTG                         GAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGGTCAAAAAAG
genomic: CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTGgtaacctcac ... ctgcattcagGAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG
EST: gi|88552763|gb|CI482801.1|CI482801
EST:     GTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTG                         GAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTTTAGGTTCAAAAAAG
genomic: CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTGgtaacctcac ... ctgcattcagGAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG
EST: gi|29642963|gb|CB647970.1|CB647970
EST:     CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTG                         GAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG
genomic: CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTGgtaacctcac ... ctgcattcagGAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG
EST: gi|29659992|gb|CB656267.1|CB656267
EST:     CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTG                         GAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG
genomic: CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTGgtaacctcac ... ctgcattcagGAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG
EST: gi|88661888|gb|CI461859.1|CI461859
EST:     CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTG                         GAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG
genomic: CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTGgtaacctcac ... ctgcattcagGAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG
EST: gi|88532797|gb|CI461430.1|CI461430
EST:     CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTG                         GAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG
genomic: CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTGgtaacctcac ... ctgcattcagGAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG

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: 74 (upstream exon), 75 (downstream exon)
Score: 53

CCTGTGACCCATTCTGTTGCCAACTGTGTCAAACGAGTTGTGGTCATCGTCTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTGgtaacctcac ... ctgcattcagGAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAGCTAAACCAAAGGCTAAGACTGCATGAGTCAACATACACAGCTGCAATTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagctcgcttttcaatttacccgtactgaattttgtccttttttctgcattcagGAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAGCTAAACCAAAGGCTAAGACTGCATGAGTCAACATACACAGCTGCAATTT
 tcctaac  putative branch site (score: 53)
                               ttttgtccttttttct  putative PPT
         ttttcaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacctcacaaccaaattcaactgatcctaacagctcgcttttcaatttacccgtactgaattttgtccttttttctgcattcagGAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAGCTAAACCAAAGGCTAAGACTGCATGAGTCAACATACACAGCTGCAATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC