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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCGTGAATATGAGCTTAATCTCCCAAATTCAAACCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCCgtaagatctttttcttatgttacatgatatgaggcacattaatttttttgtcatatcatgtttgcataaaaatgtttctttcaattaagaaactcatgagcatcaagtagatttactagactagttaagataaacaaatactgaacatgcag

Basic information

species Oryza sativa
transcript LOC_Os09g06499.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g06499.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G068212_T01 (Zea mays), 5'ss of exon 15
GTTGCGTGAATATGAGCTTAATCTCCCAAATTCAAACCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCCgtaagatctttttcttatg-ttacatgatatgaggcacattaatttttttgtcatatcatgtttgcataaaaatgtttctttcaattaagaaactcatgagcatcaagtagatttactagactagttaagataaacaaatactgaacatgcag
||||||||| |||||||| ||||| |||| ||||||| |||| |||||| ||||| ||||| |||||||||||||||||||||||||||| | | || | | ||| | | || ||| | | | | | || || || | ||| | || |||| | || | ||| | ||| | | || ||||| || || |||||||
GTTGCGTGAGTATGAGCTCAATCTTCCAAGTTCAAACAAGGGACTTGATGTTGGAAGGGTGTATTTTGTGATCCTCGAGATGTCCCgtaagactctgattttctaatcgcattgtcagcatcagattgttcccctcggt-tgtgggcatttcagaaggaaattt-------atgagcttctcaagggctttctgta---tcacttgttaaatt--gataa--aatctttggtcatgcag
















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|86898998|gb|CI296194.1|CI296194
EST:     CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCC                         CTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
genomic: CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCCgtaagatctt ... gaacatgcagCTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
EST: gi|86491278|gb|CI133911.1|CI133911
EST:     CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCC                         CTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
genomic: CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCCgtaagatctt ... gaacatgcagCTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
EST: gi|58680269|gb|CK068956.1|CK068956
EST:     CGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCC                         CTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
genomic: CGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCCgtaagatctt ... gaacatgcagCTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
EST: gi|29643061|gb|CB648068.1|CB648068
EST:     CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCC                         CTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
genomic: CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCCgtaagatctt ... gaacatgcagCTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
EST: gi|29614649|gb|CB619662.1|CB619662
EST:     CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCC                         CTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
genomic: CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCCgtaagatctt ... gaacatgcagCTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
EST: gi|87007390|gb|CI279061.1|CI279061
EST:     CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCC                         CTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
genomic: CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCCgtaagatctt ... gaacatgcagCTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
EST: gi|29661764|gb|CB658039.1|CB658039
EST:     CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCC                         CTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
genomic: CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCCgtaagatctt ... gaacatgcagCTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
EST: gi|29661763|gb|CB658038.1|CB658038
EST:     CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCC                         CTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATN
genomic: CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCCgtaagatctt ... gaacatgcagCTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTAT-
EST: gi|29674507|gb|CB670782.1|CB670782
EST:     CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCC                         CTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
genomic: CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCCgtaagatctt ... gaacatgcagCTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
EST: gi|88963699|gb|CI029474.1|CI029474
EST:     CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCC                         CTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
genomic: CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCCgtaagatctt ... gaacatgcagCTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
EST: gi|29613615|gb|CB618628.1|CB618628
EST:     CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCC                         CTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
genomic: CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCCgtaagatctt ... gaacatgcagCTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
EST: gi|86900178|gb|CI300201.1|CI300201
EST:     CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCC                         CTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCA
genomic: CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCCgtaagatctt ... gaacatgcagCTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCA
EST: gi|22304910|gb|BQ906132.1|BQ906132
EST:     CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCC                         CTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
genomic: CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCCgtaagatctt ... gaacatgcagCTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
EST: gi|29630278|gb|CB635287.1|CB635287
EST:     CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCC                         CTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
genomic: CCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCCgtaagatctt ... gaacatgcagCTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
EST: gi|86592891|gb|CI270448.1|CI270448
EST:     ATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCGC                         CTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC
genomic: ATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCCgtaagatctt ... gaacatgcagCTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATC

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), 67 (downstream exon)
Score: 15

GTTGCGTGAATATGAGCTTAATCTCCCAAATTCAAACCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCCgtaagatctt ... gaacatgcagCTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCGTGAATATGAGCTTAATCTCCCAAATTCAAACCGTGGACCTGATGTCGGAAGAGTGTACTTTGTGATCCTCGAGATGTCCCgtaagatctttttcttatgttacatgatatgaggcacattaatttttttgtcatatcatgtttgcataaaaatgtttctttcaattaagaaactcatgagcatcaagtagatttactagactagttaagataaacaaatactgaacatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG