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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggcacttcttctaattaattgaacgagtgaaaagtagaaacaaatgtgtacaggtatggcattaaatcattgagtactactgattggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCGGGCATCATAGACATGATTGGTACTGGGTGGTGCTTCGTGCGAGTGCACG

Basic information

species Oryza sativa
transcript LOC_Os09g06499.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g06499.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G068212_T01 (Zea mays), 3'ss of exon 16
gttggcacttcttctaattaattgaacgagtgaaaagtagaaacaaatgtgtacaggtatggcattaaatcattgagtactactgattggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCGGGCATCATAGACATGATTGGTACTGGGTGGTGCTTCGTGCGAGTGCACG
   | |  |||   || | |  |    ||    |  | |   | |||  ||||||  | |    || |      |  || |  | | ||  |||||||||| ||||| ||||| |||||||| ||  |||| ||| | || |||||||||||||| ||| || | ||  ||||||||||||| ||||||||||| |
---gtcctttcccatagtcacatt--tgaaactattgcaccgagaaacttgtacaactgtt---ttcagaagcagcatattctttactgactgcagATTGCCATAGCTAACCCGAACCGGCAAGTGTACCTTCTGTTGTCAAGATCGGGCATCATTGACTTGGTAGGAGCTGGGTGGTGCTTTGTGCGAGTGCATG
















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:     TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAG                         ATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
genomic: TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAGgttggcactt ... ttggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
EST: gi|86491278|gb|CI133911.1|CI133911
EST:     TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAG                         ATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
genomic: TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAGgttggcactt ... ttggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
EST: gi|29678821|gb|CB675096.1|CB675096
EST:     ACAGGGATCGCCATATCCAG                         ATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
genomic: ACAGGGATCGCCATATCCAGgttggcactt ... ttggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
EST: gi|58680269|gb|CK068956.1|CK068956
EST:     TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAG                         ATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
genomic: TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAGgttggcactt ... ttggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
EST: gi|29643061|gb|CB648068.1|CB648068
EST:     TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAG                         ATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
genomic: TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAGgttggcactt ... ttggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
EST: gi|29614649|gb|CB619662.1|CB619662
EST:     TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAG                         ATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
genomic: TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAGgttggcactt ... ttggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
EST: gi|87007390|gb|CI279061.1|CI279061
EST:     TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAG                         ATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
genomic: TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAGgttggcactt ... ttggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
EST: gi|29661764|gb|CB658039.1|CB658039
EST:     TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAG                         ATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
genomic: TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAGgttggcactt ... ttggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
EST: gi|86491018|gb|CI133651.1|CI133651
EST:     TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAG                         ATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
genomic: TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAGgttggcactt ... ttggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
EST: gi|29614647|gb|CB619660.1|CB619660
EST:     TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAG                         ATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
genomic: TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAGgttggcactt ... ttggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
EST: gi|29661763|gb|CB658038.1|CB658038
EST:     TCAGGCTCTCAAGGACTTGTATNCA-GAATACAGGGATCGCCATATCCAG                         ATTGCAATAGCGAACCCCAACCGGCAGGTACACCTGCTGCTTT
genomic: TCAGGCTCTCAAGGACTTGTAT-CAAGAATACAGGGATCGCCATATCCAGgttggcactt ... ttggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTT
EST: gi|29674507|gb|CB670782.1|CB670782
EST:     TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAG                         ATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
genomic: TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAGgttggcactt ... ttggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
EST: gi|88963699|gb|CI029474.1|CI029474
EST:     TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAG                         ATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
genomic: TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAGgttggcactt ... ttggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
EST: gi|29613615|gb|CB618628.1|CB618628
EST:     TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAG                         ATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
genomic: TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAGgttggcactt ... ttggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
EST: gi|22304910|gb|BQ906132.1|BQ906132
EST:     TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAG                         ATTGCAATAGCGAACCC-AACCGGCAGGTACACCTGCTGCTTTCGAGATCG
genomic: TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAGgttggcactt ... ttggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
EST: gi|29630278|gb|CB635287.1|CB635287
EST:     TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAG                         ATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
genomic: TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAGgttggcactt ... ttggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
EST: gi|86592891|gb|CI270448.1|CI270448
EST:     TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAG                         ATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG
genomic: TTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAGgttggcactt ... ttggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCG

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: 71 (upstream exon), 73 (downstream exon)
Score: 19

CTGTTACATACATCGATTCAAGTGCTGTTCAGGCTCTCAAGGACTTGTATCAAGAATACAGGGATCGCCATATCCAGgttggcactt ... ttggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCGGGCATCATAGACATGATTGGTACTGGGTGGTGCTTCGTGCGAGTGCACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaaatgtgtacaggtatggcattaaatcattgagtactactgattggttgcagATTGCAATAGCGAACCCAAACCGGCAGGTACACCTGCTGCTTTCGAGATCGGGCATCATAGACATGATTGGTACTGGGTGGTGCTTCGTGCGAGTGCACG
                                       tactgat  putative branch site (score: 19)
                      attaaatcatt  TA-rich tract