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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtttcttgcatgacctctctcattttcatatcagttctgagtattgtgttcagatgtatgtttcaccctcttgttattcattattatggctttgctctttgtttgatgtgtcttggaatttctcagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g12590.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G012501_T03 (Zea mays), 3'ss of exon 2
gtaagtgtttcttgcatgacctctctcattttcatatcagttctgagtattgtgttc-agatgtatgtttcaccctcttgttattcattattatggctttgctctttgtttgatgtgtcttggaatttct--cagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
|||||  || ||||||     |||| ||||||   ||   || | |     || ||  |||  ||  ||| |||||||| || |   |  ||    || ||||   ||       ||| | | | ||| |  ||||||||||  |||||||| |||||||| || ||||| ||||||||||| |||
gtaagaattccttgcac--tttctcccattttgtcattctttgtaacctgagtttttgagacata-atttgaccctcttattttctttgctttcttctctgcttcctgccc----tgtttggaactttgttgcagGTCATCATCAAGCTATTATATTTACTTAATCAAGGAGAGACATTCACCAAG
















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|88692689|gb|CI736264.1|CI736264
EST:     AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAA                         GTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
genomic: AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAAgtaagtgttt ... aatttctcagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
EST: gi|88401623|gb|CI588564.1|CI588564
EST:     AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAA                         GTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
genomic: AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAAgtaagtgttt ... aatttctcagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
EST: gi|88388647|gb|CI683432.1|CI683432
EST:     AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAA                         GTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
genomic: AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAAgtaagtgttt ... aatttctcagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
EST: gi|88377051|gb|CI597835.1|CI597835
EST:     AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGC-AGGAAGTGCTCGCAA                         GTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGAGATTCACAAAG
genomic: AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAAgtaagtgttt ... aatttctcagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
EST: gi|88443658|gb|CI591883.1|CI591883
EST:     AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAA                         GTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
genomic: AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAAgtaagtgttt ... aatttctcagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
EST: gi|88414473|gb|CI691639.1|CI691639
EST:     AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAA                         GTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
genomic: AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAAgtaagtgttt ... aatttctcagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
EST: gi|88454333|gb|CI569905.1|CI569905
EST:     AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAA                         GTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
genomic: AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAAgtaagtgttt ... aatttctcagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
EST: gi|88333728|gb|CI643760.1|CI643760
EST:     AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAA                         GTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
genomic: AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAAgtaagtgttt ... aatttctcagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
EST: gi|88405887|gb|CI591282.1|CI591282
EST:     AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAA                         GTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
genomic: AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAAgtaagtgttt ... aatttctcagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
EST: gi|88328220|gb|CI651227.1|CI651227
EST:     AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAA                         GTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
genomic: AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAAgtaagtgttt ... aatttctcagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
EST: gi|88394604|gb|CI605945.1|CI605945
EST:     AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGCAAGTGCTCGCAA                         GTAATCACTAAGCTA
genomic: AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAAgtaagtgttt ... aatttctcagGTCATCACTAAGCTA
EST: gi|88311189|gb|CI570263.1|CI570263
EST:     AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAA                         GTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
genomic: AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAAgtaagtgttt ... aatttctcagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
EST: gi|88370130|gb|CI585135.1|CI585135
EST:     AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAA                         GTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
genomic: AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAAgtaagtgttt ... aatttctcagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
EST: gi|88313845|gb|CI597476.1|CI597476
EST:     AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAA                         GTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
genomic: AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAAgtaagtgttt ... aatttctcagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
EST: gi|88387536|gb|CI583054.1|CI583054
EST:     AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAA                         GTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
genomic: AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAAgtaagtgttt ... aatttctcagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
EST: gi|88574218|gb|CI665987.1|CI665987
EST:     AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAA                         GTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
genomic: AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAAgtaagtgttt ... aatttctcagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
EST: gi|88310289|gb|CI659079.1|CI659079
EST:     AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAA                         GTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
genomic: AGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAAgtaagtgttt ... aatttctcagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG

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), 51 (downstream exon)
Score: 39

TTGAGTACTCGCCATTTTATGGGATTGAGAAGGGAGCCGTTCTGCAGGAGGCAAGGGCTTTCCATGATCCGCAGCTTGATGCCAGGAAGTGCTCGCAAgtaagtgttt ... aatttctcagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttattcattattatggctttgctctttgtttgatgtgtcttggaatttctcagGTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG
                             gtttgat  putative branch site (score: 39)
                                               tttctc  putative PPT
     ttcattattat  TA-rich tract