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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcaacaaagctctttgatacgcctgaccatcagttttttctgttaatattatttattgtacgtcatctttgcagCATGTTCGTGTTATTGATAAATCCAAGTTGAGAATTTATCCAGCTGGAATAGATAAGTCCAAACTTCTATATGAGTTACATCATCTCAAATCCATGCTTC

Basic information

species Oryza sativa
transcript LOC_Os04g41490.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41490.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G178236_T01 (Zea mays), 3'ss of exon 3
gtatcaacaaagctc----tttgatacgcctg-----------accatcagttttttctgttaatattatttattgtacgtcatctttgcagCATGTTCGTGTTATTGATAAATCCAAGTTGAGAATTTATCCAGCTGGAATAGATAAGTCCAAACTTCTATATGAGTTACATCATCTCAAATCCATGCTTC
|||| ||||||| ||    ||||||||  | |           |  || |||| | | ||||   | | |  | |  |     | |||||||||||| || || ||||||| | |||||||| |||| |||||||||||||  || |||  ||||||||    |||  | ||| | ||||||||||| ||||
gtataaacaaagttccaagtttgatacatcaggtggaaaatttattattagttatctgtgtttgcaatttacagtcaaatgattttttgcagCATGTCCGAGTCATTGATAGAGCCAAGTTGCGAATATATCCAGCTGGAACTGACAAGCTCAAACTTCAGCTTGAACTGCATAACCTCAAATCCATCCTTC
















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|396941292|gb|HO188501.1|HO188501
EST:     CTGTGCAGCTGTCAATATTGAATCATCCAAAAATAAAGCTAAAATCTGAG                         CATGTTCGTGTTATCGATAAATCCAAGTTGAGAATTTATCCAGCTGGAATA
genomic: CTGTGCAGCTGTCAATATTGAATCATCCAAAAATAAAGCTAAAATCTGAGgtatcaacaa ... atctttgcagCATGTTCGTGTTATTGATAAATCCAAGTTGAGAATTTATCCAGCTGGAATA
EST: gi|58669395|gb|CK058081.1|CK058081
EST:     CTGTGCAGCTGTCAATATTGAATCATCCAAAAATAAAGCTAAAATCTGAG                         CATGTTCGTGTTATCGATAAATCCAAGTTGAGAATTTATCCAGCTGGAATA
genomic: CTGTGCAGCTGTCAATATTGAATCATCCAAAAATAAAGCTAAAATCTGAGgtatcaacaa ... atctttgcagCATGTTCGTGTTATTGATAAATCCAAGTTGAGAATTTATCCAGCTGGAATA
EST: gi|13165135|gb|AU173932.1|AU173932
EST:     CTGTGCAGCTGTCAATATTGAATCATCCAAAAATAAAGCTAAAATCTGAG                         CATGTTCGTGTTATTGATAAATCCAAGTTGAGAATTTATCCAGCTGGAATA
genomic: CTGTGCAGCTGTCAATATTGAATCATCCAAAAATAAAGCTAAAATCTGAGgtatcaacaa ... atctttgcagCATGTTCGTGTTATTGATAAATCCAAGTTGAGAATTTATCCAGCTGGAATA
EST: gi|396941602|gb|HO188259.1|HO188259
EST:     CTGTGCAGCTGTCAATATTGAATCATCCAAAAATAAAGCTAAAATCTGAG                         CATGTTCGTGTTATCGATAAATCCAAGTTGAGAATTTATCCAGCTGGAATA
genomic: CTGTGCAGCTGTCAATATTGAATCATCCAAAAATAAAGCTAAAATCTGAGgtatcaacaa ... atctttgcagCATGTTCGTGTTATTGATAAATCCAAGTTGAGAATTTATCCAGCTGGAATA

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: 50 (upstream exon), 62 (downstream exon)
Score: 11

ACTCGATATGCAACGTATAGAAGCCCTGCACATGGGCATCTCTGCTGACTCTGTGCAGCTGTCAATATTGAATCATCCAAAAATAAAGCTAAAATCTGAGgtatcaacaa ... atctttgcagCATGTTCGTGTTATTGATAAATCCAAGTTGAGAATTTATCCAGCTGGAATAGATAAGTCCAAACTTCTATATGAGTTACATCATCTCAAATCCATGCTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcctgaccatcagttttttctgttaatattatttattgtacgtcatctttgcagCATGTTCGTGTTATTGATAAATCCAAGTTGAGAATTTATCCAGCTGGAATAGATAAGTCCAAACTTCTATATGAGTTACATCATCTCAAATCCATGCTTC
                     tgttaat  putative branch site (score: 11)
                                           tcatcttt  putative PPT
         atcagttttttctgtt  TA-rich tract