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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacactgtggatcattagcgctatgtatgcatgtgtttggttccttcccacagttaatatttaatatacctcctctcttctatctatatgatgtgaacattaaggactgacctttgcctttatgttgcagCCAAGTGAAAGCCTGTATGATCAGAAACCTGAAGAGCCAAAACCTGCTGCCCCAGTAATGACTACTTCCACCACAAAAAGTGGCCCGTCCTTGCATTCAC

Basic information

species Oryza sativa
transcript LOC_Os03g63710.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G176612_T01 (Zea mays), 3'ss of exon 3
gtaacactgtggatcattagcgctatgtatgcatgtgtttggttccttcccacagttaatatttaatatacctcctctcttctatctatatgatgtgaacattaaggactgacctttgcctttatgttgcagCCAAGTGAAAGCCTGTATGATCAGAAACCTGAAGAGCCAAAACCTGCTGCCCCAGTAATGACTACTTCCACCACAAAAAGTGGCCCGTCCTTGCATTCAC
          | |    | ||  ||| |  | | | | |   ||  | |   |    |   | | | | |  |   |  || |  | || |||  | | | ||  |  ||    |||   ||| || ||||||||| ||||||||||||||| |||||||| |||||||||||||||||||  || |   || || |||| || | |||| |||| | | ||||||||||||
----------gtaaagcttgca-tatat-cgaaagggctaaatttatgcttcc---caggctctcacaaaattatacaatttt--caatttgaactaaccctt--gccctcttttttcaatttgtgctgcagCCAAATGAAAGCCTGTATGAGCAGAAACCAGAAGAGCCAAAACCTGCTGTACCTGCCTTGGCTGCTTCAACTAAAAAAGGTGGTCAGGCCTTGCATTCAC

upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G083546_T01 (Zea mays), 3'ss of exon 3
gtaacactgtggatcattagcgctatgtatgcatgtgtttggttccttcccacagttaatatttaatatacctcctctcttctatctatatgatgtgaacattaaggactgacctttgcctttatgttgcagCCAAGTGAAAGCCTGTATGATCAGAAACCTGAAGAGCCAAAACCTGCTGCCCCAGTAATGACTACTTCCACCACAAAAAGTGGCCCGTCCTTGCATTCAC
                                  ||| | | || |   ||| |     || ||  |    | | |   ||  || |   ||   | | |  |   | || |  |||    || |  ||||||||| ||||||||||||||| |||||||| ||||||||||||||||||   || |   ||||| || | ||  ||||| |||| || |||||||||||||
----------------------------------gtgat-gcttgcagaccaaatgagctaatttgtgcttcccatgattttcattt---tggactaacccct---gccttatatttcaaattgtactgcagCCAAATGAAAGCCTGTATGAGCAGAAACCAGAAGAGCCAAAACCTGCTATACCTGCCTTGACTGCTCCAACTGCAAAAGGTGGTCCATCCTTGCATTCAC
















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|29677839|gb|CB674114.1|CB674114
EST:     AGATTGGAGGCAAGACTGGAGGGCTTGGTGTTAAAAAGCTCACCACAAAG                         CCAAGTGAAAGCCTGTATGATCAGAAACCTGAAGAGCCAAAACCTGCTGCC
genomic: AGATTGGAGGCAAGACTGGAGGGCTTGGTGTTAAAAAGCTCACCACAAAGgtaacactgt ... tatgttgcagCCAAGTGAAAGCCTGTATGATCAGAAACCTGAAGAGCCAAAACCTGCTGCC
EST: gi|29679055|gb|CB675330.1|CB675330
EST:     AGATTGGAGGCAAGACTGGAGGGCTTGGTGTTAAAAAGCTCACCACAAAG                         CCAAGTGAAAGCCTGTATGATCAGAAACCTGAAGAAGC-AAAACCTGCTGC
genomic: AGATTGGAGGCAAGACTGGAGGGCTTGGTGTTAAAAAGCTCACCACAAAGgtaacactgt ... tatgttgcagCCAAGTGAAAGCCTGTATGATCAGAAACCTGAAGA-GCCAAAACCTGCTGC
EST: gi|58670961|gb|CK059647.1|CK059647
EST:     AGATTGGAGGCAAGACTGGAGGGCTTGGTGTTAAAAAGCTCACCACAAAG                         CCAAAGTGAAAGCCTGTATGATCAGAAACCTGAA
genomic: AGATTGGAGGCAAGACTGGAGGGCTTGGTGTTAAAAAGCTCACCACAAAGgtaacactgt ... tatgttgcagCCAA-GTGAAAGCCTGTATGATCAGAAACCTGAA

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), 75 (downstream exon)
Score: 46

TACTCATCCCACTTTTGCCACTTCTGTAAAGAAGTCCATTGGTGCGAAGAAGATTGGAGGCAAGACTGGAGGGCTTGGTGTTAAAAAGCTCACCACAAAGgtaacactgt ... tatgttgcagCCAAGTGAAAGCCTGTATGATCAGAAACCTGAAGAGCCAAAACCTGCTGCCCCAGTAATGACTACTTCCACCACAAAAAGTGGCCCGTCCTTGCATTCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttctatctatatgatgtgaacattaaggactgacctttgcctttatgttgcagCCAAGTGAAAGCCTGTATGATCAGAAACCTGAAGAGCCAAAACCTGCTGCCCCAGTAATGACTACTTCCACCACAAAAAGTGGCCCGTCCTTGCATTCAC
                             gactgac  putative branch site (score: 46)
                                   cctttgccttt  CT-rich tract
     tatctatat  TA-rich tract