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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggaaattttccagtaatttgttattattttattaattgctatgcgtttatgattgacagaaatacttataagttataagctattttgaactccatgtatagGTGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAG

Basic information

species Oryza sativa
transcript LOC_Os03g21950.1
intron # 6
splice site 3'
intron type U2

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|58692734|gb|CK081421.1|CK081421
EST:     ATGCCACCCCATTGACCCTTGGCCAAGAGTTCAGCGGTTACGCCACACAA                         GTGAAATATGGAATTGATAGAATNGTTTGTACCTTACCACGGATGTATCAG
genomic: ATGCCACCCCATTGACCCTTGGCCAAGAGTTCAGCGGTTACGCCACACAAgtaggaaatt ... ccatgtatagGTGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAG
EST: gi|33795747|gb|CF323743.1|CF323743
EST:     ATGCCACCCCATTGACCCTTGGCCAAGAGTNCAGCGGTTACGCCACACAA                         GTGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAG
genomic: ATGCCACCCCATTGACCCTTGGCCAAGAGTTCAGCGGTTACGCCACACAAgtaggaaatt ... ccatgtatagGTGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAG
EST: gi|58662738|gb|CK051424.1|CK051424
EST:     ATGCCACCCCATTGACCCTTGGCCAAGAGTTCAGCGGTTACGCCACACAA                         GTGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAG
genomic: ATGCCACCCCATTGACCCTTGGCCAAGAGTTCAGCGGTTACGCCACACAAgtaggaaatt ... ccatgtatagGTGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAG
EST: gi|33676561|gb|CF304800.1|CF304800
EST:     ATGCCACCCCATTGACCCTTGGCCAAGAGTTCAGCGGTTACGCCACACAA                         GTGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAG
genomic: ATGCCACCCCATTGACCCTTGGCCAAGAGTTCAGCGGTTACGCCACACAAgtaggaaatt ... ccatgtatagGTGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAG
EST: gi|33674910|gb|CF303149.1|CF303149
EST:     ATGCCACCCCATTGACCCTTGGCCAAGAGTTCAGCGGTTACGCCACACAA                         GTGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAG
genomic: ATGCCACCCCATTGACCCTTGGCCAAGAGTTCAGCGGTTACGCCACACAAgtaggaaatt ... ccatgtatagGTGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAG
EST: gi|58681064|gb|CK069751.1|CK069751
EST:     ATGCCACCCCATTGACCCTTGGCCAAGAGTTCAGCGGTTACGCCACACAA                         GTGAAATATGGAATTGATAGAATTGTTTGTACCTTACCA
genomic: ATGCCACCCCATTGACCCTTGGCCAAGAGTTCAGCGGTTACGCCACACAAgtaggaaatt ... ccatgtatagGTGAAATATGGAATTGATAGAATTGTTTGTACCTTACCA
EST: gi|33676642|gb|CF304881.1|CF304881
EST:     ATGCCACCCCATTGACCCTTGGCCAAGAGTTCAACGGTTACGCCACACAA                         GTGAAATATGGAATTGAT
genomic: ATGCCACCCCATTGACCCTTGGCCAAGAGTTCAGCGGTTACGCCACACAAgtaggaaatt ... ccatgtatagGTGAAATATGGAATTGAT

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: 51 (upstream exon), 67 (downstream exon)
Score: 42

TCTGTTGAATTTCAAGACATAATTAAAATTGGGCGTACACATACCCAAGATGCCACCCCATTGACCCTTGGCCAAGAGTTCAGCGGTTACGCCACACAAgtaggaaatt ... ccatgtatagGTGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgattgacagaaatacttataagttataagctattttgaactccatgtatagGTGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAG
    gattgac  putative branch site (score: 42)
             aaatacttataagtta  TA-rich tract