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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcgttcggcggctgtcgcggaccggggttgcgtcagctgttcgtagacacgagagttttctcctcgatcgagaggttattgattgattctctattttgttgacagGACAACGCCGGCGGTGGCATCGGCGGGCGGATGCTCGGCGGCGGCGCTGGCGCTGGTTCTAGCGCGGGCGGCGCGATGACGAGGGACACTGAGGCGGAGA

Basic information

species Oryza sativa
transcript LOC_Os02g45250.1
intron # 1
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|88695603|gb|CI737641.1|CI737641
EST:     TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTG                         GACAACGCCGGCGGTGGCATCGGCGGGCGG
genomic: TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTGgtatgcgttc ... ttgttgacagGACAACGCCGGCGGTGGCATCGGCGGGCGG
EST: gi|88314063|gb|CI600065.1|CI600065
EST:     TCC-TTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTG                         GACAACGCCGGCGGTGGCATCGGCGGGCGGATGCTCGGC
genomic: TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTGgtatgcgttc ... ttgttgacagGACAACGCCGGCGGTGGCATCGGCGGGCGGATGCTCGGC
EST: gi|88415175|gb|CI583998.1|CI583998
EST:     TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTG                         GACAACGCCGGCGGTGGCATCGGCGGGCGGATGC
genomic: TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTGgtatgcgttc ... ttgttgacagGACAACGCCGGCGGTGGCATCGGCGGGCGGATGC
EST: gi|88415131|gb|CI583954.1|CI583954
EST:     TCC-TTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTG                         GACAACGCCGGCGGTGGCATGGGCGGTG-GGATGCTCGGCGG
genomic: TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTGgtatgcgttc ... ttgttgacagGACAACGCCGGCGGTGGCATCGGCGG-GCGGATGCTCGGCGG
EST: gi|88359555|gb|CI621086.1|CI621086
EST:     TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTG                         GACAACGCCGGGGGTGGCATCGG
genomic: TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTGgtatgcgttc ... ttgttgacagGACAACGCCGGCGGTGGCATCGG
EST: gi|88394875|gb|CI607602.1|CI607602
EST:     TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCC-TCGCGCTG                         GA-AACGCCGGAGGTGGCATCGGCGGGGGGATGCTC
genomic: TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTGgtatgcgttc ... ttgttgacagGACAACGCCGGCGGTGGCATCGGCGGGCGGATGCTC
EST: gi|88362538|gb|CI623878.1|CI623878
EST:     TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTG                         GACAACGCCGG
genomic: TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTGgtatgcgttc ... ttgttgacagGACAACGCCGG
EST: gi|88400203|gb|CI590893.1|CI590893
EST:     TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTG                         GACAACGCCGGCGGTGGCCTCGGCGGGCGGATGATCGGAGGCGGTGCTGGC
genomic: TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTGgtatgcgttc ... ttgttgacagGACAACGCCGGCGGTGGCATCGGCGGGCGGATGCTCGGCGGCGGCGCTGGC
EST: gi|88389897|gb|CI626666.1|CI626666
EST:     TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTG                         GACAACGCCGGCGGTGGAATCGGCGGGCGGATGCTCGGCGGAGGCGC
genomic: TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTGgtatgcgttc ... ttgttgacagGACAACGCCGGCGGTGGCATCGGCGGGCGGATGCTCGGCGGCGGCGC
EST: gi|88350873|gb|CI619131.1|CI619131
EST:     TCCCTTTCGCCAGTGGCTTCCCGTCCTCGCCGGCGCTCTCCCTCGCGCTG                         GAAAACGCCGGGGGTGG
genomic: TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTGgtatgcgttc ... ttgttgacagGACAACGCCGGCGGTGG
EST: gi|88393812|gb|CI621307.1|CI621307
EST:     TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTG                         GACAACGCCGGCGGTGGCATCGGCGGGCGGATGCTCGGCGGCGGGGCTGGT
genomic: TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTGgtatgcgttc ... ttgttgacagGACAACGCCGGCGGTGGCATCGGCGGGCGGATGCTCGGCGGCGGCGCTGGC
EST: gi|88411106|gb|CI606325.1|CI606325
EST:     TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTG                         GACAACGCCGGCGGTGGCATCGGCGGGCGGATGCTCGGCGGCGGCGCTGGC
genomic: TCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTGgtatgcgttc ... ttgttgacagGACAACGCCGGCGGTGGCATCGGCGGGCGGATGCTCGGCGGCGGCGCTGGC

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), 63 (downstream exon)
Score: 23

CATGAGCTTTGGGGGCCTCTTTGACGGCGGCGGCGGGGGAGGCATGCAGTTCCCTTTCGCCAGTGGCTTCGCGTCCTCGCCGGCGCTCTCCCTCGCGCTGgtatgcgttc ... ttgttgacagGACAACGCCGGCGGTGGCATCGGCGGGCGGATGCTCGGCGGCGGCGCTGGCGCTGGTTCTAGCGCGGGCGGCGCGATGACGAGGGACACTGAGGCGGAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagagttttctcctcgatcgagaggttattgattgattctctattttgttgacagGACAACGCCGGCGGTGGCATCGGCGGGCGGATGCTCGGCGGCGGCGCTGGCGCTGGTTCTAGCGCGGGCGGCGCGATGACGAGGGACACTGAGGCGGAGA
                                    ttctctattttgtt  CT-rich tract
                         ttattgatt  TA-rich tract