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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttcttgtgttcatgtaaaggacaattgcgattgtggctttgcatgatccctatttatttctataacaaactgtatcccattgcagAAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACACTCTTCAGAT

Basic information

species Oryza sativa
transcript LOC_Os01g43070.1
intron # 5
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|89163919|gb|CI101007.1|CI101007
EST:     ATTTTGGCTGAAAAATCTTCACTG                         AAGGTGACGACGGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
genomic: ATTTTGGCTGAAAAATCTTCACTGgtaatttctt ... cccattgcagAAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
EST: gi|27577239|gb|CA999933.1|CA999933
EST:     GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACT-                         --GGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
genomic: GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTGgtaatttctt ... cccattgcagAAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
EST: gi|218495434|gb|FG956077.1|FG956077
EST:     GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTG                         AAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
genomic: GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTGgtaatttctt ... cccattgcagAAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
EST: gi|86415980|gb|CI029991.1|CI029991
EST:     GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTG                         AAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
genomic: GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTGgtaatttctt ... cccattgcagAAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
EST: gi|88843742|gb|CI011000.1|CI011000
EST:     GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTG                         AAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
genomic: GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTGgtaatttctt ... cccattgcagAAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
EST: gi|58606651|gb|CK034684.1|CK034684
EST:     GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTG                         AAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
genomic: GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTGgtaatttctt ... cccattgcagAAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
EST: gi|88991038|gb|CI108425.1|CI108425
EST:     GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTG                         AAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
genomic: GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTGgtaatttctt ... cccattgcagAAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
EST: gi|58605125|gb|CK033158.1|CK033158
EST:     GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTG                         AAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
genomic: GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTGgtaatttctt ... cccattgcagAAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
EST: gi|86827940|gb|CI274869.1|CI274869
EST:     GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTG                         AAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
genomic: GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTGgtaatttctt ... cccattgcagAAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
EST: gi|66915473|gb|CX102321.1|CX102321
EST:     AAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTG                         AAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
genomic: AAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTGgtaatttctt ... cccattgcagAAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
EST: gi|86259241|gb|CI010542.1|CI010542
EST:     GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTG                         AAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
genomic: GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTGgtaatttctt ... cccattgcagAAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
EST: gi|2801088|gb|AA754382.1|AA754382
EST:     AAAAGATGTTGCTGATTGGATTTTRGCTGAAAAATCTTCACTG                         AAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
genomic: AAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTGgtaatttctt ... cccattgcagAAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
EST: gi|8335555|gb|BE040446.1|BE040446
EST:     GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTG                         AAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGAGGCGCAC
genomic: GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTGgtaatttctt ... cccattgcagAAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
EST: gi|88981435|gb|CI027053.1|CI027053
EST:     AAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTG                         AAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
genomic: AAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTGgtaatttctt ... cccattgcagAAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
EST: gi|86528789|gb|CI168995.1|CI168995
EST:     GGGATCCAAAAGATGTTGCTAATTGGATTTTGGCTGAAAAATCTTCACTG                         AAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC
genomic: GGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTGgtaatttctt ... cccattgcagAAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACAC

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: 67 (upstream exon), 60 (downstream exon)
Score: 42

ATTGGGCCGCCAAATTCACGTTTTCCGCCTTCCAAGGACAAGAGCAAGTGGGATCCAAAAGATGTTGCTGATTGGATTTTGGCTGAAAAATCTTCACTGgtaatttctt ... cccattgcagAAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACACTCTTCAGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtggctttgcatgatccctatttatttctataacaaactgtatcccattgcagAAGGTGACGACAGGCCAACGCATGACAGAGAGTTCTGTCCTTGATGCACACTCTTCAGAT
                             ctataac  putative branch site (score: 42)
                                            tcccatt  putative PPT
                    tatttatttctataac  TA-rich tract