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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCCATGGCCTTTTTGACCCTCAAGATGTAAGGCCTAATGGGGCAAGGAACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctacctgcttgttccttcattcgatttatgtgtcctgaaatgcaatctaacaaataactgttctcctcaaacag

Basic information

species Oryza sativa
transcript LOC_Os03g27010.1
intron # 4
splice site 5'
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|87026012|gb|CI257170.1|CI257170
EST:     ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|29661138|gb|CB657413.1|CB657413
EST:     ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|29661239|gb|CB657514.1|CB657514
EST:     ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|87012920|gb|CI297147.1|CI297147
EST:     ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|66916849|gb|CX103697.1|CX103697
EST:     ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|86854155|gb|CI252146.1|CI252146
EST:     CACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: CACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|29665112|gb|CB661387.1|CB661387
EST:     ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|11025516|gb|AU162117.1|AU162117
EST:     ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|58680529|gb|CK069216.1|CK069216
EST:     ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|38475431|gb|CF959564.1|CF959564
EST:     ACACAGCAAATGGCAC-GGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|29640214|gb|CB645223.1|CB645223
EST:     ACCCAGCAAATGGCCCCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|86498964|gb|CI141597.1|CI141597
EST:     ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
EST: gi|11025517|gb|AU162118.1|AU162118
EST:     CACAGCAAATGGCACCGGTGCCTCACACACACTTGTGAGAAATGCAAAT                         GTGAGCCAGCTTCTCGTTTGGGGAGGCCAACA-TGACAGCGTGNCGAAAAC
genomic: CACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGC-AGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAAC
EST: gi|86417826|gb|CI032035.1|CI032035
EST:     ACACACACCTGTGAGAAATGCAAAT                         GTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT
genomic: ACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACT

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: 54

TGGCCATGGCCTTTTTGACCCTCAAGATGTAAGGCCTAATGGGGCAAGGAACACAGCAAATGGCACCGGTGCCTCACACACACCTGTGAGAAATGCAAATgtactgctac ... cctcaaacagGTGAGCAGCTTCTCGTTTGGGGAGGCCAACACTGACAGCGTGACGAAAACTGCAAAGAAGATAACTGGCAAGAAATTCACCGATCTCACAGGCAACAACA




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