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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgagtgccgcgccgccgctaatcccttcctctccgttcttgctccggcccgccgtgctggcctatcttctcttcggctcgatttggtttggtttggtttgatttgattcggtttggtttgggcagGATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGACGGGAGCGTCGTCAACCTCGGCCTCTGGGACACTGCAG

Basic information

species Oryza sativa
transcript LOC_Os01g12900.1
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|7134828|gb|AU082694.1|AU082694
EST:     TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACC                         GATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
genomic: TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACCgttgagtgcc ... gtttgggcagGATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
EST: gi|7134839|gb|AU082699.1|AU082699
EST:     TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACC                         GATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
genomic: TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACCgttgagtgcc ... gtttgggcagGATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
EST: gi|88396989|gb|CI578138.1|CI578138
EST:     TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACC                         GATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
genomic: TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACCgttgagtgcc ... gtttgggcagGATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
EST: gi|38478868|gb|CF963001.1|CF963001
EST:     TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACC                         GATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
genomic: TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACCgttgagtgcc ... gtttgggcagGATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
EST: gi|33693104|gb|CF321343.1|CF321343
EST:     TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCTACAAGTTCCCCACC                         GATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
genomic: TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACCgttgagtgcc ... gtttgggcagGATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
EST: gi|88740975|gb|CI764483.1|CI764483
EST:     TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACC                         GATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
genomic: TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACCgttgagtgcc ... gtttgggcagGATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
EST: gi|88313328|gb|CI594958.1|CI594958
EST:     TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACC                         GATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
genomic: TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACCgttgagtgcc ... gtttgggcagGATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
EST: gi|218486326|gb|FG948103.1|FG948103
EST:     TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACC                         GATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
genomic: TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACCgttgagtgcc ... gtttgggcagGATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
EST: gi|38482617|gb|CF966571.1|CF966571
EST:     TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACC                         GATTACGTCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
genomic: TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACCgttgagtgcc ... gtttgggcagGATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
EST: gi|55439594|gb|CV733107.1|CV733107
EST:     TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACC                         GATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
genomic: TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACCgttgagtgcc ... gtttgggcagGATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
EST: gi|427824|gb|D23963.1|D23963
EST:     TGGGGAAGACGTGCATCCTCATCTGCTACACCTGCAACAAGTTCCCCACC                         GATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC
genomic: TGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACCgttgagtgcc ... gtttgggcagGATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGAC

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), 74 (downstream exon)
Score: 7

GGCGGCGGCGACGAGGTTCATCAAGTGCGTCACCGTGGGGGACGGCGCGGTGGGGAAGACGTGCATGCTCATCTGCTACACCTGCAACAAGTTCCCCACCgttgagtgcc ... gtttgggcagGATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGACGGGAGCGTCGTCAACCTCGGCCTCTGGGACACTGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcggctcgatttggtttggtttggtttgatttgattcggtttggtttgggcagGATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGACGGGAGCGTCGTCAACCTCGGCCTCTGGGACACTGCAG
                              atttgat  putative branch site (score: 7)
                          tttgattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgagtgccgcgccgccgctaatcccttcctctccgttcttgctccggcccgccgtgctggcctatcttctcttcggctcgatttggtttggtttggtttgatttgattcggtttggtttgggcagGATTACATCCCCACCGTGTTCGACAACTTCAGCGCCAATGTCTCCGTGGACGGGAGCGTCGTCAACCTCGGCCTCTGGGACACTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG