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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtagatcaatttggaatggagggagtacgacattaagatagatagattagattagattaattaatgacctgcacattgatttgaatgcatatgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG

Basic information

species Oryza sativa
transcript LOC_Os02g01150.2
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|38477990|gb|CF962123.1|CF962123
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCGCTGTGACATGGAAG
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGC-CTGTGACATGGAAG
EST: gi|29674134|gb|CB670409.1|CB670409
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGANAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
EST: gi|29680605|gb|CB676880.1|CB676880
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGA
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGA
EST: gi|58693460|gb|CK082147.1|CK082147
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
EST: gi|29616322|gb|CB621334.1|CB621334
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
EST: gi|10794734|gb|AU108700.1|AU108700
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
EST: gi|29682953|gb|CB679228.1|CB679228
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAAC
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAAC
EST: gi|29682997|gb|CB679272.1|CB679272
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
EST: gi|29655664|gb|CB651939.1|CB651939
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
EST: gi|117233241|gb|CT848054.1|CT848054
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
EST: gi|11442863|gb|BF430762.1|BF430762
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
EST: gi|29621567|gb|CB626578.1|CB626578
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
EST: gi|29660668|gb|CB656943.1|CB656943
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
EST: gi|86906454|gb|CI294577.1|CI294577
EST:     AGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: AGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
EST: gi|29678225|gb|CB674500.1|CB674500
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
EST: gi|38481826|gb|CF965897.1|CF965897
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
EST: gi|29613448|gb|CB618461.1|CB618461
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCC
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCC
EST: gi|29676108|gb|CB672383.1|CB672383
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA

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: 69 (upstream exon), 73 (downstream exon)
Score: 60

ATCGAGGGCTTCAAGATGAACTTGATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagattagattaattaatgacctgcacattgatttgaatgcatatgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG
     attagattaattaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagatcaatttggaatggagggagtacgacattaagatagatagattagattagattaattaatgacctgcacattgatttgaatgcatatgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG