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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctaatgtagaacatctacaatcaggcatattaaacatttgacaacctgtagttattgattgacgctactaattgtttcttcacaatcgggttttgcagGATTGTTCTGGAAACAGATGCAAAGGCGATTCTTGAAAAGGTATCAGGTCATGGATTGGAAGGATCCGGGTCTCTCACTGAGCAG

Basic information

species Oryza sativa
transcript LOC_Os01g62150.1
intron # 4
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|33688267|gb|CF316506.1|CF316506
EST:     GAAAACTTGGATCTTATCTTCTTATGCCTTGACGAAGTTGTTGATGGAGG                         GATTGTTCTGGAAACAGATGCAAAGGCGATTCTTGAAAAGGTATCAGGTCA
genomic: GAAAACTTGGATCTTATCTTCTTATGCCTTGACGAAGTTGTTGATGGAGGgtaattacta ... ggttttgcagGATTGTTCTGGAAACAGATGCAAAGGCGATTCTTGAAAAGGTATCAGGTCA
EST: gi|88265041|gb|CI368815.1|CI368815
EST:     GAAAACTTGGATCTTATCTTCTTATGCCTTGACGAAGTTGTTGATGGAGG                         GATTGTTCT-GAAACAGATGCAAAGGCGATTCTTGAAAAGGTATCAGGTCA
genomic: GAAAACTTGGATCTTATCTTCTTATGCCTTGACGAAGTTGTTGATGGAGGgtaattacta ... ggttttgcagGATTGTTCTGGAAACAGATGCAAAGGCGATTCTTGAAAAGGTATCAGGTCA
EST: gi|86822723|gb|CI251806.1|CI251806
EST:     GAAAACTTGGATCTTATCTTCTTATGCCTTGACGAAGTTGTTGATGGAGG                         GATTGTTCTGGAAACAGATGCAAAGGCGATTCTTGAAAAGGTATCAGGTCA
genomic: GAAAACTTGGATCTTATCTTCTTATGCCTTGACGAAGTTGTTGATGGAGGgtaattacta ... ggttttgcagGATTGTTCTGGAAACAGATGCAAAGGCGATTCTTGAAAAGGTATCAGGTCA
EST: gi|25807173|gb|CA763128.1|CA763128
EST:     GAAAACTTGGATCTTATCTTCTTATGCCTTGACGAAGTTGTTGATGGAGG                         GATTGTTCTGGAAACAGATGCAAAGGCGATTCTTGAAAAGGTATCAGGTCA
genomic: GAAAACTTGGATCTTATCTTCTTATGCCTTGACGAAGTTGTTGATGGAGGgtaattacta ... ggttttgcagGATTGTTCTGGAAACAGATGCAAAGGCGATTCTTGAAAAGGTATCAGGTCA
EST: gi|163928249|gb|EG714641.1|EG714641
EST:     GAAAACTTGGATCTTATCTTCTTATGCCTTGACGAAGTTGTTGATGGAGG                         GATTGTTCTGGAAACAGATGCAAAGGCGATTCTTGAAAAGGTATCAGGTCA
genomic: GAAAACTTGGATCTTATCTTCTTATGCCTTGACGAAGTTGTTGATGGAGGgtaattacta ... ggttttgcagGATTGTTCTGGAAACAGATGCAAAGGCGATTCTTGAAAAGGTATCAGGTCA
EST: gi|58686756|gb|CK075443.1|CK075443
EST:     GAAAACTTGGATCTTATCTTCTTATGCCTTGACGAAGTTGTTGATGGAGG                         GATTGTTCTGGAAACAGATGCAA
genomic: GAAAACTTGGATCTTATCTTCTTATGCCTTGACGAAGTTGTTGATGGAGGgtaattacta ... ggttttgcagGATTGTTCTGGAAACAGATGCAA
EST: gi|33656563|gb|CF279177.1|CF279177
EST:     GAAAACTTGGATCTTATCTTCTTATGCCTTGACGAAGTTGTTGATGGAGG                         GGATTGTTCTGGAAACAGATGCAAAGGCGATTCTTGAAA
genomic: GAAAACTTGGATCTTATCTTCTTATGCCTTGACGAAGTTGTTGATGGAGGgtaattacta ... ggttttgcagG-ATTGTTCTGGAAACAGATGCAAAGGCGATTCTTGAAA
EST: gi|86599370|gb|CI251328.1|CI251328
EST:     GAAAACTTGGATCTTATCTTCTTATGCCTTGACGAAGTTGTTGATGGAGG                         GATTGTTCTGGAAACAGATGCAAAGGCGATTCTTGAAAAGGTATCAGGTCA
genomic: GAAAACTTGGATCTTATCTTCTTATGCCTTGACGAAGTTGTTGATGGAGGgtaattacta ... ggttttgcagGATTGTTCTGGAAACAGATGCAAAGGCGATTCTTGAAAAGGTATCAGGTCA
EST: gi|33656564|gb|CF279178.1|CF279178
EST:     GAAAACTTGGATCTTATCTTCTTATGCCTTGACGAAGTTGTTGATGGAGG                         GATTGTTCTGGAAACAGATGCAAAGGCGATTCTTGAAAAGGTATCAGGTCA
genomic: GAAAACTTGGATCTTATCTTCTTATGCCTTGACGAAGTTGTTGATGGAGGgtaattacta ... ggttttgcagGATTGTTCTGGAAACAGATGCAAAGGCGATTCTTGAAAAGGTATCAGGTCA

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: 52 (upstream exon), 69 (downstream exon)
Score: 13

AAACAAAGTGCACAGAAGGGCTGCGCTTGAAAACTTGGATCTTATCTTCTTATGCCTTGACGAAGTTGTTGATGGAGGgtaattacta ... ggttttgcagGATTGTTCTGGAAACAGATGCAAAGGCGATTCTTGAAAAGGTATCAGGTCATGGATTGGAAGGATCCGGGTCTCTCACTGAGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctgtagttattgattgacgctactaattgtttcttcacaatcgggttttgcagGATTGTTCTGGAAACAGATGCAAAGGCGATTCTTGAAAAGGTATCAGGTCATGGATTGGAAGGATCCGGGTCTCTCACTGAGCAG
                      tactaat  putative branch site (score: 13)
        ttattgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctaatgtagaacatctacaatcaggcatattaaacatttgacaacctgtagttattgattgacgctactaattgtttcttcacaatcgggttttgcagGATTGTTCTGGAAACAGATGCAAAGGCGATTCTTGAAAAGGTATCAGGTCATGGATTGGAAGGATCCGGGTCTCTCACTGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
-gctaatg
- - - - - - -catctac
- - - - - - - - - - - -caggcat
- - - - - - - - - - - - - - - - - -acatttg
- - - - - - - - - - - - - - - - - - - - - - - cctgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgctact