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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctatatacttacctgaccgccaagttctattattataagagttataaaccgcattgctaactacatgtaactaaactgcttgcttgtgtcgattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGACATACCACCTTAGCTGCCTTAAGTTCTCCGCCCACTATCAATTTTTGTA

Basic information

species Oryza sativa
transcript LOC_Os02g13530.1
intron # 3
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|89165150|gb|CI255207.1|CI255207
EST:     AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
genomic: AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
EST: gi|87031413|gb|CI261787.1|CI261787
EST:     AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
genomic: AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
EST: gi|88213743|gb|CI213592.1|CI213592
EST:     AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
genomic: AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
EST: gi|55411479|gb|CV723855.1|CV723855
EST:     AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
genomic: AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
EST: gi|427216|gb|D23298.1|D23298
EST:     AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATT
genomic: AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATT
EST: gi|87007097|gb|CI277172.1|CI277172
EST:     AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
genomic: AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
EST: gi|88558939|gb|CI489471.1|CI489471
EST:     AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATNCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
genomic: AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
EST: gi|87011719|gb|CI281421.1|CI281421
EST:     AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
genomic: AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
EST: gi|86416175|gb|CI030186.1|CI030186
EST:     AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
genomic: AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
EST: gi|3762404|gb|C99652.1|C99652
EST:     AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
genomic: AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
EST: gi|86510587|gb|CI153220.1|CI153220
EST:     AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
genomic: AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
EST: gi|88208253|gb|CI208102.1|CI208102
EST:     AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
genomic: AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
EST: gi|88524829|gb|CI453780.1|CI453780
EST:     AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
genomic: AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
EST: gi|38471297|gb|CF955428.1|CF955428
EST:     AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
genomic: AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
EST: gi|86420572|gb|CI056561.1|CI056561
EST:     AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
genomic: AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
EST: gi|88242685|gb|CI242534.1|CI242534
EST:     AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
genomic: AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
EST: gi|8336460|gb|BE040907.1|BE040907
EST:     GATGAAGGAGAGGAAGAACAGAGCAAAGGAAGATCCGGGGTGTGAAGAAG                         ACAAAGGCCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTG
genomic: GATGAAGGAGAGGAAGAACAGAGCAAAG-AAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGC-TGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTG
EST: gi|88241783|gb|CI241632.1|CI241632
EST:     AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
genomic: AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
EST: gi|87022540|gb|CI267677.1|CI267677
EST:     AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA
genomic: AGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGA

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: 75 (upstream exon), 74 (downstream exon)
Score: 78

AATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatac ... gattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGACATACCACCTTAGCTGCCTTAAGTTCTCCGCCCACTATCAATTTTTGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaccgcattgctaactacatgtaactaaactgcttgcttgtgtcgattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGACATACCACCTTAGCTGCCTTAAGTTCTCCGCCCACTATCAATTTTTGTA
                      taactaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctatatacttacctgaccgccaagttctattattataagagttataaaccgcattgctaactacatgtaactaaactgcttgcttgtgtcgattttgcagACAAAGGCTGGAGATGCAGGCAAGAAGAAGTAAGCAATGGTGTTGAATTGACATACCACCTTAGCTGCCTTAAGTTCTCCGCCCACTATCAATTTTTGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC