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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatgtaatttgtgataaaattggtgaacctctggtgctacatataccgtttgcctctataattgtgataacatctatggtaccacacatcatttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGAACCCCGTTATTACTAGAACAGGATCTGACCCACAAACTCTTGACAGCCG

Basic information

species Oryza sativa
transcript LOC_Os02g56210.1
intron # 7
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|218489304|gb|FG963268.1|FG963268
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|88279030|gb|CI400030.1|CI400030
EST:     GCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGACCGGCCCCTGTTGAG
genomic: GCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCT-GCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAG
EST: gi|88320989|gb|CI530341.1|CI530341
EST:     ACAGTATCAGAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGANCGGCGCCTGTTGAGA
genomic: ACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|66916903|gb|CX103751.1|CX103751
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|88485092|gb|CI422363.1|CI422363
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|88446823|gb|CI528866.1|CI528866
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|88530937|gb|CI459368.1|CI459368
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|88514234|gb|CI441740.1|CI441740
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|86886462|gb|CI322694.1|CI322694
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|86908161|gb|CI300653.1|CI300653
EST:     CACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: CACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|88518671|gb|CI446325.1|CI446325
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|88969175|gb|CI382724.1|CI382724
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|89196512|gb|CI399098.1|CI399098
EST:     CATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: CATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|88277428|gb|CI398230.1|CI398230
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGGTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|88269261|gb|CI380559.1|CI380559
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGGTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|88284026|gb|CI405472.1|CI405472
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|218495675|gb|FG954247.1|FG954247
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|25803115|gb|CA759076.1|CA759076
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|88460383|gb|CI531856.1|CI531856
EST:     CGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: CGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|218484683|gb|FG956662.1|FG956662
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAAAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGC
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGC
EST: gi|86433955|gb|CI094298.1|CI094298
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|86593586|gb|CI264465.1|CI264465
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|88906305|gb|CI375377.1|CI375377
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|88277759|gb|CI398561.1|CI398561
EST:     CCCACAGTATCACAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: CCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|88846726|gb|CI373494.1|CI373494
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGGTAGAG                         TTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGGCGGCGCCTTTTGAG
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGA-GCGGCGCCTGTTGAG
EST: gi|88490387|gb|CI427659.1|CI427659
EST:     AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG                         GTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
genomic: AGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA
EST: gi|88504795|gb|CI432301.1|CI432301
EST:     CACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGGTAGAG                         GTACTGTGTGGAAGGCGAAGAATTCCTCAACTGGAGCGGCCCCTGTTGAGA
genomic: CACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGA

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: 73 (upstream exon), 31 (downstream exon)
Score: 9

GGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAGgtttcttctg ... catttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGAACCCCGTTATTACTAGAACAGGATCTGACCCACAAACTCTTGACAGCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accgtttgcctctataattgtgataacatctatggtaccacacatcatttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGAACCCCGTTATTACTAGAACAGGATCTGACCCACAAACTCTTGACAGCCG
                    tgataac  putative branch site (score: 9)
            tataattgtgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtaatttgtgataaaattggtgaacctctggtgctacatataccgtttgcctctataattgtgataacatctatggtaccacacatcatttgacagGTACTGTGTGGAAAGCGAAGAATTCCTCAACTGGAGCGGCGCCTGTTGAGAACCCCGTTATTACTAGAACAGGATCTGACCCACAAACTCTTGACAGCCG

- - - - -ttgtgat
- - - - - - - - - - - - - - - -ctggtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtaccac