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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcgcctttggaaacccaccttatcttgagctttaattcataattgtaattcataatgcttttatcttgtttttgcttgtttcctcgatttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGTCGATTCCTAAGGCACAACACAACAACGCCTTGTACGGTTTTAGTCTGGT

Basic information

species Oryza sativa
transcript LOC_Os01g32439.1
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|88550788|gb|CI480785.1|CI480785
EST:     GAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCG                         GAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
genomic: GAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCGgtaagaatct ... ttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
EST: gi|88239873|gb|CI239035.1|CI239035
EST:     AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCG                         GAATAAGGTTGGTCTGCATCGGCACGACCAACAGCCCACAAAGAGGTGTGT
genomic: AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCGgtaagaatct ... ttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
EST: gi|88325352|gb|CI675149.1|CI675149
EST:     AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCG                         GAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
genomic: AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCGgtaagaatct ... ttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
EST: gi|88583743|gb|CI701246.1|CI701246
EST:     AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCG                         GAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCC
genomic: AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCGgtaagaatct ... ttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCC
EST: gi|88581053|gb|CI698024.1|CI698024
EST:     AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCG                         GAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
genomic: AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCGgtaagaatct ... ttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
EST: gi|88547120|gb|CI477396.1|CI477396
EST:     AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCG                         GAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
genomic: AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCGgtaagaatct ... ttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
EST: gi|88588569|gb|CI706394.1|CI706394
EST:     AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCG                         GAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
genomic: AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCGgtaagaatct ... ttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
EST: gi|88545574|gb|CI475143.1|CI475143
EST:     GCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCG                         GAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
genomic: GCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCGgtaagaatct ... ttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
EST: gi|88352868|gb|CI678896.1|CI678896
EST:     AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCG                         GAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
genomic: AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCGgtaagaatct ... ttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
EST: gi|88526422|gb|CI453158.1|CI453158
EST:     AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCG                         GAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
genomic: AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCGgtaagaatct ... ttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
EST: gi|88463549|gb|CI696015.1|CI696015
EST:     AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCG                         GAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
genomic: AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCGgtaagaatct ... ttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
EST: gi|88577083|gb|CI673636.1|CI673636
EST:     AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCG                         GAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
genomic: AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCGgtaagaatct ... ttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
EST: gi|88550424|gb|CI478397.1|CI478397
EST:     GGGCTCCAAGTCCG                         GAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
genomic: GGGCTCCAAGTCCGgtaagaatct ... ttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
EST: gi|88523650|gb|CI451495.1|CI451495
EST:     AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCG                         GAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
genomic: AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCGgtaagaatct ... ttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
EST: gi|88581811|gb|CI699021.1|CI699021
EST:     AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCG                         GAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
genomic: AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCGgtaagaatct ... ttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
EST: gi|55408279|gb|CV720655.1|CV720655
EST:     AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCG                         GAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT
genomic: AGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCGgtaagaatct ... ttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGT

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: 29 (upstream exon), 33 (downstream exon)
Score: 3

GCATGGGCAAGCCCGTATGGCGCCGACGGCGGCGATACCGCTTCTCGACGAGACCAACACCGCAGTGAGGTTTCCCGGTAGAATTAGGGCTCCAAGTCCGgtaagaatct ... ttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGTCGATTCCTAAGGCACAACACAACAACGCCTTGTACGGTTTTAGTCTGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaattcataatgcttttatcttgtttttgcttgtttcctcgatttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGTCGATTCCTAAGGCACAACACAACAACGCCTTGTACGGTTTTAGTCTGGT
                                            tttgctt  CT-rich tract
               ttttatcttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcgcctttggaaacccaccttatcttgagctttaattcataattgtaattcataatgcttttatcttgtttttgcttgtttcctcgatttgcttgcagGAATAAGGTTGGTCTGCATCGGCACGATCAACAGCCCACAAAGAGGTGTGTCGATTCCTAAGGCACAACACAACAACGCCTTGTACGGTTTTAGTCTGGT

- - - - - - aaaccca