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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattagcttactgatgcttatataaattctttttcattacatatggctggagaactatctaatcaaataatgattataattccaatcgttctttttatgccattatgatcttctgaaatttccttctttggacacttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTTGGTTGAATCATATGATGCCAAAACTATTATTGGAGGCACAAATAGCTTG

Basic information

species Oryza sativa
transcript LOC_Os05g22940.1
intron # 34
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|88831260|gb|CI082070.1|CI082070
EST:     GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAG                         ATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
genomic: GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAGgtaattagct ... acttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
EST: gi|58695714|gb|CK084401.1|CK084401
EST:     GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAG                         ATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
genomic: GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAGgtaattagct ... acttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
EST: gi|89168891|gb|CI020972.1|CI020972
EST:     GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAG                         ATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
genomic: GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAGgtaattagct ... acttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
EST: gi|58658504|gb|CK047184.1|CK047184
EST:     TCCATGTTACTAGATAAG                         ATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
genomic: TCCATGTTACTAGATAAGgtaattagct ... acttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
EST: gi|58694968|gb|CK083655.1|CK083655
EST:     GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAG                         ATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
genomic: GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAGgtaattagct ... acttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
EST: gi|88840936|gb|CI000898.1|CI000898
EST:     GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAG                         ATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
genomic: GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAGgtaattagct ... acttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
EST: gi|88571714|gb|CI663087.1|CI663087
EST:     GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAG                         ATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
genomic: GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAGgtaattagct ... acttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
EST: gi|33678131|gb|CF306370.1|CF306370
EST:     GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAG                         ATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
genomic: GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAGgtaattagct ... acttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
EST: gi|58655652|gb|CK044332.1|CK044332
EST:     GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAG                         ATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
genomic: GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAGgtaattagct ... acttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
EST: gi|88592407|gb|CI710509.1|CI710509
EST:     GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAG                         ATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
genomic: GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAGgtaattagct ... acttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
EST: gi|32948002|gb|BP184574.1|BP184574
EST:     GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAG                         ATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
genomic: GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAGgtaattagct ... acttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
EST: gi|88218215|gb|CI218064.1|CI218064
EST:     GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAG                         ATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
genomic: GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAGgtaattagct ... acttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
EST: gi|25803623|gb|CA759584.1|CA759584
EST:     GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAG                         ATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
genomic: GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAGgtaattagct ... acttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
EST: gi|29629331|gb|CB634342.1|CB634342
EST:     GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAG                         ATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
genomic: GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAGgtaattagct ... acttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
EST: gi|29624334|gb|CB629345.1|CB629345
EST:     GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAG                         ATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
genomic: GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAGgtaattagct ... acttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
EST: gi|88218267|gb|CI218116.1|CI218116
EST:     GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAG                         ATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
genomic: GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAGgtaattagct ... acttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
EST: gi|89179908|gb|CI044187.1|CI044187
EST:     GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAG                         ATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
genomic: GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAGgtaattagct ... acttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
EST: gi|88218276|gb|CI218125.1|CI218125
EST:     GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAG                         ATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT
genomic: GCTCAGATTTGCAAGCCCTGCCACAGGGTCTTTCCATGTTACTAGATAAGgtaattagct ... acttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttttatgccattatgatcttctgaaatttccttctttggacacttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTTGGTTGAATCATATGATGCCAAAACTATTATTGGAGGCACAAATAGCTTG
                                              cttattc  CT-rich tract
             attatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattagcttactgatgcttatataaattctttttcattacatatggctggagaactatctaatcaaataatgattataattccaatcgttctttttatgccattatgatcttctgaaatttccttctttggacacttattcagATGGATCCCTCTAGAAGAGCTCAACTTGTTGAAGAAATCAGGAAGGTCCTTGGTTGAATCATATGATGCCAAAACTATTATTGGAGGCACAAATAGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG