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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgaacaaatttccttcacttctgttggacgaaaaacttgaattttcatgttcccttgctagccgcgttagctgatcagaaaattgcgtgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCTGACGAGGTGGACCAGTAACATGTACCTGGTGTATATGGCGCGGTTGCCA

Basic information

species Oryza sativa
transcript LOC_Os05g28180.3
intron # 10
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|29675538|gb|CB671813.1|CB671813
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|58670237|gb|CK058923.1|CK058923
EST:     TTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: TTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|88833424|gb|CI076905.1|CI076905
EST:     AAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: AAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|88906221|gb|CI375293.1|CI375293
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTTTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|89198377|gb|CI007437.1|CI007437
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|88964769|gb|CI084767.1|CI084767
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTAAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|27548799|gb|CA767547.2|CA767547
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|29638453|gb|CB643462.1|CB643462
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|86481338|gb|CI123971.1|CI123971
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|88842057|gb|CI081313.1|CI081313
EST:     TGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: TGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|29637475|gb|CB642484.1|CB642484
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|88841548|gb|CI080804.1|CI080804
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|86536752|gb|CI176958.1|CI176958
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|87022773|gb|CI269709.1|CI269709
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatgttcccttgctagccgcgttagctgatcagaaaattgcgtgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCTGACGAGGTGGACCAGTAACATGTACCTGGTGTATATGGCGCGGTTGCCA
                          agctgat  putative branch site (score: 4)
                                                ttttc  putative PPT
                                  agaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgaacaaatttccttcacttctgttggacgaaaaacttgaattttcatgttcccttgctagccgcgttagctgatcagaaaattgcgtgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCTGACGAGGTGGACCAGTAACATGTACCTGGTGTATATGGCGCGGTTGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA