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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtataagttcaacgaactccatatgcattatttcttgtctaaagaatatgctcacctgaacatgttgatctgactggataagcttcctttggatctgcagATAAGTTTAGATCAGATCTCATGAACATTGCCATGACTACACTTAGTTCAAAAATCCTCTCTCAGGACAAGGAGTACTTTGCTGAACTTGCTGTTGATGC

Basic information

species Oryza sativa
transcript LOC_Os03g42220.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g42220.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 14
--gtataagttcaacgaactccatatgcattatttcttgtctaaagaatatgctcacctgaacatgttgatctgactggataagcttcctttggat----ctgcagATAAGTTTAGATCAGATCTCATGAACATTGCCATGACTACACTTAGTTCAAAAATCCTCTCTCAGGACAAGGAGTACTTTGCTGAACTTGCTGTTGATGC
| || |||| | || | || || ||| | |||||||| | || ||| |||| | || || ||| ||| || |||||||||| || ||||| ||||||||||| ||||| |||||||| |||||||||||||| || || || |||||||||||||| ||||||||||| ||||||||
ggattcaaattcacttcatcttgcatc--tcatggattctctcaggaatatgccaccatgcccat--caatctcat--gacaatattctttttcattcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTCGCTGAACTTGCGGTTGATGC

upper sequence: LOC_Os03g42220.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G058276_T01 (Zea mays), 3'ss of exon 5
gtataagttcaa--cgaactccatatgcattatttc--ttgtctaaagaatatgctcacctgaacatgttgatctgactggataagcttcctttggatctgcagATAAGTTTAGATCAGATCTCATGAACATTGCCATGACTACACTTAGTTCAAAAATCCTCTCTCAGGACAAGGAGTACTTTGCTGAACTTGCTGTTGATGC
|| || ||||| | ||| |||| | | || | | | ||||||| || ||| ||||| | || || | | ||| |||||||||||||| ||| | ||||||||||| ||||| |||||||| |||||||||||||| || || || |||||||||||||||||||||||||| ||||||||
ataaaaattcaaattcacttcctcttgcaacacatggattcttttagaaatatgccattatgctcat--cgatctcat--gacaatatccttttccttctgcagATAAGTTCAGAGCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTTGCTGAACTTGCGGTTGATGC
















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|58684862|gb|CK073549.1|CK073549
EST:     TGCTAGAAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAG                         ATAAGTTTAGATCAGATCTCATGAAC
genomic: TGCTAGAAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAGgtaactatgt ... ggatctgcagATAAGTTTAGATCAGATCTCATGAAC
EST: gi|58685627|gb|CK074314.1|CK074314
EST:     GCTAGAAACGC-TTGCTGGAGAGGACCATGGACAACAAAGAAAATATAG                         ATAAGTTTAGATCAGATCTCATGAACATTGCCATGACTACACTTAGTTCAA
genomic: GCTAGAAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAGgtaactatgt ... ggatctgcagATAAGTTTAGATCAGATCTCATGAACATTGCCATGACTACACTTAGTTCAA
EST: gi|66918817|gb|CX105665.1|CX105665
EST:     GAAACGC-TTGCTGGAGAGGA-CATGGAC-ACAAAGAAAATATAG                         ATAAGTTTAGATCAGATCTCATGAACANTTG-CATGACTACACTTAGTTCA
genomic: GAAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAGgtaactatgt ... ggatctgcagATAAGTTTAGATCAGATCTCATGAACA-TTGCCATGACTACACTTAGTTCA
EST: gi|29676853|gb|CB673128.1|CB673128
EST:     TGCTAGAAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAG                         ATAAGTTTAGATCAGATCTCATGAACATTGCCATGACTACACTTAGTTCAA
genomic: TGCTAGAAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAGgtaactatgt ... ggatctgcagATAAGTTTAGATCAGATCTCATGAACATTGCCATGACTACACTTAGTTCAA
EST: gi|29657046|gb|CB653321.1|CB653321
EST:     TGCTAGAAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAG                         ATAAGTTTAGATCAGATCTCATGAACATTGCCATGACTACACTTAGTTCAA
genomic: TGCTAGAAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAGgtaactatgt ... ggatctgcagATAAGTTTAGATCAGATCTCATGAACATTGCCATGACTACACTTAGTTCAA
EST: gi|29616345|gb|CB621357.1|CB621357
EST:     TGCTAGAAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAG                         ATAAGTTTAGATCAGATCTCATGAACATTGCCATGACTACACTTAGTTCAA
genomic: TGCTAGAAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAGgtaactatgt ... ggatctgcagATAAGTTTAGATCAGATCTCATGAACATTGCCATGACTACACTTAGTTCAA
EST: gi|218488070|gb|FG946099.1|FG946099
EST:     AAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAG                         ATAAGTTTAGATCAGATCTCATGAACATTGCCATGACTACACTTAGTTCAA
genomic: AAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAGgtaactatgt ... ggatctgcagATAAGTTTAGATCAGATCTCATGAACATTGCCATGACTACACTTAGTTCAA
EST: gi|88422879|gb|CI615179.1|CI615179
EST:     TGCTAGAAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAG                         ATAAGTTTAGATCAGATCTCATGAACATTGCCATGACTACACTTAGTTCAA
genomic: TGCTAGAAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAGgtaactatgt ... ggatctgcagATAAGTTTAGATCAGATCTCATGAACATTGCCATGACTACACTTAGTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgctcacctgaacatgttgatctgactggataagcttcctttggatctgcagATAAGTTTAGATCAGATCTCATGAACATTGCCATGACTACACTTAGTTCAAAAATCCTCTCTCAGGACAAGGAGTACTTTGCTGAACTTGCTGTTGATGC
                                     cttcctttg  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataagttcaacgaactccatatgcattatttcttgtctaaagaatatgctcacctgaacatgttgatctgactggataagcttcctttggatctgcagATAAGTTTAGATCAGATCTCATGAACATTGCCATGACTACACTTAGTTCAAAAATCCTCTCTCAGGACAAGGAGTACTTTGCTGAACTTGCTGTTGATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT