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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcatggtcaaacttgttatctcactatgatctgagtatgcatttccgcacttgttcatcaaataccatgctggcatgaacgttctacagaatactgtgttcattccagatcttgcatttgttcatttatcatatcctattttcatctttgttattttttacatatgttattctccatatacagATTCCATTTTGTGTTGTCATTGGTTGGATGATGGGGCAAAAGATGGACTTGAATTTCCAACTATTCGAAACAGCAACGCTCTTCATAACAGTACTAGTCG

Basic information

species Oryza sativa
transcript LOC_Os04g55940.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 10
gtaatgcatggtcaaacttgttatctcactatgatctgagtatgcatttccgcacttgttcatcaaataccatgctggcatgaacgttctacagaatac-tgtgttcattccagatcttgcatttgttcatttatcatatcctattttcatctttgttattttttacatatgttattctccatatacagATTCCATTTTGTGTTGTCATTGGTTGGATGATGGGGCAAAAGATGGACTTGAATTTCCAACTATTCGAAACAGCAACGCTCTTCATAACAGTACTAGTCG
                                                                                |  | ||| |  || | || |  || |||| | ||  || |||      ||   | | || |   ||   ||| ||| |  ||| || |    ||| ||  | ||||||||||||||||||||||| |||||||||| |||||| |||||||||||||||||||| || ||||| || |||||||| ||||||||||||||||| || |
--------------------------------------------------------------------------------ttta-gttgtcaaggacacataagtacattactgaa-ttacataaa---atgccttaaattc---ttctgtctctgtgacatttgacgtggtatatacttta-atacagATTCCATTTTGTGTTGTTATTGGTTGGACGATGGGACAAAAGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTACTTGTGG

upper sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 9
gtaatgcatggtcaaacttgttatctcactatgatctgagtatgcatttccgcacttgttcatcaaataccatgctggcatgaacgttctacagaatactgtgttcattccagatcttgcatttgttcatttatcatatcctattttcatctttgttattttttacatatgttattctccatatacagATTCCATTTTGTGTTGTCATTGGTTGGATGATGGGGCAAAAGATGGACTTGAATTTCCAACTATTCGAAACAGCAACGCTCTTCATAACAGTACTAGTCG
                                                                               ||    ||  |  || |  | |   ||| |       || |||    || ||    | || |   ||  | ||  || |  |||  |||  | ||| ||||| || |||||||||||||||||||| ||||||||||||||||| |||| ||||||||||||||| || ||||| || |||||||| |||||||||||||| || || |
------------------------------------------------------------------------------aattttagtcattgaggaaccagaagtcaattactgaattacataaaatcctt----aaattc---ttctacctccgtgacgtttggcat--ggtatactcca-atgcagATTCCATTTTGTGTTGTTATTGGTTGGATGATGGGACAAAGGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTGCTTGTGG

upper sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G143356_T01 (Zea mays), 3'ss of exon 10
gtaatgcatggtcaaacttgttatctcactatgatctgagtatgcatttccgcacttgttcatcaaataccatgctggcatgaacgttctacagaatactgtgttcattccagatcttgcatttgttcatttatcatatcctattttcatctttgttattttttacatatgttattctccatatacagATTCCATTTTGTGTTGTCATTGGTTGGATGATGGGGCAAAAGATGGACTTGAATTTCCAACTATTCGAAACAGCAACGCTCTTCATAACAGTACTAGTCG-----------------
                                                                                                                                |  |  | ||   |  ||   ||| ||| |  ||| || |    ||| ||  | ||||||||||||||||||||||| |||||||||| |||||| |||||||||||||||||||| || ||||| || |||||||| ||||||||||||||||| || |                 
--------------------------------------------------------------------------------------------------------------------------------aaatgccttaaatt-cttctgtctctgtgacatttgacgtggtatatacttta-atacagattccattttgtgttgttattggttggacgatgggacaaaagATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAG

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|286840|gb|D15647.1|D15647
EST:     TAACACTGGGTGTTGCAATTGGGTCATCAACGCAGATATCAATGTTTGTG                         ATTCCATTTTGTGTTGTCATTGGTTGGATGATGGGGCAAAAGATGGACTTG
genomic: TAACACTGGGTGTTGCAATTGGGTCATCAACGCAGATATCAATGTTTGTGgtaatgcatg ... ccatatacagATTCCATTTTGTGTTGTCATTGGTTGGATGATGGGGCAAAAGATGGACTTG
EST: gi|66923908|gb|CX110756.1|CX110756
EST:     TAACACTGGGTGTTGCAATTGGGTCATCAACGCAGATATCAATGTTTGTG                         ATTCCATTTTGTGTTGTCATTGGTTGGATGATGGGGCAAAAGATGGACTTG
genomic: TAACACTGGGTGTTGCAATTGGGTCATCAACGCAGATATCAATGTTTGTGgtaatgcatg ... ccatatacagATTCCATTTTGTGTTGTCATTGGTTGGATGATGGGGCAAAAGATGGACTTG
EST: gi|33381504|gb|CF196847.1|CF196847
EST:     TGTTGCAATTGGGTCATCAACGCAGATATCAATGTTTGTG                         ATTCCATTTTGTGTTGTCATTGGTTGGATGATGGGGCAAAAGATGGACTTG
genomic: TGTTGCAATTGGGTCATCAACGCAGATATCAATGTTTGTGgtaatgcatg ... ccatatacagATTCCATTTTGTGTTGTCATTGGTTGGATGATGGGGCAAAAGATGGACTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatatcctattttcatctttgttattttttacatatgttattctccatatacagATTCCATTTTGTGTTGTCATTGGTTGGATGATGGGGCAAAAGATGGACTTGAATTTCCAACTATTCGAAACAGCAACGCTCTTCATAACAGTACTAGTCG
                                      ttattctcc  CT-rich tract
        tattttcatctttgtt  TA-rich tract