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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcacgttccttaagttgattactatttttcctttgcattactaaaatttccacacttgcttaataacttgtgtttttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGCAGCAAAGGCCAGAATGGCTAGTCGGATGCCGCAGATGAGCGGGATGGAT

Basic information

species Oryza sativa
transcript LOC_Os05g46290.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g46290.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G074790_T03 (Zea mays), 3'ss of exon 16
gtacgcacgttccttaagttgattact--atttttcctttgcattactaaaatttccacacttgcttaataacttgtgtttttgttt--cagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGCAGCAAAGGCCAGAATGGCTAGTCGGATGCCGCAGATGAGCGGGATGGAT
    | || || |  |||   | | |      | || |  | |  |||| |   || |  |||| |||  ||  |||| |  ||||   |||||||||  |||||||| |||| || ||||| |||||  | |||| ||| ||| | ||| ||||||| || || || ||||||||||||||||||||||| 
----gtacatttcc-aagaaaactgccccgcgtgtcttccgtacgactagacgatcaaagcttgtttacgaatctgtgatgctgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGCAACCAAGTCCAGAATAGCCAGCCGTATGCCGCAGATGAGCGGGATGGAC
















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|88289167|gb|CI553143.1|CI553143
EST:     AAAGTCATCCGAACAGCGCTACAAGATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
genomic: AAAGTCATCCGAACAGCGCTACAAGATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
EST: gi|286778|gb|D15585.1|D15585
EST:     ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTNGCTGAGCCCCCAGC
genomic: ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
EST: gi|88907793|gb|CI091191.1|CI091191
EST:     ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTATAAGATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
genomic: ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
EST: gi|89184864|gb|CI048420.1|CI048420
EST:     ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
genomic: ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
EST: gi|66913046|gb|CX099894.1|CX099894
EST:     TCATCGACCCTGTGAAAAGTCATACGAACAGCGCTACAAGATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
genomic: TCATCGACCCTGTGAAA-GTCATCCGAACAGCGCTACAAGATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
EST: gi|94362402|gb|CI052327.1|CI052327
EST:     ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
genomic: ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
EST: gi|88297143|gb|CI545233.1|CI545233
EST:     TCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
genomic: TCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
EST: gi|86539332|gb|CI179538.1|CI179538
EST:     ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
genomic: ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
EST: gi|86414356|gb|CI068759.1|CI068759
EST:     ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
genomic: ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
EST: gi|88450236|gb|CI541997.1|CI541997
EST:     AAGATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
genomic: AAGATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
EST: gi|88323532|gb|CI556163.1|CI556163
EST:     CATCCGAACAGCGCTACAAGATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
genomic: CATCCGAACAGCGCTACAAGATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
EST: gi|89183276|gb|CI045841.1|CI045841
EST:     ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
genomic: ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
EST: gi|86844247|gb|CI337622.1|CI337622
EST:     ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
genomic: ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
EST: gi|88289523|gb|CI555885.1|CI555885
EST:     TGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
genomic: TGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
EST: gi|86842098|gb|CI338451.1|CI338451
EST:     ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
genomic: ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
EST: gi|29615903|gb|CB620915.1|CB620915
EST:     ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
genomic: ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
EST: gi|86837009|gb|CI347555.1|CI347555
EST:     GATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
genomic: GATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
EST: gi|88289347|gb|CI555709.1|CI555709
EST:     CTACAAGATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
genomic: CTACAAGATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
EST: gi|89185795|gb|CI047664.1|CI047664
EST:     ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
genomic: ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
EST: gi|27920485|gb|CB096293.1|CB096293
EST:     ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAG                         TGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC
genomic: ATCATCGACCCTGTGAAAGTCATCCGAACAGCGCTACAAGATGCATCAAGgtacgcacgt ... tttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttgcattactaaaatttccacacttgcttaataacttgtgtttttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGCAGCAAAGGCCAGAATGGCTAGTCGGATGCCGCAGATGAGCGGGATGGAT
                               taataac  putative branch site (score: 1)
                                           tttttgtttc  putative PPT
       attactaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcacgttccttaagttgattactatttttcctttgcattactaaaatttccacacttgcttaataacttgtgtttttgtttcagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGCAGCAAAGGCCAGAATGGCTAGTCGGATGCCGCAGATGAGCGGGATGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA