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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTTACAGAAGCTGGGAGTGATCGTGTAATTGTATGTGATATTCATTCCACTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaacagaccaagatatgttccttttattacctaaatgctgttttcagttgtacgcaattttcttagctggatctgagttggcagcaaagtaacgattgaatctttgttatatgtag

Basic information

species Oryza sativa
transcript LOC_Os06g41360.4
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g41360.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G180863_T01 (Zea mays), 5'ss of exon 4
ACTTACAGAAGCTGGGAGTGATCGTGTAATTGTATGTGATATTCATTCCACTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaacagaccaagatatgttccttttattacctaaatgctgttttcagttgtacgcaattttcttagctggatctgagttggcagcaaagtaacgattgaatctttgttatatgtag
|||||| |||||||| ||||| ||||| |||||||||||||||||||| || ||||| ||||| ||||||||||||||||||||||||||| ||||||||||| | | |             |  | | ||||   | |      || |||||||  | |   || |  ||   |  ||   |  || |  | || ||  |     ||| ||| | | |||||
ACTTACTGAAGCTGGTAGTGACCGTGTCATTGTATGTGATATTCATTCTACGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag------------ttcttcctttacagcgt-----ttgatttcagtattgc---atctcgttg--taaattctatctgactacgaattagtgtc---atccttggtgtctgtag
















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|218499483|gb|FG945822.1|FG945822
EST:     CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAG                         CCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTGTG
genomic: CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaa ... ttatatgtagCCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTGTG
EST: gi|88444674|gb|CI694909.1|CI694909
EST:     CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAG                         CCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTGTG
genomic: CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaa ... ttatatgtagCCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTGTG
EST: gi|88589479|gb|CI707362.1|CI707362
EST:     CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAG                         CCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTGTG
genomic: CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaa ... ttatatgtagCCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTGTG
EST: gi|88591333|gb|CI708261.1|CI708261
EST:     CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAG                         CCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTA
genomic: CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaa ... ttatatgtagCCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTA
EST: gi|88321686|gb|CI672827.1|CI672827
EST:     CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAG                         CCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTGTG
genomic: CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaa ... ttatatgtagCCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTGTG
EST: gi|88585810|gb|CI701401.1|CI701401
EST:     CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAG                         CCTGTGATTCTGGATTACCTTGCCAGTAAGACAATAT
genomic: CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaa ... ttatatgtagCCTGTGATTCTGGATTACCTTGCCAGTAAGACAATAT
EST: gi|88588268|gb|CI706074.1|CI706074
EST:     CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAG                         CCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTGTG
genomic: CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaa ... ttatatgtagCCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTGTG
EST: gi|88412811|gb|CI576075.1|CI576075
EST:     CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAG                         CCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTG
genomic: CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaa ... ttatatgtagCCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTG
EST: gi|88463487|gb|CI695951.1|CI695951
EST:     CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAG                         CCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTGTG
genomic: CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaa ... ttatatgtagCCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTGTG
EST: gi|88436551|gb|CI691275.1|CI691275
EST:     CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAG                         CCTGTGATTCTG
genomic: CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaa ... ttatatgtagCCTGTGATTCTG
EST: gi|88589127|gb|CI706983.1|CI706983
EST:     CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAG                         CCTGTGATTCTGGATTACCTTGC
genomic: CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaa ... ttatatgtagCCTGTGATTCTGGATTACCTTGC
EST: gi|88579250|gb|CI688230.1|CI688230
EST:     CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAG                         CCTGTGATTCTGGATTACCTTGCCAG
genomic: CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaa ... ttatatgtagCCTGTGATTCTGGATTACCTTGCCAG
EST: gi|88588958|gb|CI706805.1|CI706805
EST:     CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAG                         CCTGTGATTCTGGATTACCTTGCCAGTA
genomic: CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaa ... ttatatgtagCCTGTGATTCTGGATTACCTTGCCAGTA
EST: gi|88588009|gb|CI705799.1|CI705799
EST:     TCAAGCCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAG                         CCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTGTG
genomic: TCAAGC-ATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaa ... ttatatgtagCCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTGTG
EST: gi|88300135|gb|CI582369.1|CI582369
EST:     CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAG                         CCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTGT
genomic: CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaa ... ttatatgtagCCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTGT
EST: gi|88444729|gb|CI694967.1|CI694967
EST:     CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAG                         CCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTGTG
genomic: CTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaa ... ttatatgtagCCTGTGATTCTGGATTACCTTGCCAGTAAGACAATATCTAAGGATCTTGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTACAGAAGCTGGGAGTGATCGTGTAATTGTATGTGATATTCATTCCACTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaacagaccaagatatgttccttttattacctaaatgctgttttcagttgtacgcaattttcttagctggatctgagttggcagcaaagtaacgattgaatctttgttatatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA