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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgtattgaagttttgtttagtttaatgtatgattgttagttattcgcataatttatattgatgcactttggtagtattaaccatcagcattggaacagGGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAATTTGAAGAATCTTATAAGCTTGGACCTGTACAAGAACAACATTTCTGGG

Basic information

species Oryza sativa
transcript LOC_Os01g59440.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59440.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G815009_T01 (Zea mays), 3'ss of exon 2
-----------gatgtattgaagttttgtttagtttaatgtatgattgttagttattcgcataatttatattgatgcactttggtagtattaaccatcagcattggaacagGGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAATTTGAAGAATCTTATAAGCTTGGACCTGTACAAGAACAACATTTCTGGG
            || | | ||  ||||   |||||| |  | ||  ||| | ||||||    |||    ||| |          | ||||| |||||  ||| || || ||||| || |||||||| |  ||||||||||| ||||| || || |||||||||||||||||||| |||||||||||| ||||||||||||||||||| |||
tgatatagttaaatatttagatatttttcatagtttgacatgtgcctgtcaattattcatccaata---attaa--------actggtattgaccattggcactgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAATTTGAAGAATCTAATAAGCTTGGACTTGTACAAGAACAACATTTCGGGG

upper sequence: LOC_Os01g59440.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G121820_T01 (Zea mays), 3'ss of exon 2
gatgtattgaagttttgtt-tagtttaatgtatgattgttagttattcgcataatttatattgatgcactttggtagtattaaccatcagcattggaacagGGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAATTTGAAGAATCTTATAAGCTTGGACCTGTACAAGAACAACATTTCTGGG
  || | | | |  |  |  ||        |   ||  | ||  |||    | | |||  ||||   | | |   |||||| ||| | |||| || |||||||| || || |||||||| ||||||||||| ||||| || || ||||| |||||||||||||| |||||||| ||| ||||||||||||||||||| |||
tttgcagttatgactcatgatacaagggcctggtatactcagacattt-tttcacttagtttgacaaattataacagtattgaccgttagcactgaaacagGGAACTTTATAAGAATAACATTCAAGGAACAATCCCTTCTGAGCTTGGCAATTTGAAGAATCTAATAAGCTTCGACTTGTACAAGAACAACATTTCGGGG
















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|87018477|gb|CI252231.1|CI252231
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCT                         GGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCTgtaagctttt ... attggaacagGGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
EST: gi|2317317|gb|C22371.1|C22371
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCT                         GGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCTgtaagctttt ... attggaacagGGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
EST: gi|29667098|gb|CB663373.1|CB663373
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCT                         GGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCTgtaagctttt ... attggaacagGGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
EST: gi|11442641|gb|BF430544.1|BF430544
EST:     CTGAGCTTGGAAAGTTGGATCATCTGCAATATCT                         GGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
genomic: CTGAGCTTGGAAAGTTGGATCATCTGCAATATCTgtaagctttt ... attggaacagGGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
EST: gi|3548933|gb|AF074734.1|AF074734
EST:     CATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCT                         GGAGCTATACAAGAATAATATTCAAGGNAACGATCCCATCGGAACTTGGTA
genomic: CATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCTgtaagctttt ... attggaacagGGAGCTATACAAGAATAATATTCAAGG-AACGATCCCATCGGAACTTGGTA
EST: gi|58602723|gb|CK013251.1|CK013251
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCT                         GTGGGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCTgtaagctttt ... attggaacagG-GAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgcataatttatattgatgcactttggtagtattaaccatcagcattggaacagGGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAATTTGAAGAATCTTATAAGCTTGGACCTGTACAAGAACAACATTTCTGGG
                               tattaac  putative branch site (score: 1)
     taatttatattgat  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgtattgaagttttgtttagtttaatgtatgattgttagttattcgcataatttatattgatgcactttggtagtattaaccatcagcattggaacagGGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAATTTGAAGAATCTTATAAGCTTGGACCTGTACAAGAACAACATTTCTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC