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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtgccaaatcaggtttctggatttctgctgtttaatttcttcttgtggttgttgacacccaaaaacttgccatttggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGCCACATATATCACCGTCTTAAAGCAAAAAAAGCCAGGGCAACAAGCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g16170.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16170.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G024733_T02 (Zea mays), 3'ss of exon 4
gtaaggtgccaaatcaggtttctggatttctgctgtttaatttc-ttcttgtggttgttgacacccaaaaacttgccatttggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGCCACATATATCACCGTCTTAAAGCAAAAAAAGCCAGGGCAACAAGCAAG
||||||    |   || |||||       ||| | |||| |||  ||| ||  ||   | |      ||  |||| | |||| |||||||||||| |||||||||||| | ||||| || | ||||||  |||||||||||||||| || || |||||| ||||||||||| |||||||| | ||||||
gtaaggcataattccaagtttcg------ctgatatttattttggttcctgcagtg--taatgattgaa--cttggcttttgcaatgcagCTATATACCATCACAACTCTAATTCTTACCGTACAGACGATATACTATAGCCACATCTACCATCGTCTTGAAGCAAAAAAATCCAGGGCAGCTAGCAAG

upper sequence: LOC_Os01g16170.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G153434_T01 (Zea mays), 3'ss of exon 4
gtaaggtgccaaatcaggtttctggatttctgctgtttaatttcttcttgtggttgttgacacccaaaaacttgccatttggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGCCACATATATCACCGTCTTAAAGCAAAAAAAGCCAGGGCAACAAGCAAG
||||||  | | | || ||||||   ||     | |||   ||| |   | |  |  ||||       |||||  | |||| |||||||||||| |||||||||||| | ||||| |||||||||||  | |||||||||||||| || || | |||||||  ||||||  |||||||| | ||||||
gtaaggcacaataccaagtttctc--ttatctttattttgattcctgcagcg--taatgact-----gaacttagcttttgcaatgcagCTATATACCATCACAACTCTGATTCTTACTGGACAGACGATCTACTATAGCCACATCTACCATCATCTTAAACTAAAAAACTCCAGGGCAGCTAGCAAG
















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|29663778|gb|CB660053.1|CB660053
EST:     CTGCCAACACAATTTTACATGGCTCTG                         CTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
genomic: CTGCCAACACAATTTTACATGGCTCTGgtaaggtgcc ... tggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
EST: gi|29677835|gb|CB674110.1|CB674110
EST:     CTGCCAACACAATTTTACATGGCTCTG                         CTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
genomic: CTGCCAACACAATTTTACATGGCTCTGgtaaggtgcc ... tggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
EST: gi|29639705|gb|CB644714.1|CB644714
EST:     CTGCCAACACAATTTTACATGGCTCTG                         CTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
genomic: CTGCCAACACAATTTTACATGGCTCTGgtaaggtgcc ... tggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
EST: gi|29679456|gb|CB675731.1|CB675731
EST:     CTGCCAACACAATTTTACATGGCTCTG                         CTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
genomic: CTGCCAACACAATTTTACATGGCTCTGgtaaggtgcc ... tggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
EST: gi|29630352|gb|CB635361.1|CB635361
EST:     CTGCCAACACAATTTTACATGGCTCTG                         CTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
genomic: CTGCCAACACAATTTTACATGGCTCTGgtaaggtgcc ... tggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
EST: gi|29629095|gb|CB634106.1|CB634106
EST:     CTGCCAACACAATTTTACATGGCTCTG                         CTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
genomic: CTGCCAACACAATTTTACATGGCTCTGgtaaggtgcc ... tggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
EST: gi|29616200|gb|CB621212.1|CB621212
EST:     CTGCCAACACAATTTTACATGGCTCTG                         CTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
genomic: CTGCCAACACAATTTTACATGGCTCTGgtaaggtgcc ... tggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
EST: gi|29672767|gb|CB669042.1|CB669042
EST:     CTGCCAACACAATTTTACATGGCTCTG                         CTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
genomic: CTGCCAACACAATTTTACATGGCTCTGgtaaggtgcc ... tggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
EST: gi|29677585|gb|CB673860.1|CB673860
EST:     CTGCCAACACAATTTTACATGGCTCTG                         CTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
genomic: CTGCCAACACAATTTTACATGGCTCTGgtaaggtgcc ... tggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
EST: gi|58587497|gb|CF985805.1|CF985805
EST:     CTGCCAACACAATTTTACATGGCTCTG                         CTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
genomic: CTGCCAACACAATTTTACATGGCTCTGgtaaggtgcc ... tggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
EST: gi|29681319|gb|CB677594.1|CB677594
EST:     CTGCCAACACAATTTTACATGGCTCTG                         CTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
genomic: CTGCCAACACAATTTTACATGGCTCTGgtaaggtgcc ... tggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
EST: gi|58657684|gb|CK046364.1|CK046364
EST:     CTGCCAACACAATTTTACATGGCTCTG                         CTATACACCATCACAACTGTTATTCTCACTGGAC
genomic: CTGCCAACACAATTTTACATGGCTCTGgtaaggtgcc ... tggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGAC
EST: gi|29624849|gb|CB629860.1|CB629860
EST:     CTGCCAACACAATTTTACATGGCTCTG                         CTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
genomic: CTGCCAACACAATTTTACATGGCTCTGgtaaggtgcc ... tggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
EST: gi|29663859|gb|CB660134.1|CB660134
EST:     CTGCCAACACAATTTTACATGGCTCTG                         CTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
genomic: CTGCCAACACAATTTTACATGGCTCTGgtaaggtgcc ... tggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
EST: gi|29641024|gb|CB646031.1|CB646031
EST:     CTGCCAACACAATTTTACATGGCTCTG                         CTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
genomic: CTGCCAACACAATTTTACATGGCTCTGgtaaggtgcc ... tggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
EST: gi|29678251|gb|CB674526.1|CB674526
EST:     CTGCCAACACAATTTTACATGGCTCTG                         CTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
genomic: CTGCCAACACAATTTTACATGGCTCTGgtaaggtgcc ... tggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
EST: gi|29664792|gb|CB661067.1|CB661067
EST:     CTGCCAACACAATTTTACATGGCTCTG                         CTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC
genomic: CTGCCAACACAATTTTACATGGCTCTGgtaaggtgcc ... tggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttaatttcttcttgtggttgttgacacccaaaaacttgccatttggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGCCACATATATCACCGTCTTAAAGCAAAAAAAGCCAGGGCAACAAGCAAG
                    tgttgac  putative branch site (score: 3)
                               aaaaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggtgccaaatcaggtttctggatttctgctgtttaatttcttcttgtggttgttgacacccaaaaacttgccatttggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGCCACATATATCACCGTCTTAAAGCAAAAAAAGCCAGGGCAACAAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG