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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtatacccaccctggatcctgggacgcagatgacatgttcagcgttcagtttgttcacgaagttggtttgtgcatgagtgcagGTGTTCAAGCACTATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAACTTTGTCGTTGTG

Basic information

species Oryza sativa
transcript LOC_Os01g50770.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G436835_T02 (Zea mays), 3'ss of exon 3
gtacgtatacccaccc--tggatcctggga--cgcagatgacatgttcagcgttcagtttgttcacgaagttggtttgtgcatgagtgcagGTGTTCAAGCACTATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAACTTTGTCGTTGTG
||||||   | | |||  ||  | | | ||  ||  |||| ||| |  |  |    ||  ||||| |     |  |||||| ||||| |||||||| |||||||| ||||| ||| |||||||||||||||| || |||||||| |||||||||
gtacgtgccctcgccccctgtttgcagagaatcgttgatggcat-tgtattgcctggt--gttcatg----cgacttgtgcgtgagtacagGTGTTTAAGCACTACTTCGAGGAGCTGGAGGAAGAGTCGCTCAGAGATAACTTCGTCGTTGTG

upper sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S300_7V6.2 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------gtacgtatacccaccctggatcctgggacgcagatgacatgttcagcgttcagtttgtt------cacgaagttggttt-----gtgcatgagtgcagGTGTTCAAGCACTATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAACTTTGTCGTTGTG
                                                                          |  ||| |  |||   |  |   || |  | | |||  | |||  | || |  ||| ||      |||  | | | |||     ||       ||||||| ||||||||||| || || |||||||| |||||||| ||| | || || ||||||||||| 
gtaagtgcttttgcccgttaccaacgacgagtttttatgaaagcttgtgtatgtcatacgtgctgacactttttgggcgt-tgtccagattcaaatttgaggag-acatgtaaagttaggagtcctttttatttgatatcacacattggctttaactggtttgcacatgcagGTTTTCAAGCACTACTTTGAGGAGTTGGAAGAAGAGTCTCTGCGTGACAATTTTGTCGTTGTT
















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|58654355|gb|CK043035.1|CK043035
EST:     GCAACTGCAACGCCGCCAGCATCCTCCTCTTCCTCCACCGCGTCGTTGAT                         GTGTTCAAGCACTATTTCGA
genomic: G-AACTGCAACGCCGCCAGCATCCTCCTCTTCCTCCACCGCGTCGTTGATgtacgtatac ... atgagtgcagGTGTTCAAGCACTATTTCGA
EST: gi|27576432|gb|CA999126.1|CA999126
EST:     AGAACTGCAACGCCGCCAGCATCCTCCTCTTCCTCCACCGCGTCGTTGAT                         GTGTTCAAGCACTATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAAC
genomic: AGAACTGCAACGCCGCCAGCATCCTCCTCTTCCTCCACCGCGTCGTTGATgtacgtatac ... atgagtgcagGTGTTCAAGCACTATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAAC
EST: gi|33793248|gb|CF322504.1|CF322504
EST:     AGAACTGCAACGCCGCCAGCATCCTCCTCTTCCTCCACCGCGTCGTTGAT                         GTGTTCAAGCACTATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAAC
genomic: AGAACTGCAACGCCGCCAGCATCCTCCTCTTCCTCCACCGCGTCGTTGATgtacgtatac ... atgagtgcagGTGTTCAAGCACTATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAAC
EST: gi|58673470|gb|CK062156.1|CK062156
EST:     AGAACTGCAACGCCGCCAGCATCCTCCTCTTCCTCCACCGCGTCGTTGAT                         GTGTTCAAGCACTATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAAC
genomic: AGAACTGCAACGCCGCCAGCATCCTCCTCTTCCTCCACCGCGTCGTTGATgtacgtatac ... atgagtgcagGTGTTCAAGCACTATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAAC
EST: gi|58665060|gb|CK053746.1|CK053746
EST:     AGAACTGCAACGCCGCCAGCATCCTCCTCTTCCTCCACCGCGTCGTTGAT                         GTGTTCAAGCACTATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAAC
genomic: AGAACTGCAACGCCGCCAGCATCCTCCTCTTCCTCCACCGCGTCGTTGATgtacgtatac ... atgagtgcagGTGTTCAAGCACTATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtatacccaccctggatcctgggacgcagatgacatgttcagcgttcagtttgttcacgaagttggtttgtgcatgagtgcagGTGTTCAAGCACTATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAACTTTGTCGTTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA