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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaccccatttgttttgtttttttttctgtccatgttggctacgtgccagcacacttgtcgatcatgtttcttgacccagttttatggctgtgggtgcagGGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGGGGTCATCGCCAACAGGGA

Basic information

species Oryza sativa
transcript LOC_Os03g09250.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 1
tcaccccatttgttttgtttttttttctgtccatgttggctacgtgccagcacacttgtcgat-catgtttcttgac-ccagttttatggctgtgg--gtgcagGGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGGGGTCATCGCCAACAGGGA
      | |  ||   | |  || |  |||  ||| || |    || |||| | ||||||  |   ||     |||  |||  |||   | | |||  ||||||||||||||| ||||||||||| ||||||||||| || |||||||||||||||||||| |||||||||||
-tgttgcctacgtgcagctcgttgtg-tgtt-atggtgtcaggctgtcagc-cgcttgtctctgtctgacggatgatgccaacttttctgttctggtggtgcagGGTGATGCTTGTGGGGTGGGGAGGCAACAACGGGTCCACGCTGACGGCTGGGGTCATTGCCAACAGGGA

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 1
tcaccccatttgttttgttttttttt--ctgtccatgttg-gctacgtgccagc-acacttgtcgatcatgtttcttgacccagttttatggctgtgggtgcagGGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGGGGTCATCGCCAACAGGGA
    || ||   | |||  |   |    ||     ||||  | |    |||| |     ||||| | |   |        |   || |    |||  |||||||||| ||||| ||||||||||| ||||||||||| || |||||||||||||||||||| |||||||||||
---tcctatgcatgttgcctacgtgcagctcgttgtgttacggtgtccgccacctgtctttgtctaacggatgatgctgtctttttctgcc-ctgatggtgcagGGTCATGCTTGTGGGGTGGGGAGGCAACAACGGGTCCACGCTGACGGCTGGGGTCATTGCCAACAGGGA

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G004528_T01 (Zea mays), 3'ss of exon 1
tcaccccatttgttt-tgtttttttttctgtccatgttggctacgtgccagcacacttgtcgatcatgtttcttgacccagttttatggctgtgggtgcagGGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGGGGTCATCGCCAACAGGGA
 ||       |   |     |  || | |  |  |||  || || || |      ||    ||| ||| |   |    | |        |||  |||||||||| ||||| ||||||||||| ||||||||||| || |||||||||||||||||||| |||||||||||
gcatgttgcctacgtgcagctcgttgtgttacggtgtccgccacctgtctttgt-ctaacggatgatgctgtctttttctgcc------ctgatggtgcagGGTCATGCTTGTGGGGTGGGGAGGCAACAACGGGTCCACGCTGACGGCTGGGGTCATTGCCAACAGGGA

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 1
tcaccccatttgttttgtttttttttctgtccatgttggctacgtgccagcacacttgtc---gatca-tgtttcttgacccagttttatggctgtgggtgcagGGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGGGGTCATCGCCAACAGGGA
 | | |   |||    |      ||||||   |  |    | |||   ||     ||| |   ||| | |  |||| |     || |  |||  ||   |||||  ||||||| || |||||||||||||||||||| || || || ||||||||  |  | || ||||| ||
-cccgctccttggcgcgcgaacatttctggaga-atgtctttcgtaatagtggttttgacacagatgaataattctgggttgtgtgtggtgg--gtacctgcagAATGATGCTTGTTGGGTGGGGCGGCAACAACGGATCCACTCTCACGGCTGGTATTCTTGCTAACAGAGA

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|29646112|gb|CB651119.1|CB651119
EST:     AAGTCCGTCCGCTACAACTTCCGGACCACCACCACCGTCCCCAAGCTCGG                         GGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGG
genomic: AAGTCCGTCCGCTACAACTTCCGGACCACCACCACCGTCCCCAAGCTCGGgtacgcaccc ... gtgggtgcagGGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGG
EST: gi|58664958|gb|CK053644.1|CK053644
EST:     AAGTCCGTCCGCTACAACTTCCGGACCACCACCACCGTCCCCAAGCTCGG                         GGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGG
genomic: AAGTCCGTCCGCTACAACTTCCGGACCACCACCACCGTCCCCAAGCTCGGgtacgcaccc ... gtgggtgcagGGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGG
EST: gi|58609519|gb|CK037552.1|CK037552
EST:     AAGTCCGTCCGCTACAACTTCCGGACCACCACCACCGTCTCCAAGCTCGG                         GGTGATGCTCGTGGGGTGGGGCGGCGACAACGGCTCAACGCTGACGGCTGG
genomic: AAGTCCGTCCGCTACAACTTCCGGACCACCACCACCGTCCCCAAGCTCGGgtacgcaccc ... gtgggtgcagGGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGG
EST: gi|58606593|gb|CK034626.1|CK034626
EST:     AAGTCCGTCCGCTACAACTTCCGGACCACCACCACCGTCCCCAAGCTCGG                         GGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGG
genomic: AAGTCCGTCCGCTACAACTTCCGGACCACCACCACCGTCCCCAAGCTCGGgtacgcaccc ... gtgggtgcagGGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGG
EST: gi|58686865|gb|CK075552.1|CK075552
EST:     AAGTCCGTCCGCTACAACTTCCGGACCACCACCACCGTCCCCAAGCTCGG                         GGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGG
genomic: AAGTCCGTCCGCTACAACTTCCGGACCACCACCACCGTCCCCAAGCTCGGgtacgcaccc ... gtgggtgcagGGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGG
EST: gi|58602603|gb|CK013131.1|CK013131
EST:     ACCGTCCCCAAGCTCGG                         GGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGG
genomic: ACCGTCCCCAAGCTCGGgtacgcaccc ... gtgggtgcagGGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGG
EST: gi|86826249|gb|CI311085.1|CI311085
EST:     AAGTCCGTCCGCTACAACTTCCGGACCACCACCACCGTCCCCAAGCTCGG                         GGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGG
genomic: AAGTCCGTCCGCTACAACTTCCGGACCACCACCACCGTCCCCAAGCTCGGgtacgcaccc ... gtgggtgcagGGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGG
EST: gi|29616445|gb|CB621457.1|CB621457
EST:     AAGTCCGTCCGCTACAACTTCCGGACCACCACCACCGTCCCCAAGCTCGG                         GGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGG
genomic: AAGTCCGTCCGCTACAACTTCCGGACCACCACCACCGTCCCCAAGCTCGGgtacgcaccc ... gtgggtgcagGGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccagcacacttgtcgatcatgtttcttgacccagttttatggctgtgggtgcagGGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGGGGTCATCGCCAACAGGGA
                        tcttgac  putative branch site (score: 3)
                                 agttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaccccatttgttttgtttttttttctgtccatgttggctacgtgccagcacacttgtcgatcatgtttcttgacccagttttatggctgtgggtgcagGGTGATGCTCGTGGGGTGGGGCGGCAACAACGGCTCAACGCTGACGGCTGGGGTCATCGCCAACAGGGA

- - - - - tgttttg
- - - - - - - - - - - ttttctg
- - - - - - - - - - - - - - - -catgttg
- - - - - - - - - - - - - - - - - - - - - -gtgccag